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Bibliographic search and citation are central to all scholarly and research activities. Within the domain of life sciences research, bibliographic citation is of particular importance for annotation of large bodies of experimentally developed and computationally derived data and the rapidly increasing corpus of research literature makes efficient and effective bibliographic searches increasingly critical.

The relevant literature may include traditional (hardcopy) research journal publications, books, theses, reviews and the like. Recent developments require researchers and scholars to use and cite a wider variety of sources, including database records, electronically published journals, World Wide Web sites and multimedia works.

While several standards exist for the representation of bibliographic citations, some of them are not readily adapted to newer forms of publication, or they are not designed to be easily extendible and customizable as the current needs require. Also, there is no common set of interfaces for distributed object implementations of bibliographic servers.

This was the motivation for proposing, defending, standardizing and finally implementing a Bibliographic Query Service, a service enabling access to heterogeneous bibliographic databases and the development of interoperable clients that make use of this access.

The package consists of three parts:

  • Few data types representing a bibliographic citation (see class BibRef),
  • An interface defining methods for connecting to a bibliographic repository, querying it and finally retrieving citations from it (see interface BibRefQuery), and
  • A supporting interface defining mainly access to the bibliographic controlled vocabularies and few other utilities (see interface BibRefSupport).
PK /*?:zs}(org/biojava/bio/AbstractAnnotation.class2 ;~ ;       ;  8  ;        < ) 8 8 8 0 / ;  8  getProperties()Ljava/util/Map;propertiesAllocated()Z getProperty&(Ljava/lang/Object;)Ljava/lang/Object;CodeLineNumberTableLocalVariableTablepropLjava/util/Map;this$Lorg/biojava/bio/AbstractAnnotation;keyLjava/lang/Object; StackMapTable Exceptions setProperty'(Ljava/lang/Object;Ljava/lang/Object;)V propertiesceLorg/biojava/utils/ChangeEvent;cs!Lorg/biojava/utils/ChangeSupport;valueremoveProperty(Ljava/lang/Object;)VcontainsProperty(Ljava/lang/Object;)Zkeys()Ljava/util/Set;toString()Ljava/lang/String;sbLjava/lang/StringBuffer;iLjava/util/Iterator;asMap()V(Lorg/biojava/bio/Annotation;)Viae$Ljava/lang/IllegalArgumentException;annLorg/biojava/bio/Annotation;(Ljava/util/Map;)VannMaphashCode()Iequalso SourceFileAbstractAnnotation.java @A >? a C java/util/NoSuchElementExceptionjava/lang/StringBuilder mn Property  unknown de m A org/biojava/utils/ChangeEvent java/lang/Object m  Can't remove key C c java/lang/StringBuffer{  A = ,} java/lang/NullPointerExceptionENull annotation not allowed. Use Annotation.EMPTY_ANNOTATION instead. s bc BC"java/lang/IllegalArgumentExceptionorg/biojava/bio/BioError)Property was there and then disappeared: m9Null annotation Map not allowed. Use an empy map instead. 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R**Y*346 B *:   @3* AB >*+ KL>*+ TU PK .*?:9i11+org/biojava/bio/alignment/ARAlignment.class2)   !"#$ ADD_LABELLorg/biojava/utils/ChangeType; REMOVE_LABEL addSequence/(Lorg/biojava/bio/alignment/AlignmentElement;)V Exceptions%&removeSequence(Ljava/lang/Object;)V()VCodeLineNumberTable SourceFileARAlignment.javaorg/biojava/utils/ChangeType"Adding a sequence to the alignment%org.biojava.bio.alignment.ARAlignment '(  %org/biojava/bio/alignment/ARAlignmentjava/lang/Object org/biojava/bio/symbol/Alignment%org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioException9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V    =!YY *0PK /*?:û=org/biojava/bio/alignment/AbstractULAlignment$ColAsList.class27 # $ % &' ( )* &+ ),-./colIlabelsLjava/util/List;this$0/Lorg/biojava/bio/alignment/AbstractULAlignment;3(Lorg/biojava/bio/alignment/AbstractULAlignment;I)VCodeLineNumberTableLocalVariableTablethis ColAsList InnerClasses9Lorg/biojava/bio/alignment/AbstractULAlignment$ColAsList;2(Lorg/biojava/bio/alignment/AbstractULAlignment;)Vget(I)Ljava/lang/Object;indxsize()I SourceFileAbstractULAlignment.java  0 1 23 4  56  7org/biojava/bio/alignment/AbstractULAlignment$ColAsListjava/util/AbstractListjava/io/Serializable()V-org/biojava/bio/alignment/AbstractULAlignment getLabels()Ljava/util/List;java/util/ListsymbolAt4(Ljava/lang/Object;I)Lorg/biojava/bio/symbol/Symbol;0   W*+***+  A*+**  J***  4 *  !"  &PK /*?:6]CCOorg/biojava/bio/alignment/AbstractULAlignment$LeftRightLocationComparator.class26 $ % &' () (*+,-this$0/Lorg/biojava/bio/alignment/AbstractULAlignment;2(Lorg/biojava/bio/alignment/AbstractULAlignment;)VCodeLineNumberTableLocalVariableTablethisLeftRightLocationComparator InnerClassesKLorg/biojava/bio/alignment/AbstractULAlignment$LeftRightLocationComparator;compare'(Ljava/lang/Object;Ljava/lang/Object;)Is1Is2o1Ljava/lang/Object;o2retloc1!Lorg/biojava/bio/symbol/Location;loc2 StackMapTable. SourceFileAbstractULAlignment.java /0 12. 34 54Iorg/biojava/bio/alignment/AbstractULAlignment$LeftRightLocationComparatorjava/lang/Objectjava/util/Comparatororg/biojava/bio/symbol/Location()V-org/biojava/bio/alignment/AbstractULAlignmentlocInAlignment5(Ljava/lang/Object;)Lorg/biojava/bio/symbol/Location;getMin()IgetMax!   4 *+*   L>*+:*,:>b>L;d`6d`6> d>: ',=BSfyRf%y w ,!!B"# &PK /*?:]  Borg/biojava/bio/alignment/AbstractULAlignment$SubULAlignment.class2 n &o pq r ps t uvw ox o y z{| } u~ u      z z z ~ u u u u $startIend subLabelsLjava/util/List;this$0/Lorg/biojava/bio/alignment/AbstractULAlignment;b(Lorg/biojava/bio/alignment/AbstractULAlignment;Ljava/util/Set;Lorg/biojava/bio/symbol/Location;)VCodeLineNumberTableLocalVariableTablethisSubULAlignment InnerClasses>Lorg/biojava/bio/alignment/AbstractULAlignment$SubULAlignment;labelsLjava/util/Set;loc!Lorg/biojava/bio/symbol/Location; StackMapTable Exceptions realPosition(I)Iposlength()IlocInAlignment5(Ljava/lang/Object;)Lorg/biojava/bio/symbol/Location;labelLjava/lang/Object;origLocminmax subAlignmentT(Ljava/util/Set;Lorg/biojava/bio/symbol/Location;)Lorg/biojava/bio/symbol/Alignment;lLjava/util/Vector;listIntersection2(Ljava/util/List;Ljava/util/List;)Ljava/util/List;iLjava/util/Iterator;s1s2commonlabelsAt(I)Ljava/util/List;column labelsInRange3(Lorg/biojava/bio/symbol/Location;)Ljava/util/List; getLabels()Ljava/util/List;symbolAt4(Ljava/lang/Object;I)Lorg/biojava/bio/symbol/Symbol;"(I)Lorg/biojava/bio/symbol/Symbol;symbolListForLabel7(Ljava/lang/Object;)Lorg/biojava/bio/symbol/SymbolList; getAlphabet#()Lorg/biojava/bio/symbol/Alphabet;symbolListIterator()Ljava/util/Iterator; SourceFileAbstractULAlignment.java -. / F () F *) EF#java/lang/IndexOutOfBoundsExceptionjava/util/ArrayList +, $org/biojava/bio/symbol/RangeLocation / _` GH BCjava/util/TreeSet /java/util/Vector ST?@ABC1= *`d23 47 D)EF16 **d`2$3  47GH11*+M,*d`>,*d`6Y2+ ,-&.341471IJ (K;L)& M)NO1]*,>*,6+Y* LY+:Y** LY*+Y25 69:*<4=F@3>4PQ]47]89]:; RL)FM)<*ARST1=Y+N+:#:, -W-2C EF$G/H8J;K3>$IJ*UV=47=W,=X, 4Y,<Z[&\]1B*Y2N347^)A_`1G*+=*+>* * Y ** *Y2S TU&V.X3*G47G:; <L)1M)<&Aab1/* 2k3 47cd1L*+* 2o3 47IJ^)ARce1A **!2s3 47 ^)ARfg1= *+"2w3 47 IJARhi12*#2{3 47jk13 $Y*%23  47lm6u5$ PK /*?:_3org/biojava/bio/alignment/AbstractULAlignment.class2 +s *tu v wxyz{ s| } ~    * * s *   * * # * ' 'SubULAlignment InnerClassesLeftRightLocationComparator ColAsListalphabet!Lorg/biojava/bio/symbol/Alphabet;()VCodeLineNumberTableLocalVariableTablethis/Lorg/biojava/bio/alignment/AbstractULAlignment;symbolAt"(I)Lorg/biojava/bio/symbol/Symbol;ire/Lorg/biojava/bio/symbol/IllegalSymbolException;indexI StackMapTableylabelsAt(I)Ljava/util/List;column labelsInRange3(Lorg/biojava/bio/symbol/Location;)Ljava/util/List;seqLoc!Lorg/biojava/bio/symbol/Location;labelLjava/lang/Object; labelIteratorLjava/util/Iterator;loclabelsLjava/util/List; labelListsymbolListIterator()Ljava/util/Iterator;debug(Ljava/lang/String;)VsLjava/lang/String;leftMost()Ljava/lang/Object;leftLoc rightMostrightLoc subAlignmentT(Ljava/util/Set;Lorg/biojava/bio/symbol/Location;)Lorg/biojava/bio/symbol/Alignment;Ljava/util/Set; Exceptions5(Ljava/util/Set;II)Lorg/biojava/bio/symbol/Alignment;minmax orderedLables-(Ljava/util/Comparator;)Ljava/util/SortedSet;compLjava/util/Comparator; orderedSetLjava/util/TreeSet; SourceFileAbstractULAlignment.java 45 237org/biojava/bio/alignment/AbstractULAlignment$ColAsList 4 -org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/BioErrorjava/lang/StringBuilder=Somehow my crossproduct alphabet is incompatible with column 4$org/biojava/bio/symbol/RangeLocation 4 FG java/util/Vector W ]  3org/biojava/bio/symbol/Alignment$SymbolListIteratorSymbolListIterator 4  Y \] `]09:0?@ASBCD6B*Y7J89:E@FG6H*MY:,:(:*N+-W7"NQS T)U0V8WEZ8H0HI)JK/LMH9:HNICOP:QPARSTTU.VW63 Y*7^8  9:XY6@+7 bc89:Z[\]6*LM::+:qN*-:, -M: -M: d d-M:*!7Jjkm n pq'r.s2t4u8xIyKzR{c|}~8H'fJKxLM9:OP\K ^I NIAPRT_SSU"RT__SSU:RT_SS`]6*LM::+:qN*-:, -M: -M: d d-M:*"7J '.248IKRc8H'fJKxLM9:OP`K aI NIAPRT_SSU"RT__SSU:RT_SSbc6I #Y*+,$78  9: Od NIefbg6S *+%&78* 9: Od h@ i@ejkl6Z'Y+(M,*)W,7 8 9:mn opqr."#*-/*0*1 PK .*?:_g0org/biojava/bio/alignment/AlignmentElement.class2getLabel()Ljava/lang/Object;getLoc#()Lorg/biojava/bio/symbol/Location; getSymbolList%()Lorg/biojava/bio/symbol/SymbolList;setLoc$(Lorg/biojava/bio/symbol/Location;)V Exceptions SourceFileAlignmentElement.java*org/biojava/bio/alignment/AlignmentElementjava/lang/Objectorg/biojava/bio/BioError    PK .*?:T)1org/biojava/bio/alignment/EditableAlignment.class2,  ! "# $%&LOCATIONLorg/biojava/utils/ChangeType;GAPSedit2(Ljava/lang/Object;Lorg/biojava/bio/symbol/Edit;)V Exceptions'shiftAtAlignmentLoc7(Ljava/lang/Object;Lorg/biojava/bio/symbol/Location;I)V()shiftAtSequenceLoc()VCodeLineNumberTable SourceFileEditableAlignment.javaorg/biojava/utils/ChangeType+The location of a sequence is being changed+org.biojava.bio.alignment.EditableAlignment *+ &The gap within a sequence are changing  +org/biojava/bio/alignment/EditableAlignmentjava/lang/Object%org/biojava/utils/ChangeVetoException7org/biojava/bio/alignment/IllegalAlignmentEditException#java/lang/IndexOutOfBoundsException9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V   =!YY  KQPK /*?:pUz1z11org/biojava/bio/alignment/FlexibleAlignment.class2 t  s  s  s  s                  s ! s" #$ s% s&'() ( * + ,-./ .0 u1 12 s3 45 46 u7 s8 9: :; < = s> s?@ @ A B CDE FH EI EJ K sL sM NO sP sQ vR vS TU sV ? sWX W Y sZ [\ \] \^ \_ \` sa sbcd ,`e fgh ij sk slmn \o p qrstudataLjava/util/Map; labelOrderLjava/util/List;alignmentRange!Lorg/biojava/bio/symbol/Location; alphaList(Ljava/util/List;)VCodeLineNumberTableLocalVariableTableelementLjava/lang/Object;ae,Lorg/biojava/bio/alignment/AlignmentElement;labellocseq#Lorg/biojava/bio/symbol/SymbolList;minImaxiLjava/util/Iterator;e'Lorg/biojava/utils/ChangeVetoException;this-Lorg/biojava/bio/alignment/FlexibleAlignment;seqListk StackMapTablervwx yz' ExceptionsgetOrder(Ljava/lang/Object;)I addSequence/(Lorg/biojava/bio/alignment/AlignmentElement;)Vcs!Lorg/biojava/utils/ChangeSupport;cevtLorg/biojava/utils/ChangeEvent;{0removeSequence(Ljava/lang/Object;)VLjava/lang/Throwable;:locInAlignment5(Ljava/lang/Object;)Lorg/biojava/bio/symbol/Location;| getLabelsAt(I)Ljava/util/List; labelIteratorcolumn labelListlength()I getAlphabet#()Lorg/biojava/bio/symbol/Alphabet; getLabels()Ljava/util/List;sortedLjava/util/TreeSet;symbolAt4(Ljava/lang/Object;I)Lorg/biojava/bio/symbol/Symbol;%Ljava/lang/IndexOutOfBoundsException;clocsymbolLorg/biojava/bio/symbol/Symbol;}@symbolListForLabel7(Ljava/lang/Object;)Lorg/biojava/bio/symbol/SymbolList;edit2(Ljava/lang/Object;Lorg/biojava/bio/symbol/Edit;)VLorg/biojava/bio/symbol/Edit;shiftAtAlignmentLoc7(Ljava/lang/Object;Lorg/biojava/bio/symbol/Location;I)Voffset sourceLocshiftAtSequenceLoccsgapcegapcslocceloc caseValue absOffsetseqLocnewLoc removeGaps.(Lorg/biojava/bio/symbol/GappedSymbolList;II)V/Lorg/biojava/bio/symbol/IllegalSymbolException;)Lorg/biojava/bio/symbol/GappedSymbolList;startgallGaps((Lorg/biojava/bio/symbol/SymbolList;II)Zendgs resetRange()VlMinlMaxcountshiftAll(I)VlListshift(Ljava/lang/Object;I)VoLocnLocgreater(II)IxygreatestlesserleastgetAE@(Ljava/lang/Object;)Lorg/biojava/bio/alignment/AlignmentElement;posInSeq(Ljava/lang/Object;I)IlocInSeqV(Ljava/lang/Object;Lorg/biojava/bio/symbol/Location;)Lorg/biojava/bio/symbol/Location;viewLoc SourceFileFlexibleAlignment.java ~java/util/ArrayList }zjava/util/Hashtable wxjava/util/Vector yz$org/biojava/bio/symbol/RangeLocation ~~ {|v w  *org/biojava/bio/alignment/AlignmentElementorg/biojava/bio/BioException2All elements of seqList must be AlignmentElements ~   z 'org/biojava/bio/symbol/GappedSymbolList-org/biojava/bio/symbol/SimpleGappedSymbolList ~0org/biojava/bio/alignment/SimpleAlignmentElement ~ y      %org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioErrorShould not have a problem here  x java/lang/Exceptiondid not find labelorg/biojava/utils/ChangeEvent  ~ {    java/lang/Throwable    #java/lang/IndexOutOfBoundsException  java/util/TreeSetIorg/biojava/bio/alignment/AbstractULAlignment$LeftRightLocationComparatorLeftRightLocationComparator InnerClasses ~ ~  ~ Not implemented yet    7org/biojava/bio/alignment/IllegalAlignmentEditException ~ java/lang/StringBuilderShifting all to left     Shifting all to right OOOPS something is wrong  -org/biojava/bio/symbol/IllegalSymbolException&We should have tested for this already   shifting shifted   +org/biojava/bio/alignment/FlexibleAlignment-org/biojava/bio/alignment/AbstractULAlignment%org/biojava/bio/alignment/ARAlignment+org/biojava/bio/alignment/EditableAlignmentjava/util/Listjava/util/Iteratorjava/lang/Objectorg/biojava/bio/symbol/Location!org/biojava/bio/symbol/SymbolListorg/biojava/utils/ChangeSupport java/util/NoSuchElementExceptionorg/biojava/bio/symbol/Symbol(II)Viterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object;(Ljava/lang/String;)VgetLabelgetLoc#()Lorg/biojava/bio/symbol/Location; getSymbolList%()Lorg/biojava/bio/symbol/SymbolList;add(Ljava/lang/Object;)Z&(Lorg/biojava/bio/symbol/SymbolList;)VY(Ljava/lang/Object;Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/Location;)V java/util/Mapput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;getMingetMax&org/biojava/bio/symbol/AlphabetManagergetCrossProductAlphabet3(Ljava/util/List;)Lorg/biojava/bio/symbol/Alphabet;alphabet!Lorg/biojava/bio/symbol/Alphabet;sizeget(I)Ljava/lang/Object;equals ADD_LABELLorg/biojava/utils/ChangeType;E(Ljava/lang/Object;Lorg/biojava/utils/ChangeType;Ljava/lang/Object;)VgetChangeSupportA(Lorg/biojava/utils/ChangeType;)Lorg/biojava/utils/ChangeSupport;firePreChangeEvent"(Lorg/biojava/utils/ChangeEvent;)VfirePostChangeEvent REMOVE_LABELremoveprintStackTrace&(Ljava/lang/Object;)Ljava/lang/Object;keySet()Ljava/util/Set; java/util/Setcontains(I)Z2(Lorg/biojava/bio/alignment/AbstractULAlignment;)V(Ljava/util/Comparator;)VaddAll(Ljava/util/Collection;)Z(Ljava/util/Collection;)V"(I)Lorg/biojava/bio/symbol/Symbol;LOCATIONGAPSjava/lang/Mathabs(I)I addGapsInViewsetLoc$(Lorg/biojava/bio/symbol/Location;)Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString()Ljava/lang/String;debug removeGaporg/biojava/bio/symbol/Alphabet getGapSymbol!()Lorg/biojava/bio/symbol/Symbol;-(Ljava/lang/Object;)Ljava/lang/StringBuilder; containsKey!stuvwxyz{|}z~ ,**Y*Y*Y * Y =+N--: Y::::*WY:Y:*W* W**  !6 ** ""#6 * Y  0**$%*&N(Y)* '~PGQR%S2U4WDXLYTZ^\e]n^w_`abcefghij klnq o!p+sz Lenw|(  ;! ,,z4L;"T ZQ 2=* +* ,+-ݻ.Y/0vw x"v(z &22 .! +:+:+:1Y*23N*24M,-5Y:YL*+W* W*W**$%**  !6** ""#6* Y *&,-6N&.3;FTam~\ .&|/T'!^1Y*7+3N*74M,-5**+89W**$% :;*+<W* +=W*&,-647:6 )479>ITX]49^^I Q7'? *+> d *? @YAYM*BC:.:*>N-D,W,& 7@LVb>L|@"-5ddGz 4@!@* "* d` /*% !^"EYFY*GHL+* IWY+J"!'*+KN*+L6:--M::"@""$H$'''!L@!? *+>  !H (YN*   '!k*+,O:*+P 4| |'W@!F1Y*Q+3:*Q4:1Y*R+3:*R4:6S6 *+T: *+>:  : , 6,"6 U @YA U-w~?`* `dV WYX5 ` Y*  d Z62* ``V WYX5* `Z Y655 ` Y Y  d " :   [*&66* ``V WYX55* `Z Y ` " :   [*&66+*  ddV WYX55*  d Z Y  "` :   [*&6655 Y Y  "` :   [*&66j*\Y]^_ `ab*+cI*\Y]d_ `ab*+c(*\Y]e_,f_g_ `abJR,-.%/.11273>4E5N7V8^9p:x<|=}?@ACFGIKL MNQ'R/T6UDVQWXX[[b\i]y^_`abcfgijklmn opqt/u7w>xEyUzn{w|{}~ DEFFF|F.%!/817 >| E N | V^Hp.0+URTQ $'W@!&6+h:(Yj*i %> &&&&B $0+k:6+M- &(.>0000 # $<=6*l:Q:*T >*T"6< *!< = *#=* Y 9* d6*m* Y* `* "` V%1>DIPV\dgjw|\ %B19>,X)>6 G'$(*lM,N--:*c$'4 ((#z '$1Y*Q+3:*Q4N*+T: Y `"` :-5*\Y]n_+f_ab*+>[*&*\Y]o_+pab-6. 8>XdhHpxi|8N|'d >  *    @d >  *    @\*+q*+r   $& *? @YA*+TN- d` *&&& | @$~$*+, L>*+,"L6 Y  4$$$|  @G FtFPK /*?:%NrV V 5org/biojava/bio/alignment/FlexibleAlignmentTest.class2 %S $T UV W XY Z[ \] $^ Z_ $` abc d Ze afg h ij k Xlm no pqrst $uvwx $y $z{| alignment[Ljava/lang/String;namesalignDNA-Lorg/biojava/bio/alignment/FlexibleAlignment; alignProt(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis1Lorg/biojava/bio/alignment/FlexibleAlignmentTest;nameLjava/lang/String;setUp()V Exceptions}testDNAsymsLjava/util/List; testProteinparseV([Ljava/lang/String;[Ljava/lang/String;Z)Lorg/biojava/bio/alignment/FlexibleAlignment;seq$Lorg/biojava/bio/seq/GappedSequence;ae,Lorg/biojava/bio/alignment/AlignmentElement;iI sequencesaltLjava/lang/Throwable;dnaZ StackMapTable~'o SourceFileFlexibleAlignmentTest.java ,- )* "org/biojava/bio/symbol/BasisSymbol ~   +* java/util/ArrayList ,6 0org/biojava/bio/alignment/SimpleAlignmentElement  , +org/biojava/bio/alignment/FlexibleAlignment ,java/lang/Throwable 6java/lang/StringA-CAGCA-A &'MOUSEHUMANSCHPO (' =>/org/biojava/bio/alignment/FlexibleAlignmentTestjunit/framework/TestCasejava/lang/Exceptionjava/util/List"org/biojava/bio/seq/GappedSequencesymbolAt"(I)Lorg/biojava/bio/symbol/Symbol; getSymbols()Ljava/util/List;get(I)Ljava/lang/Object;org/biojava/bio/seq/DNAToolsgetDNA)()Lorg/biojava/bio/symbol/FiniteAlphabet;%org/biojava/bio/symbol/FiniteAlphabet getGapSymbol!()Lorg/biojava/bio/symbol/Symbol; assertEquals'(Ljava/lang/Object;Ljava/lang/Object;)Vg'()Lorg/biojava/bio/symbol/AtomicSymbol; org/biojava/bio/seq/ProteinTools getAlphabetcreateGappedDNASequenceJ(Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/bio/seq/GappedSequence;createGappedProteinSequencelength()I$org/biojava/bio/symbol/LocationTools makeLocation%(II)Lorg/biojava/bio/symbol/Location;Y(Ljava/lang/Object;Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/Location;)Vadd(Ljava/lang/Object;)Z(Ljava/util/List;)VprintStackTrace!$%&'(')*+*,-.>*+/ '(0123456.+/>0 127896.p0L+ + /DE"F/G0012 :;78<6._# L+  /MN"O0#12:;78 =>.Vp YN6+M+2*2:+2*2:Y*2+2:-WY-:N-hi/6 WX[\&^3_MaVX\cfdifjhnj0f #?@3#?@M AB QCDaE;fF*jGHp('p&'pIJK$ L M( NNOP6.kGYSYSYSYSY SY!S""#"# /27,99:QRPK .*?:HH=org/biojava/bio/alignment/IllegalAlignmentEditException.class2    ()VCodeLineNumberTableLocalVariableTablethis9Lorg/biojava/bio/alignment/IllegalAlignmentEditException;(Ljava/lang/String;)VmessageLjava/lang/String;(Ljava/lang/Throwable;)VtLjava/lang/Throwable;*(Ljava/lang/Throwable;Ljava/lang/String;)V SourceFile"IllegalAlignmentEditException.java    7org/biojava/bio/alignment/IllegalAlignmentEditException#org/biojava/bio/BioRuntimeException*(Ljava/lang/String;Ljava/lang/Throwable;)V! /* O   :*+ Y   :*+ ]   E*,+ a  PK /*?:ȭ,,/org/biojava/bio/alignment/NeedlemanWunsch.class2l W V V V V V V V     V V V  V  # ( & % %Y  V V  %     ?  B % % % A J  M V V ? ! "# $%& CostMatrix[[D subMatrix.Lorg/biojava/bio/alignment/SubstitutionMatrix; pairalign"Lorg/biojava/bio/symbol/Alignment; alignmentLjava/lang/String;insertDdeletegapExtmatchreplace6(DDDDDLorg/biojava/bio/alignment/SubstitutionMatrix;)VCodeLineNumberTableLocalVariableTablethis+Lorg/biojava/bio/alignment/NeedlemanWunsch; gapExtendsubMatsetSubstitutionMatrix1(Lorg/biojava/bio/alignment/SubstitutionMatrix;)Vmatrix setInsert(D)Vins setDeletedel setGapExtgesetMatchma setReplacerep getInsert()D getDelete getGapExtgetMatch getReplaceprintCostMatrix([[D[C[C)Ljava/lang/String; queryChar[C targetCharlineIcoloutput StackMapTableprintAlignment(Ljava/lang/String;)Valign getAlignmentj(Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/SymbolList;)Lorg/biojava/bio/symbol/Alignment;query#Lorg/biojava/bio/symbol/SymbolList;target ExceptionsgetEditDistancemin(DDD)DxyzgetAlignmentString()Ljava/lang/String;alignAll[(Lorg/biojava/bio/seq/SequenceIterator;Lorg/biojava/bio/seq/db/SequenceDB;)Ljava/util/List;excLjava/lang/Exception;Lorg/biojava/bio/seq/Sequence;&Lorg/biojava/bio/seq/SequenceIterator;source subjectDB#Lorg/biojava/bio/seq/db/SequenceDB;lLjava/util/List;'()pairwiseAlignmentI(Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/SymbolList;)D gap_extend[Zst+Lorg/biojava/bio/seq/io/SymbolTokenization;Lorg/biojava/bio/BioException;EFijmLjava/util/Map;timeJ[Ljava/lang/String;pathsubjectsqueryssubject%*+  matchReplaceA(Lorg/biojava/bio/seq/Sequence;Lorg/biojava/bio/seq/Sequence;II)D SourceFileNeedlemanWunsch.java f, Z[ `a ba ca da ea ^_ java/lang/StringBuilder -.[ -/] 0 -1line.separator2 34 -5delta[Edit] = 678 9 \] XYjava/util/LinkedList( :; <=> ?@ ' ABjava/lang/Exception C,org/biojava/bio/seq/Sequence'org/biojava/bio/seq/impl/SimpleSequence org/biojava/bio/SimpleAnnotation fD EFG HBI EJ KL MNjava/lang/StringO P defaultQ RS TU+ VWorg/biojava/bio/BioException#org/biojava/bio/BioRuntimeException fX-org/biojava/bio/seq/impl/SimpleGappedSequence'org/biojava/bio/symbol/SimpleSymbolListtokenY fZ [ \ ]^ f_java/util/HashMap` ab&org/biojava/bio/symbol/SimpleAlignment fc ~ dePAlphabet missmatch occured: sequences with different alphabet cannot be aligned. f fgh iF jk)org/biojava/bio/alignment/NeedlemanWunsch+org/biojava/bio/alignment/SequenceAlignmentjava/util/List$org/biojava/bio/seq/SequenceIterator java/util/NoSuchElementException!org/biojava/bio/symbol/SymbolList)org/biojava/bio/seq/io/SymbolTokenization()Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString(C)Ljava/lang/StringBuilder;java/lang/System getProperty&(Ljava/lang/String;)Ljava/lang/String;(D)Ljava/lang/StringBuilder;outLjava/io/PrintStream;java/io/PrintStreamprinthasNext()Z nextSequence ()Lorg/biojava/bio/seq/Sequence;!org/biojava/bio/seq/db/SequenceDBsequenceIterator(()Lorg/biojava/bio/seq/SequenceIterator;add(Ljava/lang/Object;)ZprintStackTracef(Lorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/bio/Annotation;)V getAlphabet#()Lorg/biojava/bio/symbol/Alphabet;java/lang/Objectequals,org/biojava/bio/alignment/SubstitutionMatrix)()Lorg/biojava/bio/symbol/FiniteAlphabet;currentTimeMillis()Jlength()Ijava/lang/Math(DD)D%org/biojava/bio/symbol/FiniteAlphabetgetTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;symbolAt"(I)Lorg/biojava/bio/symbol/Symbol;tokenizeSymbol3(Lorg/biojava/bio/symbol/Symbol;)Ljava/lang/String;(Ljava/lang/Throwable;)Vorg/biojava/bio/symbol/Alphabet@(Lorg/biojava/bio/seq/io/SymbolTokenization;Ljava/lang/String;)VgetURNgetName getAnnotation()Lorg/biojava/bio/Annotation;!(Lorg/biojava/bio/seq/Sequence;)V java/util/Mapput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;(Ljava/util/Map;)V formatOutpute(Ljava/lang/String;Ljava/lang/String;[Ljava/lang/String;Ljava/lang/String;IIJIIJDJ)Ljava/lang/String; getValueAtA(Lorg/biojava/bio/symbol/Symbol;Lorg/biojava/bio/symbol/Symbol;)Iorg/biojava/bio/symbol/Symbol getMatchescontains"(Lorg/biojava/bio/symbol/Symbol;)Z!VW XYZ[\]^_`abacadaeafgh -** *** *'*)* i&  !&,jH-kl-da-ea-`a-ba-ma -n[ oph>*+i jklq[rsh>*'i jkltaush>*'i jklvawsh>*'i jklxaysh>*'i jklza{sh>*'i jkl|a}~h/*ij kl~h/*ij kl~h/*ij kl~h/*ij kl~h/*ij kl h, :6,U& Y    :' Y   ,d4 :>+- Y     :. 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Classes to generate and describe sequence alignments.

Classes can represent alignments of one or more sequences. Gaps and unequal alignments can be represented. Quality can be represented using QualitativeAlignment. Additionally implementations of the Needleman- Wunsch and Smith-Waterman algorithms are provided.

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Tools for displaying chromatograms.

PK /*?:]oo)org/biojava/bio/chromatogram/package.html

Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.

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PK .*?:YFF'org/biojava/bio/dist/Distribution.class2;+,- . /0 12345NullModelForwarder InnerClassesWEIGHTSLorg/biojava/utils/ChangeType; NULL_MODEL getAlphabet#()Lorg/biojava/bio/symbol/Alphabet; getWeight"(Lorg/biojava/bio/symbol/Symbol;)D Exceptions6 setWeight#(Lorg/biojava/bio/symbol/Symbol;D)V7 sampleSymbol!()Lorg/biojava/bio/symbol/Symbol; getNullModel%()Lorg/biojava/bio/dist/Distribution; setNullModel&(Lorg/biojava/bio/dist/Distribution;)V8registerWithTrainer4(Lorg/biojava/bio/dist/DistributionTrainerContext;)V()VCodeLineNumberTable SourceFileDistribution.javaorg/biojava/utils/ChangeTypedistribution weights changed!org.biojava.bio.dist.Distribution 9: distribution null model changed !org/biojava/bio/dist/Distributionjava/lang/Objectorg/biojava/utils/Changeable4org/biojava/bio/dist/Distribution$NullModelForwarder-org/biojava/bio/symbol/IllegalSymbolException%org/biojava/utils/ChangeVetoException/org/biojava/bio/symbol/IllegalAlphabetException9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V   !"#$%&'=!YY ( K])*   PK .*?:PIorg/biojava/bio/dist/DistributionFactory$DefaultDistributionFactory.class2Z 4567 48 9 :; < => ?@AB CD EFG H =IJK()VCodeLineNumberTableLocalVariableTablethisDefaultDistributionFactory InnerClassesELorg/biojava/bio/dist/DistributionFactory$DefaultDistributionFactory;createDistributionF(Lorg/biojava/bio/symbol/Alphabet;)Lorg/biojava/bio/dist/Distribution;alpha!Lorg/biojava/bio/symbol/Alphabet;dis#Lorg/biojava/bio/dist/Distribution;fa'Lorg/biojava/bio/symbol/FiniteAlphabet; StackMapTable Exceptions writeReplace()Ljava/lang/Object;nsfe Ljava/lang/NoSuchFieldException;FL SourceFileDistributionFactory.java %org/biojava/bio/symbol/FiniteAlphabet/org/biojava/bio/symbol/IllegalAlphabetExceptionjava/lang/StringBuilder[The default StateFactory implementation can only produce states over finite alphabets, not MNO PQ RQ S'org/biojava/bio/dist/SimpleDistribution T)org/biojava/utils/StaticMemberPlaceHolder(org/biojava/bio/dist/DistributionFactoryDEFAULTU VW Xjava/lang/NoSuchFieldException java/io/NotSerializableException YQCorg/biojava/bio/dist/DistributionFactory$DefaultDistributionFactoryjava/lang/Objectjava/io/Serializablejava/io/ObjectStreamExceptionappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;org/biojava/bio/symbol/AlphabetgetName()Ljava/lang/String;toString(Ljava/lang/String;)V*(Lorg/biojava/bio/symbol/FiniteAlphabet;)Vjava/lang/ClassgetField-(Ljava/lang/String;)Ljava/lang/reflect/Field;(Ljava/lang/reflect/Field;)V getMessage!/*T !"#7+#YY+ +N Y- M,XY'^,c5f*7!7$%5&', ()*'+,-m YLY+klm ./!*P0+123  PK .*?:WKzz.org/biojava/bio/dist/DistributionFactory.class2  DefaultDistributionFactory InnerClassesDEFAULT*Lorg/biojava/bio/dist/DistributionFactory;createDistributionF(Lorg/biojava/bio/symbol/Alphabet;)Lorg/biojava/bio/dist/Distribution; Exceptions()VCodeLineNumberTable SourceFileDistributionFactory.javaCorg/biojava/bio/dist/DistributionFactory$DefaultDistributionFactory   (org/biojava/bio/dist/DistributionFactoryjava/lang/Object/org/biojava/bio/symbol/IllegalAlphabetException    # YF  PK /*?:`f+org/biojava/bio/dist/DistributionTest.class2 Cw>h Bx? 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B{?ffffff B| }~  } B  B  B     w     ) ,L B  5    = deltaDagctdist#Lorg/biojava/bio/dist/Distribution;gapgapDist(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis'Lorg/biojava/bio/dist/DistributionTest;nameLjava/lang/String;setUp()Viae1Lorg/biojava/bio/symbol/IllegalAlphabetException;ise/Lorg/biojava/bio/symbol/IllegalSymbolException;cve'Lorg/biojava/utils/ChangeVetoException; StackMapTabletestSimpleDistributiontestAmbiguitiessymsLjava/util/Set;tottestGapDistribution testGapDistsLorg/biojava/bio/symbol/Symbol;symsiLjava/util/Iterator; [Lorg/biojava/bio/symbol/Symbol;symLLjava/util/List;o SourceFileDistributionTest.java NO DE FE GE HE IE  JK$org/biojava/bio/dist/GapDistribution N LK%org/biojava/bio/dist/PairDistribution N MK/org/biojava/bio/symbol/IllegalAlphabetException$junit/framework/AssertionFailedErrorjava/lang/StringBuilder NX$Can't initialize test distributions F G H I-org/biojava/bio/symbol/IllegalSymbolExceptionUnable to set weights: %org/biojava/utils/ChangeVetoException  Can't retrieve weight: java/util/HashSet  real-gaporg/biojava/bio/symbol/Symbol %org/biojava/bio/symbol/FiniteAlphabet  %org/biojava/bio/dist/DistributionTestjunit/framework/TestCasejava/util/Listjava/util/Iterator(org/biojava/bio/dist/DistributionFactoryDEFAULT*Lorg/biojava/bio/dist/DistributionFactory;org/biojava/bio/seq/DNAToolsgetDNA)()Lorg/biojava/bio/symbol/FiniteAlphabet;createDistributionF(Lorg/biojava/bio/symbol/Alphabet;)Lorg/biojava/bio/dist/Distribution;$(Lorg/biojava/bio/symbol/Alphabet;)VI(Lorg/biojava/bio/dist/Distribution;Lorg/biojava/bio/dist/Distribution;)Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder; getMessage()Ljava/lang/String;toString'()Lorg/biojava/bio/symbol/AtomicSymbol;!org/biojava/bio/dist/Distribution setWeight#(Lorg/biojava/bio/symbol/Symbol;D)V getAlphabet#()Lorg/biojava/bio/symbol/Alphabet;org/biojava/bio/symbol/Alphabet getGapSymbol!()Lorg/biojava/bio/symbol/Symbol; getWeight"(Lorg/biojava/bio/symbol/Symbol;)D assertEquals(Ljava/lang/String;DDD)Vjava/lang/Object getAmbiguity0(Ljava/util/Set;)Lorg/biojava/bio/symbol/Symbol; java/util/Setadd(Ljava/lang/Object;)Z&org/biojava/bio/symbol/AlphabetManagerjava/util/ArraysasList%([Ljava/lang/Object;)Ljava/util/List;iterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object; getSymbol1(Ljava/util/List;)Lorg/biojava/bio/symbol/Symbol;!BCDEFEGEHEIEJKLKMKNOPu)*+*** * *Q& !('R)ST)UVWXP**Y*Y**"LYY +! 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PK .*?:as~g-org/biojava/bio/dist/OrderNDistribution.class2getConditioningAlphabet#()Lorg/biojava/bio/symbol/Alphabet;getConditionedAlphabetconditionedDistributions()Ljava/util/Collection;setDistributionE(Lorg/biojava/bio/symbol/Symbol;Lorg/biojava/bio/dist/Distribution;)V ExceptionsgetDistributionD(Lorg/biojava/bio/symbol/Symbol;)Lorg/biojava/bio/dist/Distribution; SourceFileOrderNDistribution.java'org/biojava/bio/dist/OrderNDistributionjava/lang/Object!org/biojava/bio/dist/Distribution-org/biojava/bio/symbol/IllegalSymbolException/org/biojava/bio/symbol/IllegalAlphabetException     PK .*?:f4org/biojava/bio/dist/OrderNDistributionFactory.class2[ 2 3 4 56 57 89: ;< 5= >?@ 2 5AB ;C D E DFGDEFAULT*Lorg/biojava/bio/dist/DistributionFactory;df-(Lorg/biojava/bio/dist/DistributionFactory;)VCodeLineNumberTableLocalVariableTablethis0Lorg/biojava/bio/dist/OrderNDistributionFactory;createDistributionF(Lorg/biojava/bio/symbol/Alphabet;)Lorg/biojava/bio/dist/Distribution; conditioned!Lorg/biojava/bio/symbol/Alphabet; conditioninglLjava/util/List;alphaaList StackMapTableH ExceptionsI()V SourceFileOrderNDistributionFactory.java /  JKH LM NOP QR0org/biojava/bio/dist/IndexedNthOrderDistribution Sorg/biojava/bio/symbol/Alphabet TUV WXjava/util/ArrayList YZ0org/biojava/bio/dist/GeneralNthOrderDistribution.org/biojava/bio/dist/OrderNDistributionFactory  java/lang/Object(org/biojava/bio/dist/DistributionFactoryjava/util/List/org/biojava/bio/symbol/IllegalAlphabetException getAlphabets()Ljava/util/List;size()Iget(I)Ljava/lang/Object;org/biojava/bio/seq/DNAToolsgetDNA)()Lorg/biojava/bio/symbol/FiniteAlphabet;N(Lorg/biojava/bio/symbol/Alphabet;Lorg/biojava/bio/dist/DistributionFactory;)VsubList(II)Ljava/util/List;&org/biojava/bio/symbol/AlphabetManagergetCrossProductAlphabet3(Ljava/util/List;)Lorg/biojava/bio/symbol/Alphabet;add(Ljava/lang/Object;)Z!F **+>? @  !"+M,,Y+*,,d N,,d  : Y :W-W LY+** XY]+`=aQcZddemfsh>=C#$Q/%$Z&&' ($y)'*++,-./*Y 1 201PK .*?:2a-org/biojava/bio/dist/PairDistribution$1.class2   SourceFilePairDistribution.javaEnclosingMethod 'org/biojava/bio/dist/PairDistribution$1 InnerClassesjava/lang/Object%org/biojava/bio/dist/PairDistribution  PK .*?: %l  7org/biojava/bio/dist/PairDistribution$PairTrainer.class2w B C D EF GH I JKL EM NO EP?QRS DT U V W XY I NZ[\]this$0'Lorg/biojava/bio/dist/PairDistribution;*(Lorg/biojava/bio/dist/PairDistribution;)VCodeLineNumberTableLocalVariableTablethis PairTrainer InnerClasses3Lorg/biojava/bio/dist/PairDistribution$PairTrainer;getCountY(Lorg/biojava/bio/dist/DistributionTrainerContext;Lorg/biojava/bio/symbol/AtomicSymbol;)Ddtc1Lorg/biojava/bio/dist/DistributionTrainerContext;as%Lorg/biojava/bio/symbol/AtomicSymbol;symLLjava/util/List;fLorg/biojava/bio/symbol/Symbol;s ExceptionsaddCountT(Lorg/biojava/bio/dist/DistributionTrainerContext;Lorg/biojava/bio/symbol/Symbol;D)VsymtimesD StackMapTable^S(Lorg/biojava/bio/dist/PairDistribution;Lorg/biojava/bio/dist/PairDistribution$1;)Vx0x1)Lorg/biojava/bio/dist/PairDistribution$1; SourceFilePairDistribution.java   _` abc de fgh ijorg/biojava/bio/symbol/Symbol klm (n ol#org/biojava/bio/symbol/AtomicSymbol-org/biojava/bio/symbol/IllegalSymbolExceptionjava/lang/StringBuilder-Can't add counts for ambiguity symbols. 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You must set the weights in the underlying distributions. o~org/biojava/bio/symbol/Alphabet QR   tu -org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/BioErrorCouldn't sample symbol ojava/util/HashMap$org/biojava/utils/AbstractChangeablejava/io/Serializable'org/biojava/bio/dist/PairDistribution$1java/lang/Objectjava/util/Listjava/lang/Throwable/org/biojava/bio/symbol/IllegalAlphabetExceptionjava/util/Iteratororg/biojava/utils/ListTools'(Ljava/lang/Object;Ljava/lang/Object;)V java/util/Mapget&(Ljava/lang/Object;)Ljava/lang/Object;(Ljava/lang/Object;)Vput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;()Ljava/lang/Object;(Ljava/lang/String;)Vorg/biojava/bio/dp/ModelTrainerregisterDistributionS(Lorg/biojava/bio/dist/PairDistribution;Lorg/biojava/bio/dist/PairDistribution$1;)VregisterTrainerP(Lorg/biojava/bio/dist/Distribution;Lorg/biojava/bio/dist/DistributionTrainer;)V getSymbols()Ljava/util/List;(I)Ljava/lang/Object; getMatchesiterator()Ljava/util/Iterator;hasNext()Znextjava/util/ArraysasList%([Ljava/lang/Object;)Ljava/util/List;&org/biojava/bio/symbol/AlphabetManagergetCrossProductAlphabet3(Ljava/util/List;)Lorg/biojava/bio/symbol/Alphabet;/org/biojava/bio/dist/DistributionTrainerContext getSymbol1(Ljava/util/List;)Lorg/biojava/bio/symbol/Symbol;*(Ljava/lang/String;Ljava/lang/Throwable;)V! 45 :;<=>=?@ ABCXYM*K+LY*+N-:$ Y*+ :-Y W0 :! Y*+ :-Y W,ð:,D:JK LMN,P1Q<RRT\UaVlWZ[E><F=fGH,XIJ\(F=<=>=K'RLMN,OOOLPQRC/*DcE STAUC6 **DgE  STVWC> YDlE ST X=YZ[\Ce%+*+*+*Y*Dv wy$zE%ST%]^_`C$u+;+M,N,:*-*kI+: !":(*#cI(D2 ~(?AQ[gpsER.aH#bc(dcg deQ"fgA4hiuSTujcK ?k!Y.lmCH Y$DE  ST jc niYopC}/*%*+*,*&Y+'SY,'S()D .E /ST/<=/>=[qCI+*Y**D ESTrstuC5*+Y*,SY*,S(-L/Y0+1().D)*E* vw5STKixyzC/*D8E {T|zC/*D8E {T}~C' 2Y3D > ?86  9 PK /*?:m8/org/biojava/bio/dist/SimpleDistribution$1.class2.   !"# $%&this$0)Lorg/biojava/bio/dist/SimpleDistribution;,(Lorg/biojava/bio/dist/SimpleDistribution;)VCodeLineNumberTableLocalVariableTablethis InnerClasses+Lorg/biojava/bio/dist/SimpleDistribution$1; preChange"(Lorg/biojava/utils/ChangeEvent;)VceLorg/biojava/utils/ChangeEvent; StackMapTable Exceptions SourceFileSimpleDistribution.javaEnclosingMethod' () * +,%org/biojava/utils/ChangeVetoException9Can't allow the index to change as we have probabilities. -)org/biojava/bio/dist/SimpleDistribution$1org/biojava/utils/ChangeAdapter'org/biojava/bio/dist/SimpleDistribution readObject(Ljava/io/ObjectInputStream;)V()V hasWeights()Z4(Lorg/biojava/utils/ChangeEvent;Ljava/lang/String;)V    4 *+*`   [*Y+b ch PK /*?:a))/org/biojava/bio/dist/SimpleDistribution$2.class2.   !"# $%&this$0)Lorg/biojava/bio/dist/SimpleDistribution;,(Lorg/biojava/bio/dist/SimpleDistribution;)VCodeLineNumberTableLocalVariableTablethis InnerClasses+Lorg/biojava/bio/dist/SimpleDistribution$2; preChange"(Lorg/biojava/utils/ChangeEvent;)VceLorg/biojava/utils/ChangeEvent; StackMapTable Exceptions SourceFileSimpleDistribution.javaEnclosingMethod' () * +,%org/biojava/utils/ChangeVetoException9Can't allow the index to change as we have probabilities. -)org/biojava/bio/dist/SimpleDistribution$2org/biojava/utils/ChangeAdapter'org/biojava/bio/dist/SimpleDistribution initialise*(Lorg/biojava/bio/symbol/FiniteAlphabet;)V()V hasWeights()Z4(Lorg/biojava/utils/ChangeEvent;Ljava/lang/String;)V    4 *+*   [*Y+  PK /*?:Ԋe)Aorg/biojava/bio/dist/SimpleDistribution$SymbolWeightMemento.class2%    !"serialVersionUIDJ ConstantValueH|GdHbӁsymbolLorg/biojava/bio/symbol/Symbol;weightD#(Lorg/biojava/bio/symbol/Symbol;D)VCodeLineNumberTableLocalVariableTablethisSymbolWeightMemento InnerClasses=Lorg/biojava/bio/dist/SimpleDistribution$SymbolWeightMemento;s SourceFileSimpleDistribution.java # $;org/biojava/bio/dist/SimpleDistribution$SymbolWeightMementojava/lang/Objectjava/io/Serializable()V'org/biojava/bio/dist/SimpleDistribution    Y**+*(DE FG    PK /*?:jc115org/biojava/bio/dist/SimpleDistribution$Trainer.class2 !a "bc de f !g hijkl m hn hop q hr ds !t uv dwx y z{ z| d} d~  ! ucountsLorg/biojava/bio/dist/Count;this$0)Lorg/biojava/bio/dist/SimpleDistribution;,(Lorg/biojava/bio/dist/SimpleDistribution;)VCodeLineNumberTableLocalVariableTablethisTrainer InnerClasses1Lorg/biojava/bio/dist/SimpleDistribution$Trainer;addCountZ(Lorg/biojava/bio/dist/DistributionTrainerContext;Lorg/biojava/bio/symbol/AtomicSymbol;D)Vcve'Lorg/biojava/utils/ChangeVetoException;dtc1Lorg/biojava/bio/dist/DistributionTrainerContext;sym%Lorg/biojava/bio/symbol/AtomicSymbol;timesD StackMapTablej ExceptionsgetCountY(Lorg/biojava/bio/dist/DistributionTrainerContext;Lorg/biojava/bio/symbol/AtomicSymbol;)D clearCounts4(Lorg/biojava/bio/dist/DistributionTrainerContext;)ViIsizetrain5(Lorg/biojava/bio/dist/DistributionTrainerContext;D)VceLorg/biojava/utils/ChangeEvent; changeSupport!Lorg/biojava/utils/ChangeSupport;weight trainImpls nullModel#Lorg/biojava/bio/dist/Distribution;weights[Dtotalsumsum_invise/Lorg/biojava/bio/symbol/IllegalSymbolException;V SourceFileSimpleDistribution.java &' (!org/biojava/bio/dist/IndexedCount ( $% %org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioError0Assertion Failure: Change to Count object vetoed ( > %org/biojava/bio/symbol/FiniteAlphabet D QF org/biojava/utils/ChangeEvent (  #org/biojava/bio/symbol/AtomicSymbol >? 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Trainer InnerClassesSymbolWeightMementoserialVersionUIDJ ConstantValuedM#Qpindexer&Lorg/biojava/bio/symbol/AlphabetIndex;weights[D nullModel#Lorg/biojava/bio/dist/Distribution;alpha'Lorg/biojava/bio/symbol/FiniteAlphabet; writeObject(Ljava/io/ObjectOutputStream;)VCodeLineNumberTableLocalVariableTablewIswm>[Lorg/biojava/bio/dist/SimpleDistribution$SymbolWeightMemento;this)Lorg/biojava/bio/dist/SimpleDistribution;oosLjava/io/ObjectOutputStream; StackMapTable Exceptions readObject(Ljava/io/ObjectInputStream;)Vex/Lorg/biojava/bio/symbol/IllegalSymbolException;mstreamLjava/io/ObjectInputStream; getAlphabet#()Lorg/biojava/bio/symbol/Alphabet; getNullModel%()Lorg/biojava/bio/dist/Distribution;setNullModelImpl&(Lorg/biojava/bio/dist/Distribution;)V hasWeights()Z getWeights()[Di getWeightImpl((Lorg/biojava/bio/symbol/AtomicSymbol;)Dindexs%Lorg/biojava/bio/symbol/AtomicSymbol; setWeightImpl)(Lorg/biojava/bio/symbol/AtomicSymbol;D)VDP initialise*(Lorg/biojava/bio/symbol/FiniteAlphabet;)VeLjava/lang/Exception;alphabetalfaSizeisedistregisterWithTrainer4(Lorg/biojava/bio/dist/DistributionTrainerContext;)Vdtc1Lorg/biojava/bio/dist/DistributionTrainerContext; access$000Q(Lorg/biojava/bio/dist/SimpleDistribution;)Lorg/biojava/bio/symbol/AlphabetIndex;x0 access$100,(Lorg/biojava/bio/dist/SimpleDistribution;)Z SourceFileSimpleDistribution.java v MN OP;org/biojava/bio/dist/SimpleDistribution$SymbolWeightMemento U ST )org/biojava/bio/dist/SimpleDistribution$1 d -org/biojava/bio/symbol/IllegalSymbolExceptionjava/io/IOExceptionjava/lang/StringBuilder Symbol in serialized stream:   can't be found in the alphabet   m QR mn%org/biojava/bio/symbol/FiniteAlphabet uv wx"java/lang/IllegalArgumentException$Can't set weight to negative score:  -> )org/biojava/bio/dist/SimpleDistribution$2(org/biojava/bio/dist/UniformDistribution  rjava/lang/Exceptionorg/biojava/bio/BioError-This should never fail. Something is screwed!      an impossible error surely!   /org/biojava/bio/dist/SimpleDistribution$Trainer 'org/biojava/bio/dist/SimpleDistribution)org/biojava/bio/dist/AbstractDistributionjava/io/Serializable java/lang/ClassNotFoundException/org/biojava/bio/symbol/IllegalAlphabetException%org/biojava/utils/ChangeVetoException!org/biojava/bio/dist/Distribution hasListenersjava/io/ObjectOutputStreamdefaultWriteObject()V$org/biojava/bio/symbol/AlphabetIndexsymbolForIndex"(I)Lorg/biojava/bio/symbol/Symbol;#(Lorg/biojava/bio/symbol/Symbol;D)V(Ljava/lang/Object;)Vjava/io/ObjectInputStreamdefaultReadObject&org/biojava/bio/symbol/AlphabetManagergetAlphabetIndexO(Lorg/biojava/bio/symbol/FiniteAlphabet;)Lorg/biojava/bio/symbol/AlphabetIndex;,(Lorg/biojava/bio/dist/SimpleDistribution;)VINDEXLorg/biojava/utils/ChangeType;addChangeListenerC(Lorg/biojava/utils/ChangeListener;Lorg/biojava/utils/ChangeType;)Vsize()I()Ljava/lang/Object;symbolLorg/biojava/bio/symbol/Symbol;indexForSymbol"(Lorg/biojava/bio/symbol/Symbol;)Iweightappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;org/biojava/bio/symbol/SymbolgetName()Ljava/lang/String;toString(Ljava/lang/String;)V)()Lorg/biojava/bio/symbol/FiniteAlphabet;#org/biojava/bio/symbol/AtomicSymbol(D)Ljava/lang/StringBuilder; 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Probability distributions over Alphabets. Distributions are useful in many aspects of bioinformatics, especially when performing statistical methods. They are used to encapsulate emission spectra in weight matrices and Hidden Markov Models.

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EmissionWrapper InnerClassesDotStateWrapperWrappersource Lorg/biojava/bio/dp/MarkovModel;delegate addAState(Lorg/biojava/bio/dp/State;)VCodeLineNumberTableLocalVariableTablecve'Lorg/biojava/utils/ChangeVetoException;thisLorg/biojava/bio/dp/FlatModel;ourStateLorg/biojava/bio/dp/State; StackMapTable Exceptionsadvance()[IemissionAlphabet#()Lorg/biojava/bio/symbol/Alphabet; stateAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;heads()I magicalState#()Lorg/biojava/bio/dp/MagicalState; getWeights?(Lorg/biojava/bio/dp/State;)Lorg/biojava/bio/dist/Distribution;containsTransition7(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)ZfromtotransitionsFromC(Lorg/biojava/bio/dp/State;)Lorg/biojava/bio/symbol/FiniteAlphabet; transitionsTo setWeights@(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dist/Distribution;)Vdist#Lorg/biojava/bio/dist/Distribution;#(Lorg/biojava/bio/dp/MarkovModel;)Vdsw.Lorg/biojava/bio/dp/FlatModel$DotStateWrapper;esw.Lorg/biojava/bio/dp/FlatModel$EmissionWrapper;tjLjava/util/Iterator;mis!Lorg/biojava/bio/dp/ModelInState;flatMstartendsisOrigsModelswrapper&Lorg/biojava/bio/dp/FlatModel$Wrapper;swrappedsubModeltOrig-Lorg/biojava/bio/dist/TranslatedDistribution;table9Lorg/biojava/bio/symbol/SimpleReversibleTranslationTable;modeltoMLjava/util/Map;inModelmisStartmisEnd modelStartmodelEndcreateTransition7(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)Va!Lorg/biojava/bio/symbol/Alphabet;destroyTransitionaddStatetoAdd removeStatetoGoregisterWithTrainer$(Lorg/biojava/bio/dp/ModelTrainer;)V modelTrainer!Lorg/biojava/bio/dp/ModelTrainer; SourceFileFlatModel.java ON Q%org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioError+This model should be ours with no listeners u ^_ `a bc de fg hi jk no po#Can't set weights in immutable view u u MN$org/biojava/bio/dp/SimpleMarkovModelflat ujava/util/HashMap   org/biojava/bio/dp/Stateorg/biojava/bio/dp/DotState,org/biojava/bio/dp/FlatModel$DotStateWrapper uQ PQ    org/biojava/bio/dp/EmissionStateorg/biojava/bio/dp/MagicalState,org/biojava/bio/dp/FlatModel$EmissionWrapper u org/biojava/bio/dp/ModelInState     u$org/biojava/bio/dp/FlatModel$Wrapper -org/biojava/bio/symbol/IllegalSymbolExceptionjava/lang/StringBuilder Don't know how to handle state:    u org/biojava/bio/dp/MarkovModel 7org/biojava/bio/symbol/SimpleReversibleTranslationTable qrCouldn't edit delegate model  !"'java/lang/UnsupportedOperationException+createTransition not supported by FlatModel,destroyTransition not supported by FlatModel#addState not supported by FlatModel&removeState not supported by FlatModel# $vorg/biojava/bio/dp/FlatModel$org/biojava/utils/AbstractChangeablejava/io/Serializable java/util/Mapjava/util/Iterator+org/biojava/bio/dist/TranslatedDistribution/org/biojava/bio/symbol/IllegalAlphabetException*(Ljava/lang/String;Ljava/lang/Throwable;)V(Ljava/lang/String;)V()V7(ILorg/biojava/bio/symbol/Alphabet;Ljava/lang/String;)V%org/biojava/bio/symbol/FiniteAlphabetiterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object;put8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;%(Lorg/biojava/bio/dp/EmissionState;)VgetModel"()Lorg/biojava/bio/dp/MarkovModel;org/biojava/bio/dp/DPflatViewB(Lorg/biojava/bio/dp/MarkovModel;)Lorg/biojava/bio/dp/MarkovModel;/(Lorg/biojava/bio/dp/State;Ljava/lang/String;)V getWrapped()Lorg/biojava/bio/dp/State;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;getName()Ljava/lang/String;toString4(Lorg/biojava/bio/symbol/Symbol;Ljava/lang/String;)Vget&(Ljava/lang/Object;)Ljava/lang/Object;getTable5()Lorg/biojava/bio/symbol/ReversibleTranslationTable;setTranslationM(Lorg/biojava/bio/symbol/AtomicSymbol;Lorg/biojava/bio/symbol/AtomicSymbol;)Vorg/biojava/bio/symbol/Alphabetvalidate"(Lorg/biojava/bio/symbol/Symbol;)Vorg/biojava/bio/dp/ModelTrainer registerModel FG7HMNONPQR}*+MY, SI L JKMT  UVWXYZ[M\ ].^_R4 *SPT  WX`aR4 *STT  WXbcR4 * SXT  WXdeR4 * S\T  WXfgR4 * S`T  WXhiR? 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Y" 1 2>?  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F %org/biojava/utils/ChangeVetoExceptionCould not modify model.-org/biojava/bio/symbol/IllegalSymbolException-org/biojava/bio/dp/IllegalTransitionException Everything (org/biojava/bio/dist/UniformDistribution  %org/biojava/bio/symbol/FiniteAlphabet F  No architecture event: One parameter events:  Two parameter events: 'org/biojava/bio/dp/MarkovModelEventTestjunit/framework/TestCaseorg/biojava/bio/seq/DNAToolsgetDNA)()Lorg/biojava/bio/symbol/FiniteAlphabet;7(ILorg/biojava/bio/symbol/Alphabet;Ljava/lang/String;)V(Ljava/lang/String;)Vorg/biojava/bio/dp/MarkovModel ARCHITECTURELorg/biojava/utils/ChangeType;addChangeListenerC(Lorg/biojava/utils/ChangeListener;Lorg/biojava/utils/ChangeType;)V PARAMETERorg/biojava/bio/AnnotationEMPTY_ANNOTATIONLorg/biojava/bio/Annotation;(org/biojava/bio/dist/DistributionFactoryDEFAULT*Lorg/biojava/bio/dist/DistributionFactory;createDistributionF(Lorg/biojava/bio/symbol/Alphabet;)Lorg/biojava/bio/dist/Distribution;V(Ljava/lang/String;Lorg/biojava/bio/Annotation;[ILorg/biojava/bio/dist/Distribution;)VaddState(Lorg/biojava/bio/dp/State;)Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString()Ljava/lang/String; 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SourceFileModelInState.javaorg/biojava/bio/dp/ModelInStatejava/lang/Objectorg/biojava/bio/dp/StatePK .*?:%org/biojava/bio/dp/ModelTrainer.class2    registerModel#(Lorg/biojava/bio/dp/MarkovModel;)V SourceFileModelTrainer.javaorg/biojava/bio/dp/ModelTrainerjava/lang/Object/org/biojava/bio/dist/DistributionTrainerContextPK /*?:^bJo#org/biojava/bio/dp/ProfileHMM.class2 ,jkl mn o pq r s ,tu ,vw ,xy ,z -{|} ,~ ,  , s , $ , , , , ,advance[IcolumnsI matchStates#[Lorg/biojava/bio/dp/EmissionState; insertStates deleteStates[Lorg/biojava/bio/dp/DotState;()ICodeLineNumberTableLocalVariableTablethisLorg/biojava/bio/dp/ProfileHMM;getMatch%(I)Lorg/biojava/bio/dp/EmissionState;indx StackMapTable Exceptions getInsert getDelete (I)Lorg/biojava/bio/dp/DotState;y(Lorg/biojava/bio/symbol/Alphabet;ILorg/biojava/bio/dist/DistributionFactory;Lorg/biojava/bio/dist/DistributionFactory;)Valpha!Lorg/biojava/bio/symbol/Alphabet; matchFactory*Lorg/biojava/bio/dist/DistributionFactory; insertFactory Deprecated(Lorg/biojava/bio/symbol/Alphabet;ILorg/biojava/bio/dist/DistributionFactory;Lorg/biojava/bio/dist/DistributionFactory;Ljava/lang/String;)VmN"Lorg/biojava/bio/dp/EmissionState;iNdNLorg/biojava/bio/dp/DotState;imOiOcve'Lorg/biojava/utils/ChangeVetoException;nameLjava/lang/String;| connectModel()VdO} SourceFileProfileHMM.java 01#java/lang/IndexOutOfBoundsExceptionjava/lang/StringBuilder Ed%Match-state index must be within (0.. ), not E 23&Insert-state index must be within (0.. 43&delete-state index must be within (1.. 56 EP E org/biojava/bio/dp/EmissionStateorg/biojava/bio/dp/DotState &org/biojava/bio/dp/SimpleEmissionStatei-0 ./ E m-i-!org/biojava/bio/dp/SimpleDotStated- cd%org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioErrorUnable to construct profile HMM E => B> 07 CDorg/biojava/bio/dp/ProfileHMM$org/biojava/bio/dp/SimpleMarkovModel-org/biojava/bio/symbol/IllegalSymbolException-org/biojava/bio/dp/IllegalTransitionException/org/biojava/bio/symbol/IllegalAlphabetExceptionorg/biojava/bio/symbol/Alphabet(org/biojava/bio/dist/DistributionFactoryjava/lang/Stringappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/String;)V7(ILorg/biojava/bio/symbol/Alphabet;Ljava/lang/String;)V magicalState#()Lorg/biojava/bio/dp/MagicalState;org/biojava/bio/AnnotationEMPTY_ANNOTATIONLorg/biojava/bio/Annotation;createDistributionF(Lorg/biojava/bio/symbol/Alphabet;)Lorg/biojava/bio/dist/Distribution;V(Ljava/lang/String;Lorg/biojava/bio/Annotation;[ILorg/biojava/bio/dist/Distribution;)VaddState(Lorg/biojava/bio/dp/State;)V*(Ljava/lang/String;Ljava/lang/Throwable;)VcreateTransition7(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)V!,-./01234356078/*9K: ;<=>8> *`,YY*` * 29\]7b:>;<>?1@(AB>8: **YY * * 29s t3y::;<:?1@ &ACD8= **YY* *d29 4:=;<=?1@ &AEF8b *+-9  :4 ;< GH 01 IJ KJALMNOEP8 8*+**` *` **:Y+:* S* S*6YY -+: YY +: YY  !: * * * *  S*  S*d S : :N* `*S*":$Y%&&)#9v !)/HPX^g "&)+7: QR TSR 7TU aV1/WRHXR+ YZ8;<8GH8018IJ8KJ8[\@>a ]^__`aa]^__`b ALMNcd8*'L*(MN*+,)*,,)6**r*':*(:*+:*+)*)*+)*)*,)*,)*-)*-)*)LMN*+*)*,*)*-*)9n &.6>EMT\cj p w ~ :R.aQR6YSR>QTUxV1;<WR XReU@5]aaf`aaf]aafA #LMNgd8#  YO9)hiPK .*?:E,org/biojava/bio/dp/ScoreType$NullModel.class2)    !"()VCodeLineNumberTableLocalVariableTablethis NullModel InnerClasses(Lorg/biojava/bio/dp/ScoreType$NullModel;calculateScoreE(Lorg/biojava/bio/dist/Distribution;Lorg/biojava/bio/symbol/Symbol;)Ddist#Lorg/biojava/bio/dist/Distribution;symLorg/biojava/bio/symbol/Symbol; Exceptions# SourceFileScoreType.java  $ %& '(&org/biojava/bio/dp/ScoreType$NullModeljava/lang/Objectorg/biojava/bio/dp/ScoreTypejava/io/Serializable-org/biojava/bio/symbol/IllegalSymbolException!org/biojava/bio/dist/Distribution getNullModel%()Lorg/biojava/bio/dist/Distribution; getWeight"(Lorg/biojava/bio/symbol/Symbol;)D!  /* V   K +, Y      PK .*?:翼'org/biojava/bio/dp/ScoreType$Odds.class2,   !"#$%()VCodeLineNumberTableLocalVariableTablethisOdds InnerClasses#Lorg/biojava/bio/dp/ScoreType$Odds;calculateScoreE(Lorg/biojava/bio/dist/Distribution;Lorg/biojava/bio/symbol/Symbol;)Ddist#Lorg/biojava/bio/dist/Distribution;symLorg/biojava/bio/symbol/Symbol;dDn Exceptions& SourceFileScoreType.java  ' () *+!org/biojava/bio/dp/ScoreType$Oddsjava/lang/Objectorg/biojava/bio/dp/ScoreTypejava/io/Serializable-org/biojava/bio/symbol/IllegalSymbolException!org/biojava/bio/dist/Distribution getWeight"(Lorg/biojava/bio/symbol/Symbol;)D getNullModel%()Lorg/biojava/bio/dist/Distribution;!  /* D   u+,J+,9)o GHJ 4   PK .*?:lUU.org/biojava/bio/dp/ScoreType$Probability.class2%   ()VCodeLineNumberTableLocalVariableTablethis Probability InnerClasses*Lorg/biojava/bio/dp/ScoreType$Probability;calculateScoreE(Lorg/biojava/bio/dist/Distribution;Lorg/biojava/bio/symbol/Symbol;)Ddist#Lorg/biojava/bio/dist/Distribution;symLorg/biojava/bio/symbol/Symbol; Exceptions! SourceFileScoreType.java " #$(org/biojava/bio/dp/ScoreType$Probabilityjava/lang/Objectorg/biojava/bio/dp/ScoreTypejava/io/Serializable-org/biojava/bio/symbol/IllegalSymbolException!org/biojava/bio/dist/Distribution getWeight"(Lorg/biojava/bio/symbol/Symbol;)D! /* 3   F+, 6    PK .*?:@"org/biojava/bio/dp/ScoreType.class2)  !  "#  $%& NullModel InnerClassesOdds Probability PROBABILITYLorg/biojava/bio/dp/ScoreType;ODDS NULL_MODELcalculateScoreE(Lorg/biojava/bio/dist/Distribution;Lorg/biojava/bio/symbol/Symbol;)D Exceptions'()VCodeLineNumberTable SourceFileScoreType.java(org/biojava/bio/dp/ScoreType$Probability ( !org/biojava/bio/dp/ScoreType$Odds &org/biojava/bio/dp/ScoreType$NullModel org/biojava/bio/dp/ScoreTypejava/lang/Object-org/biojava/bio/symbol/IllegalSymbolException ?YYY + :N      PK /*?:R$ww'org/biojava/bio/dp/SimpleDotState.class2"  2(CLjava/lang/String;Lorg/biojava/bio/Annotation;)VCodeLineNumberTableLocalVariableTablethis#Lorg/biojava/bio/dp/SimpleDotState;tokenCnameLjava/lang/String; annotationLorg/biojava/bio/Annotation; Deprecated1(Ljava/lang/String;Lorg/biojava/bio/Annotation;)V(Ljava/lang/String;)V SourceFileSimpleDotState.java  !!org/biojava/bio/dp/SimpleDotState.org/biojava/bio/symbol/FundamentalAtomicSymbolorg/biojava/bio/dp/DotStatejava/io/Serializableorg/biojava/bio/AnnotationEMPTY_ANNOTATION! S*,- 23 *  I*+, :;   A *+ >?  PK .*?:E3v,org/biojava/bio/dp/SimpleEmissionState.class2 &o &pq (r s &t uv &w xy xz x{ u| &} (~ & { & ( & &   '  & 't r  # &dis#Lorg/biojava/bio/dist/Distribution;nameLjava/lang/String;annLorg/biojava/bio/Annotation;advance[Imatches!Lorg/biojava/bio/symbol/Alphabet;annotationForwarder#Lorg/biojava/utils/ChangeForwarder; distForwarder getAnnotation()Lorg/biojava/bio/Annotation;CodeLineNumberTableLocalVariableTablethis(Lorg/biojava/bio/dp/SimpleEmissionState; setAnnotation(Lorg/biojava/bio/Annotation;)VceLorg/biojava/utils/ChangeEvent; changeSupport!Lorg/biojava/utils/ChangeSupport; StackMapTableq ExceptionsgetDistribution%()Lorg/biojava/bio/dist/Distribution;setDistribution&(Lorg/biojava/bio/dist/Distribution;)V getAdvance()[I setAdvance([I)V1getToken()CgetName()Ljava/lang/String;setName(Ljava/lang/String;)V getMatches#()Lorg/biojava/bio/symbol/Alphabet;getBases()Ljava/util/Set; getSymbols()Ljava/util/List;V(Ljava/lang/String;Lorg/biojava/bio/Annotation;[ILorg/biojava/bio/dist/Distribution;)VregisterWithTrainer$(Lorg/biojava/bio/dp/ModelTrainer;)Vtrainer!Lorg/biojava/bio/dp/ModelTrainer;getChangeSupportA(Lorg/biojava/utils/ChangeType;)Lorg/biojava/utils/ChangeSupport;ctLorg/biojava/utils/ChangeType;cs SourceFileSimpleEmissionState.java ./ org/biojava/utils/ChangeEvent k b hi 45 k *+ k 65 k k 01 k ,- 23 org/biojava/utils/SingletonList b b(org/biojava/bio/symbol/SingletonAlphabet b MN P )org/biojava/utils/ChangeForwarder$RetyperRetyper InnerClasses b 78&org/biojava/bio/dp/SimpleEmissionState$org/biojava/utils/AbstractChangeable org/biojava/bio/dp/EmissionStatejava/io/Serializableorg/biojava/bio/Annotationorg/biojava/utils/ChangeSupportjava/lang/Objectjava/lang/Throwable%org/biojava/utils/ChangeVetoException hasListeners()Z ANNOTATIONW(Ljava/lang/Object;Lorg/biojava/utils/ChangeType;Ljava/lang/Object;Ljava/lang/Object;)VfirePreChangeEvent"(Lorg/biojava/utils/ChangeEvent;)VPROPERTYremoveChangeListenerC(Lorg/biojava/utils/ChangeListener;Lorg/biojava/utils/ChangeType;)VaddChangeListenerfirePostChangeEvent DISTRIBUTION!org/biojava/bio/dist/DistributionWEIGHTS NULL_MODELADVANCEjava/lang/StringcharAt(I)Cjava/util/Collections singleton#(Ljava/lang/Object;)Ljava/util/Set;(Ljava/lang/Object;)V()V((Lorg/biojava/bio/symbol/AtomicSymbol;)Vorg/biojava/bio/dp/ModelTrainerregisterDistributionorg/biojava/bio/Annotatableorg/biojava/utils/ChangeTypeisMatchingType!(Lorg/biojava/utils/ChangeType;)Z!org/biojava/utils/ChangeForwarderT(Ljava/lang/Object;Lorg/biojava/utils/ChangeSupport;Lorg/biojava/utils/ChangeType;)V!&'()*+,-./01234565789/*:A; <=>?9h* *+[Y**+M*N-Y:-,** +* *+-, ç :-\__d_:2 FGI M(N-O2PBQORTSYTgV;* G@A(?BCh<=h./DOEFGHIJKLMN9/* :Y; <=OP9A* *+ Y** +M*N-Y:-,* #* ** *++*+**+ -, ç :-:B^_a e(f-g2h9iIjYl]mjnwp|qrt;* o@A(gBC<=*+DIGHIOJKLQR9/*:w; <=ST9K* *+>Y**+M*N-Y:-,*+-, ç :-?BBGB:* |} (-27<J;* *@A("BCK<=K01D2EUGHIJKLVW93 *:;  <=XY9/*:; <=Z[9>*+: ;<=,-\]9/*:; <=^_9/*:; <=`a93 Y*:;  <=bc9&**+*,*-* *Y*: %;4&<=&,-&./&01&*+de9C +*:  ; <= fghi9z*+ M*-+!"#*#Y*, $*%*! *=+"3*#Y*,$****,:& '7HXhx; z<=zjktlCD 7H@mn # PK .*?: )org/biojava/bio/dp/SimpleHMMTrainer.class2 TU T V W XY Z [\ ]^ ]_`a b cd ef Xg ch cijk l Xmno lp cqrs tuvwdtc1Lorg/biojava/bio/dist/DistributionTrainerContext;states'Lorg/biojava/bio/symbol/FiniteAlphabet;model Lorg/biojava/bio/dp/MarkovModel;#(Lorg/biojava/bio/dp/MarkovModel;)VCodeLineNumberTableLocalVariableTable thisEmitter"Lorg/biojava/bio/dp/EmissionState; emissionDist#Lorg/biojava/bio/dist/Distribution; thisStateLorg/biojava/bio/dp/State; transDiststateILjava/util/Iterator;this%Lorg/biojava/bio/dp/SimpleHMMTrainer; StackMapTableuxy` Exceptions startCycle()VrecordEmittedSymbol=(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/symbol/Symbol;D)VstatesymbolLorg/biojava/bio/symbol/Symbol;weightDrecordTransition8(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;D)Vise/Lorg/biojava/bio/symbol/IllegalSymbolException;sourcedestj completeCyclecve'Lorg/biojava/utils/ChangeVetoException;r SourceFileSimpleHMMTrainer.java (?5org/biojava/bio/dist/SimpleDistributionTrainerContext "# &'x z{ $%| }~y  org/biojava/bio/dp/State org/biojava/bio/dp/EmissionState   ? -org/biojava/bio/symbol/IllegalSymbolException(specified State is not an EmissionState. ( "java/lang/IllegalArgumentException3the specified transition is illegal for this model.*either source or destination are not valid ?%org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioException (#org/biojava/bio/dp/SimpleHMMTrainerjava/lang/Objectorg/biojava/bio/dp/HMMTrainerorg/biojava/bio/dp/MarkovModeljava/util/Iterator stateAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;%org/biojava/bio/symbol/FiniteAlphabetiterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object;getDistribution%()Lorg/biojava/bio/dist/Distribution;/org/biojava/bio/dist/DistributionTrainerContextregisterDistribution&(Lorg/biojava/bio/dist/Distribution;)V!org/biojava/bio/dist/DistributionregisterWithTrainer4(Lorg/biojava/bio/dist/DistributionTrainerContext;)V getWeights?(Lorg/biojava/bio/dp/State;)Lorg/biojava/bio/dist/Distribution; clearCountsaddCountF(Lorg/biojava/bio/dist/Distribution;Lorg/biojava/bio/symbol/Symbol;D)V(Ljava/lang/String;)VcontainsTransition7(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)Ztrain(Ljava/lang/Throwable;)V! !"#$%&'()*M**Y*+*+*M, [,  N- (- : :**+-:**+B,&-0213;5B6H7Q8\9g=p>{?@A,HH-.Q/0;K12p30(a4567&'8(9:;><!=>?*8 *+ E F,  67@A*-+ + :*,) Y+LMNO"P,Q,4 /0-67-B2-CD-EF8" =GH*D*+,*+:*,) Y:Y47+& XYZ'[*\4`7^9_Ca,> 309 IJD67DK2DL2DEF8 * BM =N?*p* LY+ +g k i jl, OP678LQ =RSPK .*?:n:-:-*org/biojava/bio/dp/SimpleMarkovModel.class2 { | z  z I     z z P z z z    I z       z  8 I ! ) z" # z$ 3% &' &( |)* z+ I,-./ ;0 I12 z3 4 5678 9 I: z;<=>? z@ ABCDE QFGH IJKL ZM |NO zPQR _ST cUV IWXY gZ z[ \ ] z^ __ {` p _ Pa zbc d 8e fghijkserialVersionUIDJ ConstantValuedn emissionAlpha!Lorg/biojava/bio/symbol/Alphabet; stateAlpha'Lorg/biojava/bio/symbol/FiniteAlphabet; magicalState!Lorg/biojava/bio/dp/MagicalState; transFromLjava/util/Map;transTo transWeights distForwarder#Lorg/biojava/utils/ChangeForwarder;getChangeSupportA(Lorg/biojava/utils/ChangeType;)Lorg/biojava/utils/ChangeSupport;CodeLineNumberTableLocalVariableTablees"Lorg/biojava/bio/dp/EmissionState;sLorg/biojava/bio/dp/State;siLjava/util/Iterator;this&Lorg/biojava/bio/dp/SimpleMarkovModel;ctLorg/biojava/utils/ChangeType; changeSupport!Lorg/biojava/utils/ChangeSupport; StackMapTablelmemissionAlphabet#()Lorg/biojava/bio/symbol/Alphabet; stateAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;heads()I#()Lorg/biojava/bio/dp/MagicalState;advance()[IiIadv[Iadvances getWeights?(Lorg/biojava/bio/dp/State;)Lorg/biojava/bio/dist/Distribution;sourcedist#Lorg/biojava/bio/dist/Distribution; Exceptions setWeights@(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dist/Distribution;)VceLorg/biojava/utils/ChangeEvent;csta<h*ncreateTransition7(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)Vfromtoft$destroyTransitionwDcontainsTransition7(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)ZtransitionsFromC(Lorg/biojava/bio/dp/State;)Lorg/biojava/bio/symbol/FiniteAlphabet; transitionsToaddState(Lorg/biojava/bio/dp/State;)VesheStatetoAdd doAddStatefa removeStatetoGo doRemoveState7(ILorg/biojava/bio/symbol/Alphabet;Ljava/lang/String;)VnameLjava/lang/String;%(ILorg/biojava/bio/symbol/Alphabet;)Vise/Lorg/biojava/bio/symbol/IllegalSymbolException;cve'Lorg/biojava/utils/ChangeVetoException;oD- DeprecatedtoString()Ljava/lang/String; SourceFileSimpleMarkovModel.java pq rs t)org/biojava/utils/ChangeForwarder$RetyperRetyper InnerClasses u vwm xy z{org/biojava/bio/dp/State org/biojava/bio/dp/EmissionState | }~        !org/biojava/bio/dist/Distributionorg/biojava/bio/BioErrorjava/lang/StringBuilder Model does contain  7 but the associated transition distribution is missing.   /org/biojava/bio/symbol/IllegalAlphabetException"Can't set distribution from state B as the distribution alphabet is not the alphabet of transitions:  and o y org/biojava/utils/ChangeEvent l   java/lang/Object %org/biojava/utils/ChangeVetoExceptionTransition already exists:  ->  Transition does not exists:  :Can't remove transition as its weight is not zero or NaN:  =   %org/biojava/bio/symbol/FiniteAlphabetState  is known in states ) but is not listed in the transFrom table ' but is not listed in the transTo tableorg/biojava/bio/dp/MagicalState-org/biojava/bio/symbol/IllegalSymbolExceptionCan not add a MagicalStateWe already contain  This model  has  heads, but the state  headsorg/biojava/bio/dp/ModelInState   heads, but the model-in-state %org/biojava/bio/symbol/SimpleAlphabetTransitions from Transitions to 'org/biojava/bio/dist/SimpleDistribution #You can not remove the MagicalState -org/biojava/bio/dp/IllegalTransitionExceptionTYou can not remove a state untill all transitions to and from it have been destroyed  ~  java/util/HashMap  -Assertion failure: Couldn't add magical state  :$org/biojava/bio/dp/SimpleMarkovModel$org/biojava/utils/AbstractChangeableorg/biojava/bio/dp/MarkovModeljava/io/Serializableorg/biojava/utils/ChangeSupportjava/util/Iteratorjava/lang/Throwableorg/biojava/bio/symbol/Alphabet PARAMETERorg/biojava/utils/ChangeTypeisMatchingType!(Lorg/biojava/utils/ChangeType;)Z!org/biojava/utils/ChangeForwarderT(Ljava/lang/Object;Lorg/biojava/utils/ChangeSupport;Lorg/biojava/utils/ChangeType;)Viterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object; DISTRIBUTIONaddChangeListenerC(Lorg/biojava/utils/ChangeListener;Lorg/biojava/utils/ChangeType;)V org/biojava/utils/ChangeListener ALWAYS_VETO"Lorg/biojava/utils/ChangeListener;ADVANCE getAdvancejava/lang/Mathmax(II)Ivalidate"(Lorg/biojava/bio/symbol/Symbol;)V java/util/Mapget&(Ljava/lang/Object;)Ljava/lang/Object;()Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;getName(Ljava/lang/String;)V getAlphabetequals(Ljava/lang/Object;)Z hasListenersput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;W(Ljava/lang/Object;Lorg/biojava/utils/ChangeType;Ljava/lang/Object;Ljava/lang/Object;)VfirePreChangeEvent"(Lorg/biojava/utils/ChangeEvent;)VfirePostChangeEvent ARCHITECTUREcontains"(Lorg/biojava/bio/symbol/Symbol;)Z4(Lorg/biojava/utils/ChangeEvent;Ljava/lang/String;)V addSymbol getWeight"(Lorg/biojava/bio/symbol/Symbol;)Djava/lang/DoubleisNaN(D)Z(D)Ljava/lang/StringBuilder; removeSymbol-(Ljava/lang/Object;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;getModel"()Lorg/biojava/bio/dp/MarkovModel;*(Lorg/biojava/bio/symbol/FiniteAlphabet;)VsizeI(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;Ljava/lang/String;)VremoveChangeListenerremovesetNamegetMagicalStateE(Lorg/biojava/bio/symbol/Alphabet;I)Lorg/biojava/bio/dp/MagicalState;*(Ljava/lang/String;Ljava/lang/Throwable;)VgetClass()Ljava/lang/Class;java/lang/Class!z{|}~~*+M+ +e*^*Y*,*N- ;-  : % :* ,. KM!R1TDUOVWW^XlYy[|^>^O*;A~~x =/*b /*f 3 *j  /*n +m* L=+ +O*M, B,  N- .- :6+++..O+6 rtutx,y6z={H|R}b|hkH KH 62#Hmf"  'C*+*+M,(YY !+"!#!$%, A CC+AQ*+&N,'-(D)YY*!+"!+!-,!-!,'.!$/*0*+,1WR*2:Y:»3Y*,*+4:5*+,1W6ç :y6 T[jsy>sF(TFQ); *+*,3Y*78Y+SY,S4N*+&:*,9:,:2;Y-Y<!+"!=!,"!$>*0,?+?<*72:Y:-5,?+?-6ç :J -4;Fu|H0-4;4u0Q;9 **+*,*+&N3Y*78Y+SY,S4:-,:3;YY@!+"!=!,"!$>*+A:,B9EC=;YYD!+"!=!,"!E!F$>*0*+&,G*,9+GD*72:Y: 5*+&,G*,9+G6 ç :   !!&!V 4>nu     )R8***4u9nY8 Q;X*,*+&,:   QT*+*H+IM,9YYJ!+"!K!*,!L!$%, R$ TT<RQO*+*M+IM,4YYJ!+NK!*,!O!$%,) +,-M4 OO7MQ+P+* QYRS*+:#QYYT!+"!$S+ a+ =*NQYYU!*,!V!*WX!+"!V!WY!$S+Zf+Z[\=*NQYYU!*,!V!*W]!+"!V!WY!$S*0 *+^c*72M,YN»3Y*7+4:,5+ $+ :* *+^,6-ç :-0z}}}j9:=&>FAMBXC`DLMNOWX$Z,[0\?aEbLcRd`emgrhxikHXSSR?9,X0,diHQ;~*+?_YY`!+"!$aM*H+,1W*M+_YYb!+"!$a1W*+cY,d1W*+?o p*q6r`sst}u ~~*TQ;*++P QYeS*+&YMfgY+,  hi*+9YMfgY,  +hi*0 *+jf*72N-Y:»3Y*7+4:-5+ $+ :* kk*+j-6ç :Vy z{~*CRkrz>9["3''IQg;a!*+G*H+lW*M+lW  !!Q;b*,m*_-n*b*o*pYqH*pYqM*pYq*,*_Yr*,s**tNYu-vNYu-v>FIQ>FU;:EFG%*5>FIJUVa4J V bbbIK P&Y*wx!y!*,!$ &  PK /*?:+org/biojava/bio/dp/SimpleModelInState.class2  model Lorg/biojava/bio/dp/MarkovModel;getModel"()Lorg/biojava/bio/dp/MarkovModel;CodeLineNumberTableLocalVariableTablethis'Lorg/biojava/bio/dp/SimpleModelInState;5(Lorg/biojava/bio/dp/MarkovModel;Ljava/lang/String;)VnameLjava/lang/String; SourceFileSimpleModelInState.java  %org/biojava/bio/dp/SimpleModelInState.org/biojava/bio/symbol/FundamentalAtomicSymbolorg/biojava/bio/dp/ModelInState1(Ljava/lang/String;Lorg/biojava/bio/Annotation;)V!  /* %   R *,*+ )* +    PK .*?:XiW+org/biojava/bio/dp/SimpleModelTrainer.class2b 45 4 6 78 9: ;< => =?@ 9A BCDE FG HIJKLmodelsLjava/util/Set;()VCodeLineNumberTableLocalVariableTablethis'Lorg/biojava/bio/dp/SimpleModelTrainer; registerModel#(Lorg/biojava/bio/dp/MarkovModel;)Vdist#Lorg/biojava/bio/dist/Distribution;ise/Lorg/biojava/bio/symbol/IllegalSymbolException;sLorg/biojava/bio/dp/State;iLjava/util/Iterator;model Lorg/biojava/bio/dp/MarkovModel; StackMapTableMIN@C SourceFileSimpleModelTrainer.java java/util/HashSet O PQN RST UVM WX YZorg/biojava/bio/dp/State [\ ]^-org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/BioError#Couldn't register states from model _ org/biojava/bio/dp/EmissionState `a%org/biojava/bio/dp/SimpleModelTrainer5org/biojava/bio/dist/SimpleDistributionTrainerContextorg/biojava/bio/dp/ModelTrainerjava/io/Serializablejava/util/Iteratororg/biojava/bio/dp/MarkovModel java/util/Setcontains(Ljava/lang/Object;)Z stateAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;%org/biojava/bio/symbol/FiniteAlphabetiterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object; getWeights?(Lorg/biojava/bio/dp/State;)Lorg/biojava/bio/dist/Distribution;registerDistribution&(Lorg/biojava/bio/dist/Distribution;)V*(Ljava/lang/String;Ljava/lang/Throwable;)VgetDistribution%()Lorg/biojava/bio/dist/Distribution;!>**Y '*  !1h*+]+M,H,  N+- :* :Y--:* ,;> 6 - ."/,152;5>3@4L6S7^8d:g<H5"#@ $%^"#,8&'N()hh*+,%-$./-01 23PK .*?: 4+KK(org/biojava/bio/dp/SimpleStatePath.class2 _ `a ` b cd e fg h i jk jl jm jn jo jp jq jr js jt ju jvwx yz }~scoreDdelegate"Lorg/biojava/bio/symbol/Alignment;getScore()DCodeLineNumberTableLocalVariableTablethis$Lorg/biojava/bio/dp/SimpleStatePath;m(DLorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/SymbolList;)Vsequence#Lorg/biojava/bio/symbol/SymbolList;statesscoresmapLjava/util/Map; Exceptions getAlphabet#()Lorg/biojava/bio/symbol/Alphabet; getLabels()Ljava/util/List;length()I subAlignmentT(Ljava/util/Set;Lorg/biojava/bio/symbol/Location;)Lorg/biojava/bio/symbol/Alignment;labelsLjava/util/Set;loc!Lorg/biojava/bio/symbol/Location;symbolAt"(I)Lorg/biojava/bio/symbol/Symbol;colI4(Ljava/lang/Object;I)Lorg/biojava/bio/symbol/Symbol;labelLjava/lang/Object;symbolListForLabel7(Ljava/lang/Object;)Lorg/biojava/bio/symbol/SymbolList;iterator()Ljava/util/Iterator;subList'(II)Lorg/biojava/bio/symbol/SymbolList;startendtoList seqString()Ljava/lang/String;subStr(II)Ljava/lang/String;edit (Lorg/biojava/bio/symbol/Edit;)VLorg/biojava/bio/symbol/Edit;symbolListIterator SourceFileSimpleStatePath.java !" ,java/util/HashMap J J J&org/biojava/bio/symbol/SimpleAlignment , #$ 67 89 :; <= CD CH KL MN OP S9 TU VW%org/biojava/utils/ChangeVetoExceptionCan't edit SimpleStatePath ,3org/biojava/bio/symbol/Alignment$SymbolListIteratorSymbolListIterator InnerClasses ,"org/biojava/bio/dp/SimpleStatePathorg/biojava/utils/Unchangeableorg/biojava/bio/dp/StatePathjava/io/Serializable"java/lang/IllegalArgumentException java/util/NoSuchElementException#java/lang/IndexOutOfBoundsException/org/biojava/bio/symbol/IllegalAlphabetException()VSEQUENCE java/util/Mapput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;STATESSCORES(Ljava/util/Map;)V org/biojava/bio/symbol/Alignment(Ljava/lang/String;)V%(Lorg/biojava/bio/symbol/Alignment;)V! !"#$%&'/*(=) *+,-'F**'Y:-WWW* Y ("EF GHI+J8KEL)>F*+F!"F./F0/F1/4234567'4 * (O)  *+89'4 * (S)  *+:;'4 * (W)  *+<='J * +,(\)  *+ >? @A4BCD'? * (a) *+ EF4GCH'J * +(f)  *+ IJ EF4GBKL'? * +(k) *+ IJ4BMN'4 * (o)  *+OP'J * (s)  *+ QF RFS9'4 * (w)  *+TU'4 * ({)  *+VW'J * ()  *+ QF RF4GXY'> Y() *+ XZ4[G\N'3 Y*()  *+]^| j{ PK .*?:BP P +org/biojava/bio/dp/SimpleWeightMatrix.class2l I J KL MN OPQ KR S TUV W X YZ [ [ O O \ \ ]^_`serialVersionUIDJ ConstantValueycolumns$[Lorg/biojava/bio/dist/Distribution;alpha!Lorg/biojava/bio/symbol/Alphabet; getAlphabet#()Lorg/biojava/bio/symbol/Alphabet;CodeLineNumberTableLocalVariableTablethis'Lorg/biojava/bio/dp/SimpleWeightMatrix;()I getColumn&(I)Lorg/biojava/bio/dist/Distribution;columnIO(Lorg/biojava/bio/symbol/Alphabet;ILorg/biojava/bio/dist/DistributionFactory;)VidFact*Lorg/biojava/bio/dist/DistributionFactory; StackMapTable^ab Exceptions'([Lorg/biojava/bio/dist/Distribution;)Vc"hashCodehcequals(Ljava/lang/Object;)Zwm!Lorg/biojava/bio/dp/WeightMatrix;oLjava/lang/Object;Z SourceFileSimpleWeightMatrix.java #$ !" 1c!org/biojava/bio/dist/Distributionb de %&/org/biojava/bio/symbol/IllegalAlphabetExceptionjava/lang/StringBuilder3All columns must emit the same alphabet. Expecting fga hi , but found ji 1k >,org/biojava/bio/dp/WeightMatrix !, -. @A%org/biojava/bio/dp/SimpleWeightMatrixjava/lang/Objectjava/io/Serializableorg/biojava/bio/symbol/Alphabet(org/biojava/bio/dist/DistributionFactory()VcreateDistributionF(Lorg/biojava/bio/symbol/Alphabet;)Lorg/biojava/bio/dist/Distribution;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;getName()Ljava/lang/String;toString(Ljava/lang/String;)V!!"#$%&'/*(*) *+!,'0*(.) *+-.';*2(2)*+/012'/**+*6*-+S(67 89:(9.<)430/*+/#$/!0/456789:1;'k**+2=+P+2*;YY  *   +2  *+("?@AB'C_AeIjJ) S<0k*+k!"67=L:>,'$<=*h*2`<(MN ON"Q) <0$*+"?06 @A'R+L+M,*,*>**,(2 UV WXZ([*^4_F`H^NcPe)*,"<0 DBCR*+RDE6FGHPK .*?:[borg/biojava/bio/dp/State.class2  SourceFile State.javaorg/biojava/bio/dp/Statejava/lang/Object#org/biojava/bio/symbol/AtomicSymbolPK .*?:"org/biojava/bio/dp/StatePath.class2   SEQUENCELjava/lang/Object;STATESSCORESgetScore()D()VCodeLineNumberTable SourceFileStatePath.java org/biojava/bio/dp/StatePathjava/lang/Object org/biojava/bio/symbol/Alignment    0IN SPK .*?:ހ3)org/biojava/bio/dp/StoppingCriteria.class2 isTrainingComplete)(Lorg/biojava/bio/dp/TrainingAlgorithm;)Z SourceFileStoppingCriteria.java#org/biojava/bio/dp/StoppingCriteriajava/lang/ObjectPK .*?:`ul"org/biojava/bio/dp/Trainable.class2   registerWithTrainer$(Lorg/biojava/bio/dp/ModelTrainer;)V Exceptions  SourceFileTrainable.javaorg/biojava/bio/dp/Trainablejava/lang/Objectorg/biojava/bio/BioExceptionPK .*?:G2*org/biojava/bio/dp/TrainerTransition.class2," # $ % & '()trainer&Lorg/biojava/bio/dp/TransitionTrainer;fromLorg/biojava/bio/dp/State;toequals(Ljava/lang/Object;)ZCodeLineNumberTableLocalVariableTablethis&Lorg/biojava/bio/dp/TrainerTransition;oLjava/lang/Object;t StackMapTable" Exceptions*hashCode()I](Lorg/biojava/bio/dp/TransitionTrainer;Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)V SourceFileTrainerTransition.java$org/biojava/bio/dp/TrainerTransition  +java/lang/Objectjava/io/Serializablejava/lang/ClassCastException()V!   ~,+M*,*,*, ,- ,,' *@B***4 l**+*,*-78 9:;*    !PK .*?:7e/*org/biojava/bio/dp/TrainingAlgorithm.class2getDP()Lorg/biojava/bio/dp/DP; getLastScore()DgetCurrentScoregetCycle()ItrainL(Lorg/biojava/bio/seq/db/SequenceDB;DLorg/biojava/bio/dp/StoppingCriteria;)V Exceptions SourceFileTrainingAlgorithm.java$org/biojava/bio/dp/TrainingAlgorithmjava/lang/Object-org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/BioException    PK .*?:;``#org/biojava/bio/dp/Transition.class2(  ! " #$%fromLorg/biojava/bio/dp/State;toequals(Ljava/lang/Object;)ZCodeLineNumberTableLocalVariableTablethisLorg/biojava/bio/dp/Transition;oLjava/lang/Object;t StackMapTable Exceptions&hashCode()I7(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)V SourceFileTransition.javaorg/biojava/bio/dp/Transition   'java/lang/Objectjava/io/Serializablejava/lang/ClassCastException()V!    s!+M*,*, *+ !! @ :**2  Y**+*,56 78   PK .*?:v*org/biojava/bio/dp/TransitionTrainer.class2addCount8(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;D)V Exceptionstrain(DD)V clearCounts()V SourceFileTransitionTrainer.java$org/biojava/bio/dp/TransitionTrainerjava/lang/Object-org/biojava/bio/symbol/IllegalSymbolException-org/biojava/bio/dp/IllegalTransitionException    PK .*?:@++org/biojava/bio/dp/WMAsMM.class2 @ @ @  @  @ @ @       @ @ A @ B # @ '  * *   @ /   9 * =advance[Iwm!Lorg/biojava/bio/dp/WeightMatrix; stateAlpha'Lorg/biojava/bio/symbol/FiniteAlphabet; magicalState!Lorg/biojava/bio/dp/MagicalState;states#[Lorg/biojava/bio/dp/EmissionState; transFromLjava/util/Map;transTo transWeights distForwarder#Lorg/biojava/utils/ChangeForwarder;()[ICodeLineNumberTableLocalVariableTablethisLorg/biojava/bio/dp/WMAsMM;emissionAlphabet#()Lorg/biojava/bio/symbol/Alphabet; stateAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;heads()I#()Lorg/biojava/bio/dp/MagicalState; getWeights?(Lorg/biojava/bio/dp/State;)Lorg/biojava/bio/dist/Distribution;sourceLorg/biojava/bio/dp/State; Exceptions setWeights@(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dist/Distribution;)Vdist#Lorg/biojava/bio/dist/Distribution;transitionsFromC(Lorg/biojava/bio/dp/State;)Lorg/biojava/bio/symbol/FiniteAlphabet;fromsAlpha!Lorg/biojava/bio/symbol/Alphabet; transitionsTotoregisterWithTrainer$(Lorg/biojava/bio/dp/ModelTrainer;)V modelTrainer!Lorg/biojava/bio/dp/ModelTrainer;createTransition7(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)VdestroyTransitionaddState(Lorg/biojava/bio/dp/State;)VtoAdd StackMapTable removeStatecontainsTransition7(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)Zindex(Lorg/biojava/bio/dp/State;)IiIs$(Lorg/biojava/bio/dp/WeightMatrix;)Vprevcurrentfa changeSupport!Lorg/biojava/utils/ChangeSupport;sa'Lorg/biojava/bio/symbol/SimpleAlphabet;cve'Lorg/biojava/utils/ChangeVetoException;ise/Lorg/biojava/bio/symbol/IllegalSymbolException;()V SourceFile WMAsMM.java FG [ HI JK QO !org/biojava/bio/dist/Distribution%org/biojava/utils/ChangeVetoException-Can't replace distribution in immutable model \] NO%org/biojava/bio/symbol/FiniteAlphabet POjava/lang/StringBuilder #destroyTransition not supported by  -org/biojava/bio/symbol/IllegalSymbolException5Can't add a state to a model that already contains it addState not supported by removeState not supported by jk LM  )org/biojava/utils/ChangeForwarder$RetyperRetyper InnerClasses   RSjava/util/HashMap  %org/biojava/bio/symbol/SimpleAlphabet   _ org/biojava/bio/dp/EmissionState&org/biojava/bio/dp/SimpleEmissionState    DE    [ (org/biojava/bio/dist/UniformDistribution Weight Matrix columns org/biojava/bio/BioErrorBAssertion Failure: Should be able to manipulate my state alphabet. org/biojava/bio/dp/WMAsMM$org/biojava/utils/AbstractChangeableorg/biojava/bio/dp/MarkovModeljava/io/Serializableorg/biojava/bio/BioExceptionorg/biojava/bio/dp/WeightMatrixorg/biojava/utils/ChangeSupportorg/biojava/bio/dp/State getAlphabetvalidate"(Lorg/biojava/bio/symbol/Symbol;)V java/util/Mapget&(Ljava/lang/Object;)Ljava/lang/Object;(Ljava/lang/String;)Vorg/biojava/bio/symbol/Alphabetappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;java/lang/ObjectgetClass()Ljava/lang/Class;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;contains"(Lorg/biojava/bio/symbol/Symbol;)Z4(Lorg/biojava/bio/symbol/Symbol;Ljava/lang/String;)Vorg/biojava/utils/ChangeTypeUNKNOWNLorg/biojava/utils/ChangeType;getChangeSupportA(Lorg/biojava/utils/ChangeType;)Lorg/biojava/utils/ChangeSupport;!org/biojava/utils/ChangeForwarder PARAMETERT(Ljava/lang/Object;Lorg/biojava/utils/ChangeSupport;Lorg/biojava/utils/ChangeType;)Vorg/biojava/bio/dp/MagicalStategetMagicalStateE(Lorg/biojava/bio/symbol/Alphabet;I)Lorg/biojava/bio/dp/MagicalState; addSymbolcolumns(I)Ljava/lang/StringBuilder;org/biojava/bio/AnnotationEMPTY_ANNOTATIONLorg/biojava/bio/Annotation; getColumn&(I)Lorg/biojava/bio/dist/Distribution;V(Ljava/lang/String;Lorg/biojava/bio/Annotation;[ILorg/biojava/bio/dist/Distribution;)VaddChangeListener%(Lorg/biojava/utils/ChangeListener;)V getMatchesput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;*(Lorg/biojava/bio/symbol/FiniteAlphabet;)VsetName*(Ljava/lang/String;Ljava/lang/Throwable;)V!@ABC DEFGHIJKLMNOPOQORSDTU2 YOVGW XYZ[U4 *VKW  XY\]U/*VOW XY^_U,VSW XYJ`U/*VWW XYabUP*+*+V \ ]WXYcdefgUH Y VbW  XY cd hie jkU`* M,+ *+Vij lW XYldmneokU`* M,+ *+Vqr tW XYpdmneqrU5V}WXYsteuvwU\ YY* VW XYldpde xwU\ YY* VW XYldpde yzU{6* +Y+ YY* V W6XY6{d|e }zU`(* + YY* V  W(XY({de ~Us* N-+ -, *+,V W*XYldpdmneU}=*+*2V W XYd| U q* *!"M*#Y*,$%&*'Y(*'Y(*'Y(*+*+)*Y+N-*,*-*+-.6+-+-I-*/YY0123+45[S,+4*&6 * *d2:+- * *2:7:*78W*8W9Y::*8W)-;<M=Y>,?M=Y>,?UX UdV~ '2=BPX`er"0;IOUXYdepWp adFd:I;hiu IXY e qXYqFG|@ u[ HFMK eU#  YO3V9 # PK .*?:zMM%org/biojava/bio/dp/WeightMatrix.class2  getAlphabet#()Lorg/biojava/bio/symbol/Alphabet;columns()I getColumn&(I)Lorg/biojava/bio/dist/Distribution; Exceptions SourceFileWeightMatrix.javaorg/biojava/bio/dp/WeightMatrixjava/lang/Object#java/lang/IndexOutOfBoundsException    PK .*?:誇չ .org/biojava/bio/dp/WeightMatrixAnnotator.class2R S T UVX YZ [ \ ] ^_ ` ab cd ef g hi Y3j k lm n ^o !Y pqr stuvwmatrix!Lorg/biojava/bio/dp/WeightMatrix; thresholdD scoreTypeLorg/biojava/bio/dp/ScoreType;wmIDLjava/lang/String;annotate>(Lorg/biojava/bio/seq/Sequence;)Lorg/biojava/bio/seq/Sequence;CodeLineNumberTableLocalVariableTableann"Lorg/biojava/bio/SimpleAnnotation;scoreqoffsetIthis*Lorg/biojava/bio/dp/WeightMatrixAnnotator;seqLorg/biojava/bio/seq/Sequence;colstemplateTemplate InnerClasses&Lorg/biojava/bio/seq/Feature$Template; StackMapTableX ExceptionsxyzU(Lorg/biojava/bio/dp/WeightMatrix;Lorg/biojava/bio/dp/ScoreType;DLjava/lang/String;)Vwm%(Lorg/biojava/bio/dp/WeightMatrix;D)VC(Lorg/biojava/bio/dp/WeightMatrix;Lorg/biojava/bio/dp/ScoreType;D)VgetWeightMatrixID()Ljava/lang/String;setWeightMatrixID(Ljava/lang/String;)Vid SourceFileWeightMatrixAnnotator.java%org/biojava/bio/seq/impl/ViewSequence F{ $%| }~$org/biojava/bio/seq/Feature$Template FWeightMatrixAnnotator + *+ + ~ ()  &'$org/biojava/bio/symbol/RangeLocation F  org/biojava/bio/SimpleAnnotationjava/lang/Double F  weightMatrix  )hit FG(org/biojava/bio/dp/WeightMatrixAnnotatorjava/lang/Object%org/biojava/bio/seq/SequenceAnnotatorjava/io/Serializable/org/biojava/bio/symbol/IllegalAlphabetExceptionorg/biojava/bio/BioException%org/biojava/utils/ChangeVetoException!(Lorg/biojava/bio/seq/Sequence;)Vorg/biojava/bio/dp/WeightMatrixcolumns()Iorg/biojava/bio/seq/Feature()Vsourcetypeorg/biojava/bio/seq/Sequencelengthorg/biojava/bio/dp/DPscoreWeightMatrixf(Lorg/biojava/bio/dp/WeightMatrix;Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/dp/ScoreType;I)Djava/lang/Mathexp(D)D(II)Vlocation!Lorg/biojava/bio/symbol/Location;(D)V setProperty'(Ljava/lang/Object;Ljava/lang/Object;)V annotationLorg/biojava/bio/Annotation; createFeatureE(Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;org/biojava/bio/dp/ScoreType PROBABILITY! !"#$%&'()*+,-.s Y+L*=YN--* 6+ d`o*+*  99*H-Y`dY:  Y *- +-W+/J$ &'(!))*,+;-K.R/\0o1x2345,80Rx)12 KV3'RO4',{56789:;6<?@,AtBCDEFG.**+*)* * /DE FGHI0478H%()&'*+FI.N *+(/ R S0  78 H% &'FJ.v**+*, *)* /^_ `abc0*78H%()&'KL./* /j0 78MN.>*+ / rs078O+PQ> W= PK .*?:c̈́z.z.'org/biojava/bio/dp/XmlMarkovModel.class2                       ! "# $% &'()* + +,- . 0/0 41 234 8 5 ;6 47 89:;< = >? >@ AB  C DE FG KHIJK 8LM +L 4NOP 8QR 4ST 4U "VW X YZ "[\ ]^ _ `a `bcd je &f ghi jk lm lno lpqrs Yt {uv w lxyz lU{|}~()VCodeLineNumberTableLocalVariableTablethis#Lorg/biojava/bio/dp/XmlMarkovModel; readMatrix8(Lorg/w3c/dom/Element;)Lorg/biojava/bio/dp/WeightMatrix;indxIisymLorg/biojava/bio/symbol/Symbol;cve'Lorg/biojava/utils/ChangeVetoException;weightELorg/w3c/dom/Element;symNameLjava/lang/String;jcolEweightsLorg/w3c/dom/NodeList;rootalphaEsa!Lorg/biojava/bio/symbol/Alphabet;seqAlpha'Lorg/biojava/bio/symbol/FiniteAlphabet; symParser+Lorg/biojava/bio/seq/io/SymbolTokenization; nameParsercolumnscolLwm!Lorg/biojava/bio/dp/WeightMatrix; StackMapTablec( Exceptions readModel7(Lorg/w3c/dom/Element;)Lorg/biojava/bio/dp/MarkovModel;nsee"Ljava/util/NoSuchElementException;dFact*Lorg/biojava/bio/dist/DistributionFactory;ise/Lorg/biojava/bio/symbol/IllegalSymbolException;stateEnamedis#Lorg/biojava/bio/dist/Distribution;state"Lorg/biojava/bio/dp/EmissionState;ite transitionEfromLorg/biojava/bio/dp/State;toprobDheadsmodel&Lorg/biojava/bio/dp/SimpleMarkovModel;advance[I symbolParser nameToStateLjava/util/Map;states transitions02tIR writeMatrix9(Lorg/biojava/bio/dp/WeightMatrix;Ljava/io/PrintStream;)VssiLjava/util/Iterator;matrixoutLjava/io/PrintStream;symA writeModel8(Lorg/biojava/bio/dp/MarkovModel;Ljava/io/PrintStream;)VsymIesstateI Lorg/biojava/bio/dp/MarkovModel;stateAprintTransitionsR(Lorg/biojava/bio/dp/MarkovModel;Lorg/biojava/bio/dp/State;Ljava/io/PrintStream;)V SourceFileXmlMarkovModel.java alphabet  org/w3c/dom/Element  %org/biojava/bio/symbol/FiniteAlphabet/org/biojava/bio/symbol/IllegalAlphabetExceptionjava/lang/StringBuilder/Can't read WeightMatrix over infinite alphabet   of type    token col   %org/biojava/bio/dp/SimpleWeightMatrix  weightres      %org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioError4Assertion failure: Should be able to set the weights  WeightMatrixorg/biojava/bio/dp/WMAsMM $org/biojava/bio/dp/SimpleMarkovModel  java/util/NoSuchElementExceptionorg/biojava/bio/BioException$Couldn't find a parser for alphabet java/util/HashMap_start_  _end__START__END_     &org/biojava/bio/dp/SimpleEmissionState  -org/biojava/bio/symbol/IllegalSymbolExceptionCan't extract symbol from  in 6Assertion failure: Should be able to edit distribution 8Assertion failure: Should be able to add states to model transition org/biojava/bio/dp/State MWe should have unlimited write-access to this model. Something is very wrong.        org/biojava/bio/symbol/Symbol  ?W@>?WA>?WB>?W*C: -DE1-D-DE-DFGH I: : 6   P  :  :  -J:KY LM: ?W :6: : !"#:$$%:\%:N%:%:-:8Y Y OP Q'():+YRS#T:+YUS *V: 6   i  :  WXY: ZXY:[:+Y\S:+Y\S 6   ~  :  WXY: ZXY: '(9]):+Y\S:+Y\S | oy|7~7-0NZor**N*xNx*ZVmnq&r8sDvOwTx]ycxi|l}oy|~;CHWepz"-02Zort#2@Ujx-W~@  2(t -S e9 p. z$KY   R =(r   @g URj=x/& &8xDlOaT\lDoA Hh  $<L)Z3   )W I  OM dM 8N d*^ M+ Y _,`ab>*c+ Y d`efb,g:hJij:+ Y klm*&noab+pbv+qb2  + 7 U g s >s8]Q- -/P   E*rK*sM*t N+ Y u*vefb+ Y w-`ab,g:hiY:x+ Y yzfb{g{:|:-g:hEij: + Y k lm noab+}bN,g:hiY:*+~+qbb 8Y!k"w#$%&'()* , .03(445;6>8D9z 3 L]Twa4 EE 9/Ba_ K *+gN-h-iY:, Y +x= +zx@ zm*+noab,:+Y Y +zSa!N"<=!?EBCFG>'!  ,f(NPK .*?:䊺OO/org/biojava/bio/dp/onehead/AbstractCursor.class2: & ' ( )* + ),- . /0123gapLorg/biojava/bio/symbol/Symbol; symIteratorLjava/util/Iterator; currentReslastRes!()Lorg/biojava/bio/symbol/Symbol;CodeLineNumberTableLocalVariableTablethis+Lorg/biojava/bio/dp/onehead/AbstractCursor; canAdvance()Z StackMapTableadvance()V11-(Ljava/util/Iterator;)V SourceFileAbstractCursor.java   4 5  67org/biojava/bio/symbol/Symbol !8 9)org/biojava/bio/dp/onehead/AbstractCursorjava/lang/Object#org/biojava/bio/dp/onehead/DPCursorjava/util/IteratorhasNextnext()Ljava/lang/Object;&org/biojava/bio/symbol/AlphabetManager getGapSymbol   /*+ /*/ R* *3 @y+*****78*: +d !"\**+**<= >?@!3* BC # $$%PK .*?:YRyy)org/biojava/bio/dp/onehead/DPCursor.class2symList%()Lorg/biojava/bio/symbol/SymbolList;length()I currentCol()[DlastCol currentRes!()Lorg/biojava/bio/symbol/Symbol;lastRes canAdvance()Zadvance()V SourceFile DPCursor.java#org/biojava/bio/dp/onehead/DPCursorjava/lang/Object    PK .*?:k?C-org/biojava/bio/dp/onehead/MatrixCursor.class2@ , -. /0 -1 2 3 4 5 067matrix+Lorg/biojava/bio/dp/onehead/SingleDPMatrix;dirIindexlength()ICodeLineNumberTableLocalVariableTablethis)Lorg/biojava/bio/dp/onehead/MatrixCursor;symList%()Lorg/biojava/bio/symbol/SymbolList; currentCol()[DlastColadvance()VC(Lorg/biojava/bio/dp/onehead/SingleDPMatrix;Ljava/util/Iterator;I)V symIteratorLjava/util/Iterator; StackMapTable6896 Exceptions: SourceFileMatrixCursor.java 8 ;<  =>    ?'org/biojava/bio/dp/onehead/MatrixCursor)org/biojava/bio/dp/onehead/AbstractCursor)org/biojava/bio/dp/onehead/SingleDPMatrixjava/util/Iterator"java/lang/IllegalArgumentException&()[Lorg/biojava/bio/symbol/SymbolList;!org/biojava/bio/symbol/SymbolListscores[[D(Ljava/util/Iterator;)V  ;*2`) 4 *2-  7 **21  <***d25 D**Y*`9:;  #*,*+** * dBD EF"I*## #!"##+$%&'$%&'()*+PK .*?:rd<<)org/biojava/bio/dp/onehead/SingleDP.class2 e  d d d e         d d          d  % d d * d -!" /# -$ d% d& d' d( d) d* +, d- ./ d0 d1 2 +3 +4 +5 d6 +7 d8 d9 +: d;< K= K> K? K@ +AB QCD SE UF GH IJ GKL MN KOPQ .R _S TU ^VWXY emissionsProbLjava/util/HashMap; emissionsOdds emissionsNull#(Lorg/biojava/bio/dp/MarkovModel;)VCodeLineNumberTableLocalVariableTablethis%Lorg/biojava/bio/dp/onehead/SingleDP;model Lorg/biojava/bio/dp/MarkovModel; ExceptionsZ[\update()V StackMapTable getEmissionA(Lorg/biojava/bio/symbol/Symbol;Lorg/biojava/bio/dp/ScoreType;)[D emissionsLjava/util/Map;es"Lorg/biojava/bio/dp/EmissionState;dis#Lorg/biojava/bio/dist/Distribution;iIdsistatesorg/biojava/bio/dp/State;symLorg/biojava/bio/symbol/Symbol; scoreTypeLorg/biojava/bio/dp/ScoreType;em[D]forwardE([Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/dp/ScoreType;)Dseq$[Lorg/biojava/bio/symbol/SymbolList;dpCursor%Lorg/biojava/bio/dp/onehead/DPCursor;scoreD^backward forwardMatrixa([Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/dp/ScoreType;)Lorg/biojava/bio/dp/DPMatrix;matrix+Lorg/biojava/bio/dp/onehead/SingleDPMatrix;backwardMatrix~([Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/dp/DPMatrix;Lorg/biojava/bio/dp/ScoreType;)Lorg/biojava/bio/dp/DPMatrix;Lorg/biojava/bio/dp/DPMatrix;smF(Lorg/biojava/bio/dp/onehead/DPCursor;Lorg/biojava/bio/dp/ScoreType;)Dforward_initializeF(Lorg/biojava/bio/dp/onehead/DPCursor;Lorg/biojava/bio/dp/ScoreType;)Vltkkctr[Itrsciconstantv transitions[[ItransitionScore[[D currentColW_`backward_initializeforward_recurseweightlastColabackward_recurselc stateCount prevScoresforward_terminationscoresbackward_terminationviterbib([Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/dp/ScoreType;)Lorg/biojava/bio/dp/StatePath;symListr#Lorg/biojava/bio/symbol/SymbolList;c(Lorg/biojava/bio/dp/onehead/DPCursor;Lorg/biojava/bio/dp/ScoreType;)Lorg/biojava/bio/dp/StatePath;sp transProbtransprevvcvlemissionbp![Lorg/biojava/bio/dp/BackPointer;j oldPointers newPointersbest Lorg/biojava/bio/dp/BackPointer; bestScorelenb2dotCemCaMapali"Lorg/biojava/bio/symbol/Alignment;symView)Lorg/biojava/bio/symbol/GappedSymbolList; stateListLjava/util/List;rigapsb<cde SourceFile SingleDP.java kljava/util/HashMap ky gh ih jh xy fy` g h iorg/biojava/bio/BioErrorjava/lang/StringBuilderUnknown ScoreType object: jk jl mn ko] pq rs tuv wx org/biojava/bio/dp/EmissionState yz {|} ~ "java/lang/IllegalArgumentExceptionseq must be 1 long, not j y&org/biojava/bio/dp/onehead/SmallCursor  k y%org/biojava/bio/dp/DP$ReverseIteratorReverseIterator InnerClasses k )org/biojava/bio/dp/onehead/SingleDPMatrix k'org/biojava/bio/dp/onehead/MatrixCursor k  _        y x {|    x org/biojava/bio/dp/BackPointer k k   &org/biojava/bio/symbol/SimpleAlignment k-org/biojava/bio/symbol/SimpleGappedSymbolListjava/util/ArrayList ke  sorg/biojava/bio/dp/MagicalState org/biojava/bio/dp/DotStated  "org/biojava/bio/dp/SimpleStatePath'org/biojava/bio/symbol/SimpleSymbolList  k  k#org/biojava/bio/dp/onehead/SingleDPorg/biojava/bio/dp/DPjava/io/Serializable-org/biojava/bio/symbol/IllegalSymbolException-org/biojava/bio/dp/IllegalTransitionExceptionorg/biojava/bio/BioException java/util/Map/org/biojava/bio/symbol/IllegalAlphabetException#org/biojava/bio/dp/onehead/DPCursororg/biojava/bio/dp/ScoreTypeorg/biojava/bio/symbol/Symbolorg/biojava/bio/dp/State org/biojava/bio/symbol/Alignment'org/biojava/bio/symbol/GappedSymbolListjava/util/Listclear PROBABILITYODDS NULL_MODELappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/String;)Vget&(Ljava/lang/Object;)Ljava/lang/Object;getDotStatesIndex()I getStates()[Lorg/biojava/bio/dp/State;&org/biojava/bio/symbol/AlphabetManager getGapSymbol!()Lorg/biojava/bio/symbol/Symbol;getDistribution%()Lorg/biojava/bio/dist/Distribution;calculateScoreE(Lorg/biojava/bio/dist/Distribution;Lorg/biojava/bio/symbol/Symbol;)Djava/lang/Mathlog(D)Dput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;(I)Ljava/lang/StringBuilder; 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F!(tu *e PK .*?:b3/org/biojava/bio/dp/onehead/SingleDPMatrix.class2Q 8 9 : ;<= > ? @ AB ACD EFGHIstatesorg/biojava/bio/dp/State;model Lorg/biojava/bio/dp/MarkovModel;symList$[Lorg/biojava/bio/symbol/SymbolList;scores[[DscoreD()[Lorg/biojava/bio/dp/State;CodeLineNumberTableLocalVariableTablethis+Lorg/biojava/bio/dp/onehead/SingleDPMatrix;"()Lorg/biojava/bio/dp/MarkovModel;&()[Lorg/biojava/bio/symbol/SymbolList;getScore()DsetScore(D)VgetCell([I)Dindex[I StackMapTable Exceptions=(Lorg/biojava/bio/dp/DP;Lorg/biojava/bio/symbol/SymbolList;)VdpLorg/biojava/bio/dp/DP;#Lorg/biojava/bio/symbol/SymbolList; SourceFileSingleDPMatrix.java    #java/lang/IndexOutOfBoundsExceptionindex must be two-dimensional 1J  1KL M% N!org/biojava/bio/symbol/SymbolList OP)org/biojava/bio/dp/onehead/SingleDPMatrixjava/lang/Objectorg/biojava/bio/dp/DPMatrixjava/io/Serializable(Ljava/lang/String;)V()Vorg/biojava/bio/dp/DPgetModel getStateslength()I! /*!/" #$% /*!3" #$& /*!7" #$'( /*!;" #$)* >*'! ?@"#$+, b+ Y*+.2+.1!DEG"#$-./012 =* *+ *+ * Y,S* *,`*!JK LM N'O<P" =#$=34=567PK .*?:,org/biojava/bio/dp/onehead/SmallCursor.class2: , -. / 0 1 2 3 4 567symList#Lorg/biojava/bio/symbol/SymbolList;currentC[DlastC%()Lorg/biojava/bio/symbol/SymbolList;CodeLineNumberTableLocalVariableTablethis(Lorg/biojava/bio/dp/onehead/SmallCursor;length()I currentCol()[DlastColadvance()VvU([Lorg/biojava/bio/dp/State;Lorg/biojava/bio/symbol/SymbolList;Ljava/util/Iterator;)Vstatesorg/biojava/bio/dp/State; symIteratorLjava/util/Iterator; canAdvance()ZlastRes!()Lorg/biojava/bio/symbol/Symbol; currentRes SourceFileSmallCursor.java 8     9 %& '( )(&org/biojava/bio/dp/onehead/SmallCursor)org/biojava/bio/dp/onehead/AbstractCursor!org/biojava/bio/symbol/SymbolList(Ljava/util/Iterator;)V!    /*) 4 *-  /*1 /*5 [**L***+9; <=>  s*-*,*+*+AB DEF*!" #$A%&/*# A'(/*# A)(/* # *+PK /*?:pY22&org/biojava/bio/dp/onehead/package.inf!!BioJavaBuildTool1 Dynamic Programming Packages PK /*?:u!org/biojava/bio/dp/package.html HMM and Dynamic Programming Algorithms.

This package deals with dynamic programming. It uses the same notions of sequences, alphabets and alignments as org.biojava.bio.seq, and extends them to incorporate HMMs, HMM states and state paths. As far as possible, the implementation detail is hidden from the casual observer, so that these objects can be used as black-boxes. Alternatively, there is scope for you to implement your own efficient representations of states and dynamic programming algorithms.

HMMs are defined by a finite set of states and a finite set of transitions. The states are encapsulated as subinterfaces of Symbols, so that we can re-use alphabets and SymbolList to store legal states and sequences of states. States that emit residues must implement EmissionState. They define a probability distribution over an alphabet. Other states may contain entire HMMs, or be non-emitting states which make the model easier to wire. An HMM contains an alphabet of states and a set of transitions with scores. They really resemble directed weighted graphs with the nodes being the states and the arcs being the transitions.

A simple HMM can be aligned to a single sequence at a time. This effectively finds the most likely way that the HMM could have emitted that sequence. More complex algorithms may align more than one sequence to a model simultaneously. For example, Smith-Waterman is a three-state model that aligns two sequences to each other and to the model. These more complex models can still be represented as producing a single sequence, but in this case the sequence is an alignment of the two input sequences against one-another (including gap characters where appropriate). PK /*?:pY22org/biojava/bio/dp/package.inf!!BioJavaBuildTool1 Dynamic Programming Packages PK .*?:f::;org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.class2 c de f gh i dj k lm n o p' q% r st uv wx y z{_| c}~pos[Iseqs$[Lorg/biojava/bio/symbol/SymbolList;columns[[[D bPointers#[[[Lorg/biojava/bio/dp/BackPointer; emissions numStatesIzeroCol[DemptyBP![Lorg/biojava/bio/dp/BackPointer;depthsMatrixeCache*Lorg/biojava/bio/dp/twohead/EmissionCache;(Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/SymbolList;IIIILorg/biojava/bio/dp/twohead/PairDPMatrix;Lorg/biojava/bio/dp/twohead/EmissionCache;)VCodeLineNumberTableLocalVariableTableijei[[Dthis7Lorg/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor;seq1#Lorg/biojava/bio/symbol/SymbolList;seq2start1start2depth1depth2matrix)Lorg/biojava/bio/dp/twohead/PairDPMatrix;symArray [Lorg/biojava/bio/symbol/Symbol;symListLjava/util/List; StackMapTable}mHHt; ExceptionsgetDepth()[Ipress%()[[Lorg/biojava/bio/dp/twohead/Cell;ci"[Lorg/biojava/bio/dp/twohead/Cell;cells#[[Lorg/biojava/bio/dp/twohead/Cell;] SourceFileAbstractMatrixPairDPCursor.java 3 )* +,org/biojava/bio/dp/BackPointer -. 0% !!org/biojava/bio/symbol/SymbolList "# /! 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89y I org/biojava/bio/dp/EmissionState I  1org/biojava/bio/dp/twohead/DPInterpreter$Backwardjava/lang/Object)org/biojava/bio/dp/twohead/CellCalculator-org/biojava/bio/symbol/IllegalSymbolException/org/biojava/bio/symbol/IllegalAlphabetException-org/biojava/bio/dp/IllegalTransitionExceptionorg/biojava/bio/dp/twohead/Cellorg/biojava/bio/dp/State()Vorg/biojava/bio/dp/DP getStates()[Lorg/biojava/bio/dp/State;getBackwardTransitions()[[IgetBackwardTransitionScores#(Lorg/biojava/bio/dp/ScoreType;)[[DgetModel"()Lorg/biojava/bio/dp/MarkovModel;org/biojava/bio/dp/MarkovModel#()Lorg/biojava/bio/dp/MagicalState;scores getAdvance()[I emissionsjava/lang/DoubleisNaN(D)Zjava/lang/Mathexp(D)Dlog(org/biojava/bio/dp/twohead/DPInterpreter  !"#$}+**+*+*+,*+  % *& +'*++,+-./01234$?*+ % &'*56/01274$?*+ % &'*56/01289$i+22N- :*d6Q*2:( * R$R*2:*2:: 6  p .6 * 2: < :+.2.2: 19  R -:9     1 cR 9 9 6U 19?7 9 19 c gc9  R  cR%, #/8AILU^ep w $%'(+,-.01,2<)B6J7U9bhD&*:;<= >?<= w`@A WB!>?huCA !D=EE=ZCA#?F!U G;^HIeJI K= }L= SMAi'*i56iNOcP? ]QIRST+U  VWSTUXTTUVWSTUXTTUSVWSTUXTTUVWSTUXTTUS VWSTUXTT +' VWST/012YZ) r( PK .*?::\6org/biojava/bio/dp/twohead/DPInterpreter$Forward.class2 $k lm #n lo #p lq #r ls tu #v #w xy xz{ |} ~   k     transitions[[ItransitionScores[[Dstatesorg/biojava/bio/dp/State; magicalStateLorg/biojava/bio/dp/State;8(Lorg/biojava/bio/dp/DP;Lorg/biojava/bio/dp/ScoreType;)VCodeLineNumberTableLocalVariableTablethisForward InnerClasses2Lorg/biojava/bio/dp/twohead/DPInterpreter$Forward;dpLorg/biojava/bio/dp/DP; scoreTypeLorg/biojava/bio/dp/ScoreType; Exceptions initialize&([[Lorg/biojava/bio/dp/twohead/Cell;)Vcells#[[Lorg/biojava/bio/dp/twohead/Cell;calcCell _calcCell'([[Lorg/biojava/bio/dp/twohead/Cell;Z)V sourceScores[DweightDadvance[IsktrcItrSccitrtrsconstantscoreeLjava/lang/Exception;Lorg/biojava/bio/BioError;curStatelinitializationHackZcurCell!Lorg/biojava/bio/dp/twohead/Cell;curCol emissions StackMapTableBGK SourceFileDPInterpreter.java . *+ &' ()  , ,- DE G _G org/biojava/bio/dp/EmissionState  java/lang/Exceptionorg/biojava/bio/BioErrorjava/lang/StringBuilderProblem with state  ->  .Error with state 0org/biojava/bio/dp/twohead/DPInterpreter$Forwardjava/lang/Object)org/biojava/bio/dp/twohead/CellCalculator-org/biojava/bio/symbol/IllegalSymbolException/org/biojava/bio/symbol/IllegalAlphabetException-org/biojava/bio/dp/IllegalTransitionExceptionorg/biojava/bio/dp/twohead/Cellorg/biojava/bio/dp/State()Vorg/biojava/bio/dp/DP getStates()[Lorg/biojava/bio/dp/State;getForwardTransitions()[[IgetForwardTransitionScores#(Lorg/biojava/bio/dp/ScoreType;)[[DgetModel"()Lorg/biojava/bio/dp/MarkovModel;org/biojava/bio/dp/MarkovModel#()Lorg/biojava/bio/dp/MagicalState;scoresjava/lang/DoubleisNaN(D)Z getAdvance()[Ijava/lang/Mathexp(D)Dlogappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;getName()Ljava/lang/String;toString*(Ljava/lang/String;Ljava/lang/Throwable;)V(org/biojava/bio/dp/twohead/DPInterpreter #$%&'()*+,-./0}+**+*+*+,*+  1FG IJK*L2 +36+78+9:;<=>?@0?*+ 1 TU236AB;<=>C@0?*+ 1 ]^236AB;<=>DE0B+22N- :- :6**2:( * R R` 9 :B19    R+: + .2 .2 :*2: *2: 9 96 \ .619@7 9  19c gc9 R c cRk:YY*2 !:YY"*2 !d(NFQFCF(NzQzCz1,fg hlm(p4q=rFtNwQ}Y~\cj{  (3CFHz|l2`FG\HI JK !LILMNEOIaPNFGjHI QK RG SI TIH2UV|2UW(X-YN36ABZ[\] ^G_G`abcdd0e  abcddedabcddedfd2'abcddeBgsh3;<=>ij5 #4 PK .*?:MK4org/biojava/bio/dp/twohead/DPInterpreter$Maker.class2  ()VCodeLineNumberTableLocalVariableTablethisMaker InnerClasses0Lorg/biojava/bio/dp/twohead/DPInterpreter$Maker;makeK(Lorg/biojava/bio/dp/DP;)Lorg/biojava/bio/dp/twohead/CellCalculatorFactory;dpLorg/biojava/bio/dp/DP; SourceFileDPInterpreter.java (org/biojava/bio/dp/twohead/DPInterpreter .org/biojava/bio/dp/twohead/DPInterpreter$Makerjava/lang/Object5org/biojava/bio/dp/twohead/CellCalculatorFactoryMaker(Lorg/biojava/bio/dp/DP;)V! 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isCollapsingZ rendForwarder#Lorg/biojava/utils/ChangeForwarder;getChangeSupportA(Lorg/biojava/utils/ChangeType;)Lorg/biojava/utils/ChangeSupport;CodeLineNumberTableLocalVariableTablecLorg/biojava/utils/Changeable;this;Lorg/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer;ctcs!Lorg/biojava/utils/ChangeSupport; StackMapTable()Vcve'Lorg/biojava/utils/ChangeVetoException;1(Lorg/biojava/bio/gui/sequence/FeatureRenderer;)VfRendgetFeatureRenderer0()Lorg/biojava/bio/gui/sequence/FeatureRenderer;setFeatureRendererceLorg/biojava/utils/ChangeEvent; Exceptions setCollapsing(Z)Vb getCollapsing()ZgetDepth7(Lorg/biojava/bio/gui/sequence/SequenceRenderContext;)Dsrc4Lorg/biojava/bio/gui/sequence/SequenceRenderContext;features#Lorg/biojava/bio/seq/FeatureHolder;filter#Lorg/biojava/bio/seq/FeatureFilter;fhgetMinimumLeadergetMinimumTrailerpaintL(Ljava/awt/Graphics2D;Lorg/biojava/bio/gui/sequence/SequenceRenderContext;)VclipLjava/awt/Shape;atLjava/awt/geom/AffineTransform;fLorg/biojava/bio/seq/Feature;iLjava/util/Iterator;gLjava/awt/Graphics2D;filtfeatsprocessMouseEvent(Lorg/biojava/bio/gui/sequence/SequenceRenderContext;Ljava/awt/event/MouseEvent;Ljava/util/List;)Lorg/biojava/bio/gui/sequence/SequenceViewerEvent;posDmeLjava/awt/event/MouseEvent;pathLjava/util/List;sMinIsMaxhits SourceFile!FeatureBlockSequenceRenderer.java NO LM?org/biojava/bio/gui/sequence/SequenceRenderer$RendererForwarderRendererForwarder InnerClasses \ HIorg/biojava/utils/Changeable F \] JK1org/biojava/bio/gui/sequence/BasicFeatureRenderer gb%org/biojava/utils/ChangeVetoException"org/biojava/utils/AssertionFailure+Assertion Failure: Should have no listeners \ r EForg/biojava/utils/ChangeEvent \ GFjava/lang/Boolean \o    y  st     w  r   org/biojava/bio/seq/Feature      !" #" $%2org/biojava/bio/seq/FeatureFilter$OverlapsLocationOverlapsLocation$org/biojava/bio/symbol/RangeLocation \& \' (0org/biojava/bio/gui/sequence/SequenceViewerEvent \)org/biojava/utils/ChangeType*The associated FeatureRenderer has changed9org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer *F \+AChanged whether the render collapses when no features are visible9org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer$org/biojava/utils/AbstractChangeable-org/biojava/bio/gui/sequence/SequenceRendererorg/biojava/utils/ChangeSupport,org/biojava/bio/gui/sequence/FeatureRendererjava/lang/Objectjava/lang/Throwable!org/biojava/bio/seq/FeatureHolder!org/biojava/bio/seq/FeatureFilterjava/util/IteratorS(Lorg/biojava/bio/gui/sequence/SequenceRenderer;Lorg/biojava/utils/ChangeSupport;)V2org/biojava/bio/gui/sequence/SequenceRenderContextREPAINTaddChangeListenerC(Lorg/biojava/utils/ChangeListener;Lorg/biojava/utils/ChangeType;)V*(Ljava/lang/String;Ljava/lang/Throwable;)V hasListenersW(Ljava/lang/Object;Lorg/biojava/utils/ChangeType;Ljava/lang/Object;Ljava/lang/Object;)VfirePreChangeEvent"(Lorg/biojava/utils/ChangeEvent;)VremoveChangeListenerfirePostChangeEvent getFeatures%()Lorg/biojava/bio/seq/FeatureHolder;getRange(()Lorg/biojava/bio/symbol/RangeLocation;org/biojava/bio/seq/FilterUtilsoverlapsLocationF(Lorg/biojava/bio/symbol/Location;)Lorg/biojava/bio/seq/FeatureFilter;I(Lorg/biojava/bio/seq/FeatureFilter;Z)Lorg/biojava/bio/seq/FeatureHolder; 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makeLabel1(Lorg/biojava/bio/seq/Feature;)Ljava/lang/String;featLorg/biojava/bio/seq/Feature;annLorg/biojava/bio/Annotation; StackMapTable4 SourceFileFeatureLabelRenderer.java   5 674 89 :; <=>Forg/biojava/bio/gui/sequence/FeatureLabelRenderer$AnnotationLabelMakerjava/lang/Object*+  /* }%+M,*,*" %% !""#$ / /3 PK .*?:)FLLBorg/biojava/bio/gui/sequence/FeatureLabelRenderer$LabelMaker.class2   makeLabel1(Lorg/biojava/bio/seq/Feature;)Ljava/lang/String; SourceFileFeatureLabelRenderer.java ()VCodeLineNumberTableLocalVariableTablethisSourceLabelMaker InnerClassesDLorg/biojava/bio/gui/sequence/FeatureLabelRenderer$SourceLabelMaker; makeLabel1(Lorg/biojava/bio/seq/Feature;)Ljava/lang/String;fLorg/biojava/bio/seq/Feature; SourceFileFeatureLabelRenderer.java   Borg/biojava/bio/gui/sequence/FeatureLabelRenderer$SourceLabelMakerjava/lang/Object()VCodeLineNumberTableLocalVariableTablethisTypeLabelMaker InnerClassesBLorg/biojava/bio/gui/sequence/FeatureLabelRenderer$TypeLabelMaker; makeLabel1(Lorg/biojava/bio/seq/Feature;)Ljava/lang/String;fLorg/biojava/bio/seq/Feature; 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AB 56 A LM%org/biojava/utils/ChangeVetoException"org/biojava/utils/AssertionFailure+Assertion Failure: Should have no listeners Aorg/biojava/utils/ChangeEvent 34java/lang/Double AM A%Can't set padding to a negative value A XY \Y ]Y  VW ^_  efjava/lang/StringBuilderPaddingRenderer(  op)org/biojava/utils/ChangeTypeThe padding has changed,org.biojava.bio.gui.sequence.PaddingRenderer 4 A,org/biojava/bio/gui/sequence/PaddingRenderer4org/biojava/bio/gui/sequence/SequenceRendererWrapper-org/biojava/bio/gui/sequence/SequenceRendererorg/biojava/utils/ChangeSupportjava/lang/Objectjava/lang/Throwablejava/awt/geom/AffineTransform0org/biojava/bio/gui/sequence/SequenceViewerEvent2(Lorg/biojava/bio/gui/sequence/SequenceRenderer;)V*(Ljava/lang/String;Ljava/lang/Throwable;)VW(Ljava/lang/Object;Lorg/biojava/utils/ChangeType;Ljava/lang/Object;Ljava/lang/Object;)V4(Lorg/biojava/utils/ChangeEvent;Ljava/lang/String;)VfirePreChangeEvent"(Lorg/biojava/utils/ChangeEvent;)VfirePostChangeEventjava/awt/Graphics2D getTransform!()Ljava/awt/geom/AffineTransform;2org/biojava/bio/gui/sequence/SequenceRenderContext getDirection()I translate(DD)V setTransform"(Ljava/awt/geom/AffineTransform;)Vjava/awt/event/MouseEventtranslatePoint(II)Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder; getRenderer1()Lorg/biojava/bio/gui/sequence/SequenceRenderer;LAYOUTW(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/utils/ChangeType;)V!12 3456 789/*:8; <=>?9:*+:<;<=@4AB9< **:EF G;  <=AC9*+*(:Y   :UW Z XY[;* DE<=FG56H IJK LM9D '- Y* Y* Y'NY-*R* N-Y:» Y* Y* Y':-*'-ç :*'Dx{{{::ij%m0r7s?tDudxjyozu{|};4% NOdNO?DPQ<=56H0JIRSTUVW9/*:; <=XY9C*+*kc:;<=Z[\Y9:*+:;<=Z[]Y9:*+:;<=Z[^_9/+N,+* +**+,+- :#).;*/<=/`a/Z[*bcH def9I*6+,t! ,t!*+,-":+ ,! ,!:& #,5?F;>I<=IZ[IghIijB5k,lmHnop9I#Y$%&*'(&)&*:; <=qB9,+Y,-./0 :.rsPK .*?:SZ!!;org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.class2} N O  N N  N      N N N N ) )  4 6   N   R =    C H H H GOUTLINELorg/biojava/utils/ChangeType;spf#Lorg/biojava/bio/seq/FeatureFilter;lineFloat InnerClassesLjava/awt/geom/Line2D$Float;outlineLjava/awt/Paint;()VCodeLineNumberTableLocalVariableTablethis7Lorg/biojava/bio/gui/sequence/PairwiseDiagonalRenderer;(Ljava/awt/Paint;)VpaintL(Ljava/awt/Graphics2D;Lorg/biojava/bio/gui/sequence/PairwiseRenderContext;)Vfh#Lorg/biojava/bio/seq/FeatureHolder;posX1FposY1posX2posY2f11Lorg/biojava/bio/seq/homol/SimilarityPairFeature;f2s1Strand,Lorg/biojava/bio/seq/StrandedFeature$Strand;s2loc1!Lorg/biojava/bio/symbol/Location;loc2min1Imax1min2max2clipLjava/awt/geom/Rectangle2D;fiLjava/util/Iterator;g2Ljava/awt/Graphics2D;context4Lorg/biojava/bio/gui/sequence/PairwiseRenderContext; StackMapTable !" getOutline()Ljava/awt/Paint; setOutlineceLorg/biojava/utils/ChangeEvent;cs!Lorg/biojava/utils/ChangeSupport;#$%& Exceptions'processMouseEvent(Lorg/biojava/bio/gui/sequence/PairwiseRenderContext;Ljava/awt/event/MouseEvent;Ljava/util/List;)Lorg/biojava/bio/gui/sequence/SequenceViewerEvent;gPosDmeLjava/awt/event/MouseEvent;pathLjava/util/List;priMinpriMaxclipLine#(FFFFLjava/awt/geom/Line2D$Float;)VdxdyxMinxMaxyMinyMax clipTypeX clipTypeY calcClipType (FFFFFF)IxyeLjava/lang/Exception; classNameLjava/lang/String;( SourceFilePairwiseDiagonalRenderer.java) *+ \c \],java/awt/geom/Line2D$Float VY Z[! -. /01%org/biojava/bio/seq/FeatureFilter$AndAnd2org/biojava/bio/seq/FeatureFilter$OverlapsLocationOverlapsLocation 23 \4 TU \5 67 83 9: ;< =>/org/biojava/bio/seq/homol/SimilarityPairFeature ?@ AB CD" E. 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isEnabled Exceptions SourceFileRectangularBeadRenderer.java 56 java/awt/geom/Rectangle2D$DoubleDouble InnerClasses 12 34 5<   ?>  U => S BA CD @A ]^ a 0 org/biojava/utils/ChangeEvent /0java/lang/Boolean 5c 5 5 org/biojava/utils/ChangeType5The height scaling policy of the features has changed4org.biojava.bio.gui.sequence.RectangularBeadRenderer 54org/biojava/bio/gui/sequence/RectangularBeadRenderer1org/biojava/bio/gui/sequence/AbstractBeadRendererjava/awt/Graphics2Dorg/biojava/bio/seq/Feature2org/biojava/bio/gui/sequence/SequenceRenderContextorg/biojava/bio/symbol/Locationorg/biojava/utils/ChangeSupportjava/lang/Objectjava/lang/Throwable%org/biojava/utils/ChangeVetoExceptionjava/awt/geom/Rectangle2D getLocation#()Lorg/biojava/bio/symbol/Location;getMin()IgetMax getDirectionsequenceToGraphics(I)DgetScale()Djava/lang/Math(DD)Dfloor(D)DsetRect(DDDD)VsetPaint(Ljava/awt/Paint;)Vfill(Ljava/awt/Shape;)V setStroke(Ljava/awt/Stroke;)Vdraw hasListenersLAYOUTgetChangeSupportA(Lorg/biojava/utils/ChangeType;)Lorg/biojava/utils/ChangeSupport;W(Ljava/lang/Object;Lorg/biojava/utils/ChangeType;Ljava/lang/Object;Ljava/lang/Object;)Vv(Ljava/lang/Object;Lorg/biojava/utils/ChangeType;Ljava/lang/Object;Ljava/lang/Object;Lorg/biojava/utils/ChangeEvent;)VfirePreChangeEvent"(Lorg/biojava/utils/ChangeEvent;)VfirePostChangeEventW(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/utils/ChangeType;)V!-./01234567K**Y*8HIJK9 :;5<7*')*Y*8\ ]^_9>:;=>?>@ABACDEF7 6,:6 6d6- v- 9* 9 `- k9 */* o9* *goc9 *9*  s* 9- 9 c- k9*/*o9  ** goc9 *9 *  +*+*+*+*+*8vlnop!t*v4w:xLzS|bl %-59bG>4iH>:cI> LQJ> G>J> 6:;6KL6MN6OP.QR%STUT!VTH>I> >J> wG>Ww XYZ[\XYZ[\T XYZ[\ XYZ[\]^7V*+I(** c8 9 :;OP_>`a7/*89 :;bc7f*\*M,YN» Y* Y*!"Y*#"Y#$%:,&*,'-ç :-*SVVZV8. @FKQ]`e9*@deNfgf:;fh4WVXijklmn67,(Y)*+,!8:opu rt PK .*?:@A~z:org/biojava/bio/gui/sequence/RectangularImapRenderer.class2 . - - - - - - @   - renderer6Lorg/biojava/bio/gui/sequence/RectangularBeadRenderer;imageMap'Lorg/biojava/bio/gui/sequence/ImageMap; urlFactory"Lorg/biojava/utils/net/URLFactory;(Lorg/biojava/bio/gui/sequence/RectangularBeadRenderer;Lorg/biojava/bio/gui/sequence/ImageMap;Lorg/biojava/utils/net/URLFactory;)VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/gui/sequence/RectangularImapRenderer; getImageMap)()Lorg/biojava/bio/gui/sequence/ImageMap; setImageMap*(Lorg/biojava/bio/gui/sequence/ImageMap;)VsetDelegateRenderer\(Lorg/biojava/bio/seq/OptimizableFilter;Lorg/biojava/bio/gui/sequence/BeadFeatureRenderer;)Vfilter'Lorg/biojava/bio/seq/OptimizableFilter;2Lorg/biojava/bio/gui/sequence/BeadFeatureRenderer;renderImageMapi(Ljava/awt/Graphics2D;Lorg/biojava/bio/seq/Feature;Lorg/biojava/bio/gui/sequence/SequenceRenderContext;)VheightDposXWposYNwidth coordinates[Ljava/lang/Integer;g2Ljava/awt/Graphics2D;fLorg/biojava/bio/seq/Feature;context4Lorg/biojava/bio/gui/sequence/SequenceRenderContext;boundsLjava/awt/Rectangle;mapWidthI mapHeighturlLjava/net/URL; beadDepthbeadDisplacement scaleHeightZtLjava/awt/geom/AffineTransform;transXtransYminmaxdifx1y1x2y2loc!Lorg/biojava/bio/symbol/Location; StackMapTable renderFeature renderBeadgetDepth7(Lorg/biojava/bio/gui/sequence/SequenceRenderContext;)D getBeadDepth()DgetBeadDisplacementgetHeightScaling()ZsetHeightScaling(Z)V isEnabled ExceptionsprocessMouseEvent(Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/gui/sequence/SequenceRenderContext;Ljava/awt/event/MouseEvent;)Lorg/biojava/bio/seq/FeatureHolder;holder#Lorg/biojava/bio/seq/FeatureHolder;mEventLjava/awt/event/MouseEvent; SourceFileRectangularImapRenderer.java 8 23 45 67 CD   } } |} ~}   } }   } g f g fjava/lang/Integer 8-org/biojava/bio/gui/sequence/ImageMap$HotSpotHotSpot InnerClassesrect 8 HI xI yI z{ 4org/biojava/bio/gui/sequence/RectangularImapRendererjava/lang/Object0org/biojava/bio/gui/sequence/BeadFeatureRenderer-org/biojava/bio/gui/sequence/ImageMapRendererjava/io/Serializablejava/awt/Graphics2Dorg/biojava/bio/seq/Feature2org/biojava/bio/gui/sequence/SequenceRenderContextjava/awt/Rectangle java/net/URLjava/awt/geom/AffineTransformorg/biojava/bio/symbol/Location%org/biojava/utils/ChangeVetoException()V4org/biojava/bio/gui/sequence/RectangularBeadRenderergetDeviceConfiguration"()Ljava/awt/GraphicsConfiguration;java/awt/GraphicsConfiguration getBounds()Ljava/awt/Rectangle;getWidth getHeight org/biojava/utils/net/URLFactory createURL"(Ljava/lang/Object;)Ljava/net/URL; getTransform!()Ljava/awt/geom/AffineTransform; getTranslateX getTranslateY getLocation#()Lorg/biojava/bio/symbol/Location;getMin()IgetMax getDirectionsequenceToGraphics(I)DgetScalejava/lang/Math(DD)Dfloor(D)D(II)I(I)V%org/biojava/bio/gui/sequence/ImageMapI(Ljava/lang/String;Ljava/net/URL;[Ljava/lang/Integer;Ljava/lang/Object;)V addHotSpot2(Lorg/biojava/bio/gui/sequence/ImageMap$HotSpot;)V!-./01234567 89:l**+*,*-;CD EFG<*=>234567?@:/*;P< =>AB:>*+; Z[<=>45CD:L *+,; f g<  => EF 2GHI:#+:6 6*, :* 9* 9 * 6 +:  9 9,:!!6!6d6-U-9 9`-k9 )o9jgoc9Y9R 9-9c-k9 )o9goc99c6c6cc6cc6{v6666:""YS"YS"YS"YS* Y!","#;/z }~%+17=DKS\elu!,:H`hpy<L!JKHLKDMK2NKJKNKKOP"=>QRSTUV WXYZ[Z%\]+^K1_K 7`a =bc DdKKeK\xfZeogZlhhZ!iZ,jZ:kZHlZ LKMKNKJKSmn!opqrstuvwpqrstuvwJpqrstuvwpqrstuvwpqrstuvwxI:b*+,-$*+,-%;<*=>QRSTUVyI:W *+,-&;  <* => QR ST UVz{:= *+';< => UV|}:2*(;< =>~}:2*);< =>:2**;< =>:A *+;   < => a:S *+,-,;<* =>  UV   PK .*?:wA ?org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.class2 !SU S X@ Y Z ![ \] ^_ ^` ab ac d ae fg h@ fi fj Tk l mn mo p mq r ms !tuvrect Ljava/awt/geom/RoundRectangle2D;arcWidthD arcHeight()VCodeLineNumberTableLocalVariableTablethis;Lorg/biojava/bio/gui/sequence/RoundRectangularBeadRenderer;8(DDLjava/awt/Paint;Ljava/awt/Paint;Ljava/awt/Stroke;DD)V beadDepthbeadDisplacement beadOutlineLjava/awt/Paint;beadFill beadStrokeLjava/awt/Stroke; renderBeadi(Ljava/awt/Graphics2D;Lorg/biojava/bio/seq/Feature;Lorg/biojava/bio/gui/sequence/SequenceRenderContext;)VposXWposYNwidthheightg2Ljava/awt/Graphics2D;fLorg/biojava/bio/seq/Feature;context4Lorg/biojava/bio/gui/sequence/SequenceRenderContext;loc!Lorg/biojava/bio/symbol/Location;minImaxdif StackMapTableuwxyzgetDepth7(Lorg/biojava/bio/gui/sequence/SequenceRenderContext;)DmaxDepth SourceFile!RoundRectangularBeadRenderer.java '({%java/awt/geom/RoundRectangle2D$DoubleDouble InnerClasses "# $% &% '|x }~z  y 0%  F /% D 32w 45 12 NO9org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer1org/biojava/bio/gui/sequence/AbstractBeadRendererjava/awt/Graphics2Dorg/biojava/bio/seq/Feature2org/biojava/bio/gui/sequence/SequenceRenderContextorg/biojava/bio/symbol/Locationjava/awt/geom/RoundRectangle2D6(DDLjava/awt/Paint;Ljava/awt/Paint;Ljava/awt/Stroke;)V getLocation#()Lorg/biojava/bio/symbol/Location;getMin()IgetMax getDirectionsequenceToGraphics(I)DgetScale()Djava/lang/Math(DD)Dfloor(D)D setRoundRect (DDDDDD)VsetPaint(Ljava/awt/Paint;)Vfill(Ljava/awt/Shape;)V setStroke(Ljava/awt/Stroke;)Vdraw! !"#$%&%'()X**Y***56789+ ,-'.) $*') *Y** *P QRS#T+R$,-$/%$0%$12$32$45$$%$&% 67) &, : 6 6d6- n-9*9 `-k9 * o9* *goc9 *  **k*9-9 c-k9 * o9**goc9*  **+*+*+*+*+**jbdef!h*j4k:lLm[qerutx{|}~ %+4^8%:X9% LF:% [7;%b8%X9% F;% 7:%&,-&<=&>?&@ABCDE FE!GEHnu IJKLMIJKLMJ IJKLMIJKLMNO)V*+I(**c* + ,-@AP%QRW TV PK .*?:B0org/biojava/bio/gui/sequence/RulerRenderer.class2 < =  <V < < @4 <@ < < < ? @ @$ @  :TICKS_UPI ConstantValue TICKS_DOWNlineLjava/awt/geom/Line2D;depthD antiQuarterLjava/awt/geom/AffineTransform; tickDirection tickHeightFhorizLabelOffsetvertLabelOffset()VCodeLineNumberTableLocalVariableTablethis,Lorg/biojava/bio/gui/sequence/RulerRenderer; Exceptions(I)V StackMapTablegetMinimumLeader7(Lorg/biojava/bio/gui/sequence/SequenceRenderContext;)Dcontext4Lorg/biojava/bio/gui/sequence/SequenceRenderContext;getMinimumTrailergetDepthsrcpaintL(Ljava/awt/Graphics2D;Lorg/biojava/bio/gui/sequence/SequenceRenderContext;)VsnapSymsPerGapoffset labelStringLjava/lang/String;halfLabelWidthindexg2Ljava/awt/Graphics2D; prevTransformvisible!Lorg/biojava/bio/symbol/Location;minmaxminXmaxXscale halfScalefMetricsLjava/awt/FontMetrics; coordWidthminGaprealSymsPerGapexponentcharacteristicminPprocessMouseEvent(Lorg/biojava/bio/gui/sequence/SequenceRenderContext;Ljava/awt/event/MouseEvent;Ljava/util/List;)Lorg/biojava/bio/gui/sequence/SequenceViewerEvent;meLjava/awt/event/MouseEvent;pathLjava/util/List;sPos SourceFileRulerRenderer.java PX PQjava/awt/geom/Line2D$DoubleDouble InnerClasses EF  IJ K@"java/lang/IllegalArgumentExceptionTTick direction may only be set to RulerRenderer.TICKS_UP or RulerRenderer.TICKS_DOWN P GH LM NM OM    n    p         0org/biojava/bio/gui/sequence/SequenceViewerEvent P *org/biojava/bio/gui/sequence/RulerRendererjava/lang/Object-org/biojava/bio/gui/sequence/SequenceRendererjava/awt/geom/AffineTransformorg/biojava/bio/symbol/Locationjava/awt/Graphics2D2org/biojava/bio/gui/sequence/SequenceRenderContextjava/awt/FontMetricsjava/lang/Stringjava/awt/geom/Line2Djava/lang/Math toRadians(D)DgetRotateInstance"(D)Ljava/awt/geom/AffineTransform;(Ljava/lang/String;)V getTransform!()Ljava/awt/geom/AffineTransform;java/awt/ColorblackLjava/awt/Color;setPaint(Ljava/awt/Paint;)V%org/biojava/bio/gui/sequence/GUIToolsgetVisibleRangel(Lorg/biojava/bio/gui/sequence/SequenceRenderContext;Ljava/awt/Graphics2D;)Lorg/biojava/bio/symbol/Location;emptygetMin()IgetMaxsequenceToGraphics(I)DgetScale()D getDirectionsetLine(DDDD)Vdraw(Ljava/awt/Shape;)VgetFontMetrics()Ljava/awt/FontMetrics;java/lang/IntegertoString(I)Ljava/lang/String; stringWidth(Ljava/lang/String;)I(II)Iceillogfloorpow(DD)DvalueOf drawString(Ljava/lang/String;FF)V translate(DD)V transform"(Ljava/awt/geom/AffineTransform;)V setTransformjava/util/Listadd(Ljava/lang/Object;)Zjava/awt/event/MouseEventgetPoint()Ljava/awt/Point;graphicsToSequence(Ljava/awt/geom/Point2D;)IS(Ljava/lang/Object;Ljava/lang/Object;ILjava/awt/event/MouseEvent;Ljava/util/List;)V!<=> ?@ABC@ADEFGHIJK@LMNMOMPQR4*S MNT UVW PXRg**Y*  * Y *****f f*** b jfS. 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PK /*?:j2org/biojava/bio/gui/sequence/SequencePanel$1.class2P * + ), )- ./ )01 + 23 )4 56 57 589:this$0,Lorg/biojava/bio/gui/sequence/SequencePanel;/(Lorg/biojava/bio/gui/sequence/SequencePanel;)VCodeLineNumberTableLocalVariableTablethis InnerClasses.Lorg/biojava/bio/gui/sequence/SequencePanel$1; mouseClicked(Ljava/awt/event/MouseEvent;)VmeLjava/awt/event/MouseEvent;dist[Isve2Lorg/biojava/bio/gui/sequence/SequenceViewerEvent; StackMapTable mousePressed mouseReleased SourceFileSequencePanel.javaEnclosingMethod;  < => ?@A BC DEjava/util/ArrayListF GH IJK LM NM OM,org/biojava/bio/gui/sequence/SequencePanel$1java/awt/event/MouseAdapter*org/biojava/bio/gui/sequence/SequencePanel()VisActive()ZcalcDist()[Ijava/awt/event/MouseEventtranslatePoint(II)V access$000](Lorg/biojava/bio/gui/sequence/SequencePanel;)Lorg/biojava/bio/gui/sequence/SequenceRenderer;-org/biojava/bio/gui/sequence/SequenceRendererprocessMouseEvent(Lorg/biojava/bio/gui/sequence/SequenceRenderContext;Ljava/awt/event/MouseEvent;Ljava/util/List;)Lorg/biojava/bio/gui/sequence/SequenceViewerEvent; access$100b(Lorg/biojava/bio/gui/sequence/SequencePanel;)Lorg/biojava/bio/gui/sequence/SequenceViewerSupport;2org/biojava/bio/gui/sequence/SequenceViewerSupportfireMouseClicked5(Lorg/biojava/bio/gui/sequence/SequenceViewerEvent;)VfireMousePressedfireMouseReleased 4 *+*  N**M+,.,.**+Y N+,.t,.t* - " 6BM*NN; 6!"# $N**M+,.,.**+Y N+,.t,.t* - " 6BM*NN; 6!"# %N**M+,.,.**+Y N+,.t,.t* - " 6BM*NN; 6!"# &'() PK /*?:u/^2org/biojava/bio/gui/sequence/SequencePanel$2.class2N ) * (+ (, -. 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Graphical displays of biological sequences and associated annotations.

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P QL RL SL%org/biojava/bio/molbio/DNAComposition"org/biojava/bio/molbio/Compositionorg/biojava/bio/seq/DNATools createDNA7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList; setSymbolList&(Lorg/biojava/bio/symbol/SymbolList;)Vjava/lang/SystemerrLjava/io/PrintStream;java/io/PrintStreamprintln(Ljava/lang/String;)VgetDistribution%()Lorg/biojava/bio/dist/Distribution;a'()Lorg/biojava/bio/symbol/AtomicSymbol;!org/biojava/bio/dist/Distribution getWeight"(Lorg/biojava/bio/symbol/Symbol;)D*(Ljava/lang/String;Ljava/lang/Throwable;)Vcgt!** L &( +)*, !i* L Y + 4 56 M"!i*  L Y + @ AB M#!i*  L Y + L MN M$!i*  L Y + X YZ M%&PK .*?:[Epp.org/biojava/bio/molbio/RestrictionEnzyme.class2 2 2 4       2 2 2 2 2 2       2  .  2 CUT_SIMPLEI ConstantValue CUT_COMPOUNDOVERHANG_5PRIMEOVERHANG_3PRIMEBLUNTnameLjava/lang/String;site#Lorg/biojava/bio/symbol/SymbolList;cutTypedsCutPositions[IusCutPositions forwardRegex reverseRegexsummary:(Ljava/lang/String;Lorg/biojava/bio/symbol/SymbolList;II)VCodeLineNumberTableLocalVariableTablethis*Lorg/biojava/bio/molbio/RestrictionEnzyme; dsForward dsReverse Exceptions<(Ljava/lang/String;Lorg/biojava/bio/symbol/SymbolList;IIII)V usForward usReverse<(Ljava/lang/String;Lorg/biojava/bio/symbol/SymbolList;[I[I)Viae1Lorg/biojava/bio/symbol/IllegalAlphabetException;iise/Lorg/biojava/bio/symbol/IllegalSymbolException;sbLjava/lang/StringBuffer; StackMapTableFgetName()Ljava/lang/String;getRecognitionSite%()Lorg/biojava/bio/symbol/SymbolList;getForwardRegexgetReverseRegex isPalindromic()Z getCutType()IgetDownstreamCut()[IgetUpstreamCutgetDownstreamEndTypegetUpstreamEndTypehashCodeequals(Ljava/lang/Object;)ZoLjava/lang/Object;toString SourceFileRestrictionEnzyme.java KX D7 K  /org/biojava/bio/symbol/IllegalAlphabetExceptionjava/lang/StringBuilderLRestrictionEnzyme site can only be a DNA SymbolList. 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G HI#J1K=LYMaNmOuQTb cfwxuso/"h,yz`B *aXb  cfo @{|` aL* .0Y*** .* .*.*.1L0Y***.*.2LM4Y5,6+PS3a"]a c4kPsSpTr_ub T }~acf_mo4B q`a*+*7* ayz{|bcfusoh,q`u8Y+9M,:? * ,:(,;<>,=>6,`,?d=>6:,YAB** * O* O* **C`O**C`Os,D<6*  *,EF*O*O0,GW*,EF*O**CdO:,YIB-JM@  Ha  &-8JMO[biq|  b\ O -}k8rkJ`k }hkcfus oN 0  -1,B h,e Jd PK .*?:aGN'N'5org/biojava/bio/molbio/RestrictionEnzymeManager.class2 g g g g g n g g   g            g  g !"# $ %& %'( ) * + ,- ./ / 0 41 234 556 $789: ;; <= >? $@A ABC DD CEF G GG GH GI GJK MLM ONOP SQ SRST XUV ZWX ZYZ[ _ _\ ] n^ _`abc _ de gfg dh _ijRebaseEnzymeBuilder InnerClassesREBASE_DATA_KEYLjava/lang/String; ConstantValueREBASE_TAG_NAMEREBASE_TAG_ISZRREBASE_TAG_SITEREBASE_TAG_METHkREBASE_TAG_ORGNlREBASE_TAG_SRCEmREBASE_TAG_COMMREBASE_TAG_REFSnloadCommercialOnlyZbundleLjava/util/ResourceBundle; nameToSiteLjava/util/Map; nameToEnzymenameToIsoschizomers sizeToCuttersenzymeToPatternenzymeToAnnotationenzymeToSuppliers()VCodeLineNumberTableLocalVariableTablethis1Lorg/biojava/bio/molbio/RestrictionEnzymeManager;loadEnzymeFile(Ljava/io/InputStream;Z)VisLjava/io/InputStream;commercialOnly getAllEnzymes()Ljava/util/Set; getEnzyme>(Ljava/lang/String;)Lorg/biojava/bio/molbio/RestrictionEnzyme;name StackMapTablegetIsoschizomers#(Ljava/lang/String;)Ljava/util/Set;resultLjava/util/Set;getRecognitionSequence&(Ljava/lang/String;)Ljava/lang/String; getNCutters(I)Ljava/util/Set;nIsizeLjava/lang/Integer; getPatternsF(Lorg/biojava/bio/molbio/RestrictionEnzyme;)[Ljava/util/regex/Pattern;enzyme*Lorg/biojava/bio/molbio/RestrictionEnzyme; getAnnotationH(Lorg/biojava/bio/molbio/RestrictionEnzyme;)Lorg/biojava/bio/Annotation; getSuppliers>(Lorg/biojava/bio/molbio/RestrictionEnzyme;)Ljava/lang/String;register<(Lorg/biojava/bio/molbio/RestrictionEnzyme;Ljava/util/Set;)VoLjava/lang/Object;iiLjava/util/Iterator; isoschizomersoregisterEnzyme-(Lorg/biojava/bio/molbio/RestrictionEnzyme;)Vscve'Lorg/biojava/utils/ChangeVetoException;sizeKeyforwardLjava/util/regex/Pattern;reverse annotationLorg/biojava/bio/Annotation;3"8loadData(Ljava/io/InputStream;)VisoNamerenibrLjava/io/BufferedReader;lsParser2Lorg/biojava/bio/program/tagvalue/LineSplitParser;builderELorg/biojava/bio/molbio/RestrictionEnzymeManager$RebaseEnzymeBuilder;iso0Lorg/biojava/bio/program/tagvalue/RegexSplitter;sitetable.Lorg/biojava/bio/program/tagvalue/ChangeTable;changer/Lorg/biojava/bio/program/tagvalue/ValueChanger; rebaseTags-Lorg/biojava/bio/program/tagvalue/TagDropper;parser)Lorg/biojava/bio/program/tagvalue/Parser;tempMaptempSeteLjava/lang/Exception;pBFKLPTV[qja access$000()Z access$100x0 access$200()Ljava/util/Map; access$300 access$400rebaseDataFileName SourceFileRestrictionEnzymeManager.java q rs tu vw"java/lang/IllegalArgumentExceptionjava/lang/StringBuilder Unknown RestrictionEnzyme name ' xy' z{ | }~(org/biojava/bio/molbio/RestrictionEnzyme java/util/Set w java/lang/Stringjava/lang/Integer  RestrictionEnzyme ' {8' is not registered. No precompiled Pattern is available[Ljava/util/regex/Pattern; /' is not registered. No Annotation is availableorg/biojava/bio/Annotation o  >Isoschizomers set may contain only RestrictionEnzymes. Found ' x    wjava/util/HashSet {  {java/util/regex/Patternorg/biojava/bio/SmallAnnotationdbxrefREBASE: %org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioError.Assertion Failure: failed to modify Annotation    java/util/HashMapjava/io/BufferedReaderjava/io/InputStreamReader 0org/biojava/bio/program/tagvalue/LineSplitParser |   Corg/biojava/bio/molbio/RestrictionEnzymeManager$RebaseEnzymeBuilder.org/biojava/bio/program/tagvalue/RegexSplitter([^,]+) (\(-?\d+/-?\d+\)|[A-Za-z^]+),org/biojava/bio/program/tagvalue/ChangeTable<2> <3>-org/biojava/bio/program/tagvalue/ValueChanger +org/biojava/bio/program/tagvalue/TagDropper <1> <7>'org/biojava/bio/program/tagvalue/Parser    java/lang/ExceptionFailed to read REBASE data file/org/biojava/bio/molbio/RestrictionEnzymeManager  rebase.data.file  java/lang/Object<4><5><6><8>java/util/Iteratorjava/io/InputStream java/util/MapkeySetjava/util/CollectionsunmodifiableSet (Ljava/util/Set;)Ljava/util/Set; containsKey(Ljava/lang/Object;)Zappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/String;)Vget&(Ljava/lang/Object;)Ljava/lang/Object;contains EMPTY_SET(I)VgetNameiterator()Ljava/util/Iterator;hasNextnext()Ljava/lang/Object;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;put8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;getRecognitionSite%()Lorg/biojava/bio/symbol/SymbolList;!org/biojava/bio/symbol/SymbolListlength()IaddgetForwardRegexcompile-(Ljava/lang/String;)Ljava/util/regex/Pattern;getReverseRegex setProperty'(Ljava/lang/Object;Ljava/lang/Object;)V*(Ljava/lang/String;Ljava/lang/Throwable;)V org/biojava/utils/ChangeListener ALWAYS_VETO"Lorg/biojava/utils/ChangeListener;org/biojava/utils/ChangeTypeUNKNOWNLorg/biojava/utils/ChangeType;addChangeListenerC(Lorg/biojava/utils/ChangeListener;Lorg/biojava/utils/ChangeType;)V(Ljava/io/Reader;)VsetEndOfRecordsetSplitOffsetsetContinueOnEmptyTag(Z)VsetMergeSameTag(Ljava/util/regex/Pattern;I)V setSplitterSplitterL(Ljava/lang/Object;Lorg/biojava/bio/program/tagvalue/ChangeTable$Splitter;)Vd(Lorg/biojava/bio/program/tagvalue/TagValueListener;Lorg/biojava/bio/program/tagvalue/ChangeTable;)V6(Lorg/biojava/bio/program/tagvalue/TagValueListener;)VaddTag(Ljava/lang/Object;)Vread(Ljava/io/BufferedReader;Lorg/biojava/bio/program/tagvalue/TagValueParser;Lorg/biojava/bio/program/tagvalue/TagValueListener;)ZgetClass()Ljava/lang/Class;java/lang/Class newInstancejava/util/ResourceBundle getBundle.(Ljava/lang/String;)Ljava/util/ResourceBundle; getStringgetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;5org/biojava/bio/program/tagvalue/ChangeTable$Splitter1gnqrsktrs\ursUvrsWwrsxyrsz{rs|}rs^~rs /* )E *  $    t9 * # YY* * , 9r, L* # YY**L++  ,9CGLr9 , t9* # YY** , 9r, w)YL+ +  )  z?* & YY* *!! / ?/ w<"* & YY*#"*$. //3 </ W* %*Z [\ )V+&M,'4,(N-# YY)-***M,++W& nprt>xAzE|J}U~4':VVJ r 6 *L +*+WY*,-M, ,N-*.W/Y0N-*.W,-+W*12N*32:*4Y-SYS+W5Y6:7Y8+9:;Y<=>?@"*+W:V!-:BEMU`hq\ :M r!hpqgG)EO AYBAYB AYBAYBAYBAYB"AYBCYDY*EFLGYHM,%I,J,K,LMYNNOYP2Q:OYR2Q:SYT:UVWVXY-Y:ZY[:\]U]W]^]_Y`:  +,aAYB: :  &:  ' (:  :b : cd:    +W&:'-(: :  .Wϧv L;Yf+=Fe1 (2<FV^dins{ $-<FN[gzrp4-w <h VV^N{1"     Y 3 0 O/*O OOOn&ghijjklKg*mL+!% r!pMgo S PK /*?:w@Ӕ9org/biojava/bio/molbio/RestrictionEnzymeManagerTest.class2 4t 1u vw 3xy 1z { 3|}~ 3 1 v 3 1 v   1   `  1 1 1 (Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis5Lorg/biojava/bio/molbio/RestrictionEnzymeManagerTest;nameLjava/lang/String;testGetAllEnzymes()VallEnzLjava/util/Set; testGetEnzymeinvalid*Lorg/biojava/bio/molbio/RestrictionEnzyme;iae$Ljava/lang/IllegalArgumentException;ecoRI StackMapTable~testGetIsoschizomersisoAvaIisoAvrIavaIavrItestGetNCutterseeiLjava/util/Iterator; all6CutterstestGetPatternsise/Lorg/biojava/bio/symbol/IllegalSymbolException;1Lorg/biojava/bio/symbol/IllegalAlphabetException;pat[Ljava/util/regex/Pattern;site#Lorg/biojava/bio/symbol/SymbolList;custom]testGetRecognitionSequence recognitiontestgetSuppliers supplierstestloadEnzymeFilehind3ecor1rebaseDataFileNameisLjava/io/InputStream;re SourceFile!RestrictionEnzymeManagerTest.java 56  EcoRI xxxx"java/lang/IllegalArgumentException!Expected IllegalArgumentException 6AvaI AvrI  (org/biojava/bio/molbio/RestrictionEnzyme   ga{2}t{2}c a -org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/BioErrorInternal error in test 5 5/org/biojava/bio/symbol/IllegalAlphabetException G^AATTC ABCEFGHIJKLMNOQRSTUVX!org/biojava/bio/molbio/rebase.dat   HindIII%IllegalArgumentException not expected)/org/biojava/bio/molbio/rebase_common.dat/org/biojava/bio/molbio/RestrictionEnzymeManager3org/biojava/bio/molbio/RestrictionEnzymeManagerTestjunit/framework/TestCase java/util/Setjava/util/Iterator!org/biojava/bio/symbol/SymbolListjava/lang/Stringjava/io/InputStream getAllEnzymes()Ljava/util/Set;size()I assertEquals(II)V getEnzyme>(Ljava/lang/String;)Lorg/biojava/bio/molbio/RestrictionEnzyme;getName()Ljava/lang/String;'(Ljava/lang/String;Ljava/lang/String;)VfailgetIsoschizomers#(Ljava/lang/String;)Ljava/util/Set;contains(Ljava/lang/Object;)Z assertTrue(Z)V getNCutters(I)Ljava/util/Set;iterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object;getRecognitionSite%()Lorg/biojava/bio/symbol/SymbolList;length getPatternsF(Lorg/biojava/bio/molbio/RestrictionEnzyme;)[Ljava/util/regex/Pattern;java/util/regex/Patternpatternorg/biojava/bio/seq/DNATools createDNA7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;*(Ljava/lang/Throwable;Ljava/lang/String;)V:(Ljava/lang/String;Lorg/biojava/bio/symbol/SymbolList;II)VgetRecognitionSequence&(Ljava/lang/String;)Ljava/lang/String; getSuppliers>(Lorg/biojava/bio/molbio/RestrictionEnzyme;)Ljava/lang/String;java/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;loadEnzymeFile(Ljava/io/InputStream;Z)V!34 567>*+8 019:;<=>?7LL(+85679:; @AB?7*L+ M,,MM " 8& ;<@AF"C#E$H)I9* CD#EF*:;$GDH II@IJIKL?7Gb L+M, N:+,- ::: BVY 8>MNPQ S&T-V8WB[I\VaY^[`\cad9HI CA[EFb:;\MALNA&<OD-5PDH9RJQQIIQAQJQQIIKR?7=L++M,,N-߱8hik!m+n9o<p9*+SD$TU=:;7VAHQW#X?7nL+M,2,2NN:Y !:Y"-#::Y !M: #),=KN$\be 8Rtu wx!z#}),.:=KNP\beghm9R. YZP E[gEFn:;hGD c\]#K^_=1`DH8,JIabc JIabId HKe?7I %L&+8 9 :;f=g?7\L+'M(,8 9 :; GD h=i?7)L**++,M,-N-.:. :/ **++,M,-N-.:.: :/ 0L1+2M,-"36 \~ 8f")368=INR\cmt~9\ ) jD8EFcjDt kDEF:;l=mnoAH 6JpqQKCKrsPK /*?:nb b 2org/biojava/bio/molbio/RestrictionEnzymeTest.class2 MN OP QR S QTU VWXYZ [ \] \^ _ Q` ab Qc d Qe Qfgh i Qjkl Qmno(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis.Lorg/biojava/bio/molbio/RestrictionEnzymeTest;nameLjava/lang/String; testGetName()VecoRI*Lorg/biojava/bio/molbio/RestrictionEnzyme; ExceptionstestGetRecognitionSiteise/Lorg/biojava/bio/symbol/IllegalSymbolException;iIsite#Lorg/biojava/bio/symbol/SymbolList;test StackMapTablenpqXtestIsPalindromicbsp24ItestGetCutTypetestGetDownstreamCutds[ItestGetUpstreamCutbeLorg/biojava/bio/BioException;us@gtestGetDownstreamEndTypeapaIsmaItestGetUpstreamEndType SourceFileRestrictionEnzymeTest.java !EcoRIr stp uv wx yzGAATTC{ |}-org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/BioErrorInternal error in test ~q  w Bsp24I w org/biojava/bio/BioExceptionExpected BioException ! ApaISmaI ,org/biojava/bio/molbio/RestrictionEnzymeTestjunit/framework/TestCase(org/biojava/bio/molbio/RestrictionEnzyme!org/biojava/bio/symbol/SymbolList/org/biojava/bio/molbio/RestrictionEnzymeManager getEnzyme>(Ljava/lang/String;)Lorg/biojava/bio/molbio/RestrictionEnzyme;getName()Ljava/lang/String; assertEquals'(Ljava/lang/String;Ljava/lang/String;)VgetRecognitionSite%()Lorg/biojava/bio/symbol/SymbolList;org/biojava/bio/seq/DNATools createDNA7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;*(Ljava/lang/Throwable;Ljava/lang/String;)Vlength()IsymbolAt"(I)Lorg/biojava/bio/symbol/Symbol;'(Ljava/lang/Object;Ljava/lang/Object;)V isPalindromic()Z assertTrue(Z)V getCutType(II)VgetDownstreamCut()[IgetUpstreamCutfailgetDownstreamEndTypegetUpstreamEndType!  !">*+# )*$%&'()*"LL+#./0$%& +,-.*"LL+MNN: Y 6, -,߱  #. 45 7 :?<>$A2CEAKE$> /0'$12L%&F+, A34 ?546 7899: #-;*"#L+M,#IJ LM"N$ #%&+,<,6 88@=*"kL+M,#RSUVW$ %&+, <,>*"hL+M,.,.#[\ ^_`$ %&+, ?@-A*"2L+M,. ,.N-M:!&)#. de ghj!m&r)o+q,t1u$4+BC2%&,<, 'D@!+,6)78E8F-G*"+L+M,N-#yz}~"*$*+%&%+,H," I,-J*"$L+M,WN#& #$*BC$%&<,+,6788F-KLPK .*?:5A: .org/biojava/bio/molbio/RestrictionMapper.class2 KL K M N OP Q RS RTUV W XY XZ R[\] K^ _ `a b c Rde Rf RghijSITE_FEATURE_SOURCELjava/lang/String; ConstantValuekSITE_FEATURE_TYPElrestrictionEnzymesLjava/util/List;mapAllZ threadPoolLorg/biojava/utils/ThreadPool;!(Lorg/biojava/utils/ThreadPool;)VCodeLineNumberTableLocalVariableTablethis*Lorg/biojava/bio/molbio/RestrictionMapper;annotate>(Lorg/biojava/bio/seq/Sequence;)Lorg/biojava/bio/seq/Sequence;enzyme*Lorg/biojava/bio/molbio/RestrictionEnzyme;iIsequenceLorg/biojava/bio/seq/Sequence;mapped StackMapTablem getMapAll()Z setMapAll(Z)Von addEnzyme-(Lorg/biojava/bio/molbio/RestrictionEnzyme;)V removeEnzyme clearEnzymes()V SourceFileRestrictionMapper.java -Hjava/util/ArrayList '( )* +,%org/biojava/bio/seq/impl/ViewSequence -no pq rs(org/biojava/bio/molbio/RestrictionEnzyme,org/biojava/bio/molbio/RestrictionSiteFinder -tu vw xH yz"java/lang/IllegalArgumentExceptionjava/lang/StringBuilder&RestrictionMapper is already mapping ' {| {}' ~ - z"RestrictionMapper is not mapping ' z H(org/biojava/bio/molbio/RestrictionMapperjava/lang/Object%org/biojava/bio/seq/SequenceAnnotatorregex misc_bindingorg/biojava/bio/seq/Sequence!(Lorg/biojava/bio/seq/Sequence;)Vjava/util/Listsize()Iget(I)Ljava/lang/Object;L(Lorg/biojava/bio/molbio/RestrictionEnzyme;ZLorg/biojava/bio/seq/Sequence;)Vorg/biojava/utils/ThreadPool addRequest(Ljava/lang/Runnable;)VwaitForThreadscontains(Ljava/lang/Object;)Zappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/String;)Vaddremoveclear! !"#$%"#&'()*+,-./^**Y**+0bcdef123+,45/OY+M>* /*  :* Y*, *,0s uw'y>uDM14'67 989O23O:; F<;=  >8?@//*01 23AB/>*0 123C*DE/9*+#YY+*+W0 -81923967=-FE/9*+#YY+*+W0 -81923967=-GH/8 *0  1  23IJPK .*?:z//5org/biojava/bio/molbio/RestrictionSite$Template.class2 enzyme*Lorg/biojava/bio/molbio/RestrictionEnzyme;()VCodeLineNumberTableLocalVariableTablethisTemplate InnerClasses1Lorg/biojava/bio/molbio/RestrictionSite$Template; SourceFileRestrictionSite.java /org/biojava/bio/molbio/RestrictionSite$Template,org/biojava/bio/seq/StrandedFeature$Template&org/biojava/bio/molbio/RestrictionSite#org/biojava/bio/seq/StrandedFeature!/* =     PK .*?:խoo,org/biojava/bio/molbio/RestrictionSite.class2 Template InnerClasses getPosition()I getEnzyme,()Lorg/biojava/bio/molbio/RestrictionEnzyme; SourceFileRestrictionSite.java&org/biojava/bio/molbio/RestrictionSitejava/lang/Object#org/biojava/bio/seq/StrandedFeature/org/biojava/bio/molbio/RestrictionSite$Template     PK .*?:FR2org/biojava/bio/molbio/RestrictionSiteFinder.class2 .` -a -b -cd e fg hi jk lk hm no hp hq nrt `u vw x yz { f| } a ~    l h y &` & & & %targetLorg/biojava/bio/seq/Sequence;findAllZenzyme*Lorg/biojava/bio/molbio/RestrictionEnzyme;L(Lorg/biojava/bio/molbio/RestrictionEnzyme;ZLorg/biojava/bio/seq/Sequence;)VCodeLineNumberTableLocalVariableTablethis.Lorg/biojava/bio/molbio/RestrictionSiteFinder;run()VusCut[IidxIpatterns[Ljava/util/regex/Pattern;siteLenseqLenusOffsetdsOffsetdsCuttTemplate InnerClasses1Lorg/biojava/bio/molbio/RestrictionSite$Template;mLjava/util/regex/Matcher;eLjava/lang/Exception;charSeq/Lorg/biojava/bio/seq/io/SymbolListCharSequence; StackMapTabledD@t SourceFileRestrictionSiteFinder.java 6> 45 23 01-org/biojava/bio/seq/io/SymbolListCharSequence 6     /org/biojava/bio/molbio/RestrictionSite$Template misc_binding regex    $org/biojava/bio/symbol/RangeLocation 6 java/lang/Exception#org/biojava/bio/BioRuntimeExceptionjava/lang/StringBuilderFailed to complete search for 6,org/biojava/bio/molbio/RestrictionSiteFinderjava/lang/Objectjava/lang/Runnablejava/util/regex/Matcherjava/lang/Throwable&(Lorg/biojava/bio/symbol/SymbolList;)V/org/biojava/bio/molbio/RestrictionEnzymeManager getPatternsF(Lorg/biojava/bio/molbio/RestrictionEnzyme;)[Ljava/util/regex/Pattern;(org/biojava/bio/molbio/RestrictionEnzymegetRecognitionSite%()Lorg/biojava/bio/symbol/SymbolList;!org/biojava/bio/symbol/SymbolListlength()Iorg/biojava/bio/seq/SequencegetDownstreamCut()[Ijava/lang/Mathmax(II)I getCutTypegetUpstreamCutmin&org/biojava/bio/molbio/RestrictionSitetypeLjava/lang/String;source#org/biojava/bio/seq/StrandedFeaturePOSITIVEStrand,Lorg/biojava/bio/seq/StrandedFeature$Strand;strand getAnnotationH(Lorg/biojava/bio/molbio/RestrictionEnzyme;)Lorg/biojava/bio/Annotation; annotationLorg/biojava/bio/Annotation;java/util/regex/Patternmatcher3(Ljava/lang/CharSequence;)Ljava/util/regex/Matcher;find()Zstart(II)Vlocation!Lorg/biojava/bio/symbol/Location; createFeatureE(Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature; isPalindromicNEGATIVEappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;*(Ljava/lang/String;Ljava/lang/Throwable;)V*org/biojava/bio/seq/StrandedFeature$Strand$org/biojava/bio/seq/Feature$Templateorg/biojava/bio/seq/Feature -./012345678l**+**-9>? @AB:*;<452301=>8Y*L*M* >* 666* :.. 6* *:..6Y:**,2+:  a `6 * ` `Y  `d *Y: *!W ç :   *"z#,2+:  a `6 * ` `Y  `d *Y: *!W ç :   #M%Y&Y'()**+,,p $9+I MO!P,Q/R2T;UHWS[\\i_r`yabcdfgilmopqr s vxy'{/}8QThp|:\ ?@RAB 8RAB yCD!lEB,aFB/^GB2[HB;RI@rJMNO PQ;< RST iUVWX<YZ,- UVWXYZ[\,- UVWXYZ[\UVB]^_LsK yK PK /*?:4~ٳ#org/biojava/bio/molbio/package.html

The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.

PK /*?:KTF F org/biojava/bio/package.html The core classes that will be used throughout the bio packages.

Throwables

The classes BioException and BioError form the basis of error-handling within the core classes. They both can optionally wrap a source Throwable and carry a message. The stack-trace printed should contain a single merged stack-trace, together with all messages inserted in the proper places. These exceptions can be nested to any depth, providing an organic and natural way to trace errors and bugs.

Annotations

The Annotation classes are used throughout the org.biojava.bio interface hierachy to indicate that there is un-typed information that may optionally be associated with an object. The Annotation object takes the form of a paranoid Map, and Annotatable flags an object as having an associated Annotation object.

Annotations would be used where the designer of an API knew that users may wish to associate further information with instances of an interface or class, but it is inapropreate to add get/set pairs and properties, either because the properties will frequently be absent, or the names and types of the properties will not be known untill objects are populated.

To help bring some order to this potential chaos, there is a loose-typing system available. AnnotationType defines an instanceOf method that will return true if an annotation is considered to be an instance of that type, and false otherwise. In practice, this choice will tend to be made on the basis of the available annotation properties, their names and values. PropertyConstraint allows restrictions on the range of property values to be bound to names within a PropertyType. These may restrict a property to being of a particular java class, within a set of possible values (enumerated type), being an annotation of a particular AnnotationType, or being a collection of one of these (set, list).

It is not expected that in the general case Annotations will publish an AnnotationType they conform to in a well-known slot such as ISA. In the general case, annotations will be dynamicaly validated by calling AnnotatoinType.instanceOf(Annotation). Annotations are symultaneously instances of all AnnotationType instances that they match to. In particular, all Annotation instances are of type AnnotationType.ANY which places no restrictions upon the presence or value of properties.

AnnotationType and PropopertyConstraint both have operators to check if another instance matches a subset of the items it matches. These are subTypeOf and subConstraintOf respectively. In the same way that the type of an Annotation is inferred as needed, these relationships will in general be proved when required. It is not likely that AnnotatoinType or PropertyConstraint instances will maintain references between super- and sub-types, but rather they will introspect the class and properties of the type or constraints and prove that the sub-type instanceOf method returns true for a subset of the cases returning true for the super-type.

This typing system is able to validate the type of an annotation by the names and types of its properties. It is unable to (and it is outside the scope of this API to attempt to) validate the type of an annotation by other annotations or objects that may refer to it. We only validate part-whole hierachies.

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NKO A *R,D*+-. /2S)TUVW1"$]0CD oD P]PK /*?:g>org/biojava/bio/program/das/DASSequence$StructureWrapper.class2? #% $'(* + , - ./012 345this$0)Lorg/biojava/bio/program/das/DASSequence;,(Lorg/biojava/bio/program/das/DASSequence;)VCodeLineNumberTableLocalVariableTablethisStructureWrapper InnerClasses:Lorg/biojava/bio/program/das/DASSequence$StructureWrapper;createFeatureHolder%()Lorg/biojava/bio/seq/FeatureHolder;exLorg/biojava/bio/BioException; StackMapTable0 SourceFileDASSequence.java 6%org/biojava/bio/seq/FeatureFilter$AndAnd 78)org/biojava/bio/seq/FeatureFilter$ByClassByClass$org/biojava/bio/seq/ComponentFeature 9 : ;< =org/biojava/bio/BioException#org/biojava/bio/BioRuntimeExceptionError fetching structure >8org/biojava/bio/program/das/DASSequence$StructureWrapper%org/biojava/bio/seq/LazyFeatureHolder!org/biojava/bio/seq/FeatureFilter top_level#Lorg/biojava/bio/seq/FeatureFilter;(Ljava/lang/Class;)VI(Lorg/biojava/bio/seq/FeatureFilter;Lorg/biojava/bio/seq/FeatureFilter;)V&(Lorg/biojava/bio/seq/FeatureFilter;)V'org/biojava/bio/program/das/DASSequence getStructure*(Ljava/lang/String;Ljava/lang/Throwable;)V P*+*YY d* L Y +    H !".$&$)PK /*?:XRR-org/biojava/bio/program/das/DASSequence.class2" Q Q Q   Q  Q  Q Q Q Q  Q  Q  Q       "    Q @ ) Q    Q Q Q Q 3    Q   : Q   Q   Q   "  " Q  @  M O   Q U @ O d d O  O d d! 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SourceFileFeatureFetcher.java NO TU ^~ FGjava/util/ArrayList HI RS PQSEGMENT id org/xml/sax/SAXExceptionMissing segment ID ^#org/biojava/bio/program/das/Segment 8org/biojava/bio/program/das/FeatureRequestManager$Ticket JM ^java/lang/StringBuilderResponse segment : , wasn't requested "?,@%&:+,:Y.Vdg-Y2 EF"G,HHIVK]LdOgMiNsPvQZ>i hi"Q,GfgVjkgw[]t'Wwvz{ |X8, 1*/**0W**A*BCYY Z[\7_Z48[]8mQ8nQ8oQ8t7|L*KD\: $%PK .*?:KkBorg/biojava/bio/program/das/FeatureFetcher$DASSegmentHandler.class2 ,Y -Z ,[ ,\ ]^_ `ab ]cdefghi jk lmn Z oqs t uv wxz{ | }~   # %Z % % t ]siol&Lorg/biojava/bio/seq/io/SeqIOListener;levelIthis$0,Lorg/biojava/bio/program/das/FeatureFetcher;g(Lorg/biojava/bio/program/das/FeatureFetcher;Lorg/biojava/bio/seq/io/SeqIOListener;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisDASSegmentHandler InnerClasses>Lorg/biojava/bio/program/das/FeatureFetcher$DASSegmentHandler; fetchEncodingLjava/lang/String; startElement{(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;Lorg/biojava/utils/stax/DelegationManager;)VsegStartsegStop segVersionex'Lorg/biojava/bio/seq/io/ParseException;xffh2Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;nsURI localNameqNameattrsLorg/xml/sax/Attributes;dm*Lorg/biojava/utils/stax/DelegationManager; 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serverurl()VCodeLineNumberTableLocalVariableTablethis=Lorg/biojava/bio/program/das/dasalignment/DASAlignmentClient;(Ljava/lang/String;)VurlsetQueryqgetQuery()Ljava/lang/String; getAlignmentsI(Ljava/lang/String;)[Lorg/biojava/bio/program/das/dasalignment/Alignment;query_ Exceptions7()[Lorg/biojava/bio/program/das/dasalignment/Alignment;alicall;Lorg/biojava/bio/program/das/dasalignment/DASAlignmentCall;ali5[Lorg/biojava/bio/program/das/dasalignment/Alignment; StackMapTable SourceFileDASAlignmentClient.java  4http://127.0.0.1:8080/dazzle/myalig/alignment?query=  "java/io/IOException+no query specified - call setQuery() first! 9org/biojava/bio/program/das/dasalignment/DASAlignmentCall ;org/biojava/bio/program/das/dasalignment/DASAlignmentClientjava/lang/Object! 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request alignments via DAS

PK .*?:?org/biojava/bio/program/das/dasstructure/DASStructureCall.class2 @ ?           ? ?  ?       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request a protein structure via DAS

PK /*?:<쯰(org/biojava/bio/program/das/package.html Development client for the Distributed Annotation System. More information about the protocol can be found on the DAS web site. 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c_ecNumber SourceFile Ligand.java 56,org/biojava/bio/program/tagvalue/ChangeTableENZYME -org/biojava/bio/program/tagvalue/ValueChanger 5.org/biojava/bio/program/tagvalue/RegexSplitter\S+ 5 /org/biojava/bio/program/tagvalue/ParserListener 12 5 /0 34 open-bio.orgformatligand/reaction 0org/biojava/bio/program/tagvalue/LineSplitParser 2 5 MN ON PN QN*org/biojava/bio/PropertyConstraint$ByClassByClassjava/lang/String 5org/biojava/bio/EcNumber#org/biojava/bio/AnnotationType$ImplImpl MS ENTRY NAME DEFINITIONEQUATIONPATHWAY/org/biojava/bio/program/formats/Ligand$Reactionjava/lang/Object&org/biojava/bio/program/formats/Format+org/biojava/bio/program/formats/FormatToolsEC_FROM_STRINGChanger6Lorg/biojava/bio/program/tagvalue/ChangeTable$Changer; setChangerK(Ljava/lang/Object;Lorg/biojava/bio/program/tagvalue/ChangeTable$Changer;)Vd(Lorg/biojava/bio/program/tagvalue/TagValueListener;Lorg/biojava/bio/program/tagvalue/ChangeTable;)Vjava/util/regex/Patterncompile-(Ljava/lang/String;)Ljava/util/regex/Pattern;(Ljava/util/regex/Pattern;I)V setSplitterSplitterL(Ljava/lang/Object;Lorg/biojava/bio/program/tagvalue/ChangeTable$Splitter;)Vg(Lorg/biojava/bio/program/tagvalue/TagValueParser;Lorg/biojava/bio/program/tagvalue/TagValueListener;)V,org/biojava/utils/lsid/LifeScienceIdentifiervalueOff(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/utils/lsid/LifeScienceIdentifier;GENBANK5(Lorg/biojava/bio/program/tagvalue/LineSplitParser;)V%org/biojava/bio/CardinalityConstraint"org/biojava/bio/PropertyConstraint(Ljava/lang/Class;)Vorg/biojava/bio/AnnotationTypesetDefaultConstraintsH(Lorg/biojava/bio/PropertyConstraint;Lorg/biojava/bio/symbol/Location;)VsetConstraintsZ(Ljava/lang/Object;Lorg/biojava/bio/PropertyConstraint;Lorg/biojava/bio/symbol/Location;)V&org/biojava/bio/program/formats/Ligand4org/biojava/bio/program/tagvalue/ChangeTable$Changer5org/biojava/bio/program/tagvalue/ChangeTable$Splitter!,-./01234567/*8w9 :=>?7QYM,Y+,NY: Y  Y-:Y8$8D9>Q:=Q@AIBC6DE$-FCD GEHI7.89 :=JK7.89 :=L67BYKLMNY :Y! :"Y#$*%&,'(+')-'*-'++'+'8F~ !%)5AKWdq~9>MN!ON%PN)|QN5pRSAdTSUV<*,; wy "}   PK /*?:bzz,org/biojava/bio/program/formats/Ligand.class2 DollarStringCatter InnerClassesCompoundReactionEnzyme()VCodeLineNumberTableLocalVariableTablethis(Lorg/biojava/bio/program/formats/Ligand; SourceFile Ligand.java &org/biojava/bio/program/formats/Ligandjava/lang/Object9org/biojava/bio/program/formats/Ligand$DollarStringCatter/org/biojava/bio/program/formats/Ligand$Compound/org/biojava/bio/program/formats/Ligand$Reaction-org/biojava/bio/program/formats/Ligand$Enzyme! /* "    PK .*?:/&~ Forg/biojava/bio/program/formats/Swissprot$SPFeatureTableListener.class2| FG HI J K L M N O P QR HS TUV TW XYZ[\]^ _` a Hbc d R eghpatLjava/util/regex/Pattern;depthItagLjava/lang/Object;6(Lorg/biojava/bio/program/tagvalue/TagValueListener;)VCodeLineNumberTableLocalVariableTablethisSPFeatureTableListener InnerClassesBLorg/biojava/bio/program/formats/Swissprot$SPFeatureTableListener;delegate3Lorg/biojava/bio/program/tagvalue/TagValueListener; startRecord()V Exceptions endRecordstartTag(Ljava/lang/Object;)V StackMapTableendTagvalueG(Lorg/biojava/bio/program/tagvalue/TagValueContext;Ljava/lang/Object;)VmLjava/util/regex/Matcher;ise!Ljava/lang/IllegalStateException;ctxt2Lorg/biojava/bio/program/tagvalue/TagValueContext;val\ SourceFileSwissprot.java '(&(\w+)\s+((?\d+)|(\?))i jk !" #$ 23 53 %& 67 93l mn opq rsTYPE tu :;STARTEND DESCRIPTIONjava/lang/IllegalStateException!org/biojava/utils/ParserExceptionjava/lang/StringBuilder '3Couldn't match: vw xn vy 'z{@org/biojava/bio/program/formats/Swissprot$SPFeatureTableListener6org/biojava/bio/program/tagvalue/SimpleTagValueWrapperjava/util/regex/Patterncompile-(Ljava/lang/String;)Ljava/util/regex/Pattern;java/lang/ObjecttoString()Ljava/lang/String;matcher3(Ljava/lang/CharSequence;)Ljava/util/regex/Matcher;java/util/regex/Matcherfind()Zgroup(I)Ljava/lang/String;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;pattern-(Ljava/lang/Object;)Ljava/lang/StringBuilder;*(Ljava/lang/String;Ljava/lang/Throwable;)V)org/biojava/bio/program/formats/Swissprot  !"#$%&'()T*+***{|+,/0123)A*Y`** + ,/453)A**Yd*+ ,/467)`* *+*+ *+,/%&8497)R ** * + ,/ %&84:;)q**** N- W* *+-* * *+-* * *+-* * *+,*ANYY**-*+, *+,ps*Z#)37=GKQ[_ekpst+4R<=t.>?,/@AB&8 sC.4DE. f- PK .*?:azWW/org/biojava/bio/program/formats/Swissprot.class2 Kxyz {| }~   x      t  % J J  1 3x  7 SPFeatureTableListener InnerClasses ANNO_TYPE Lorg/biojava/bio/AnnotationType;LSID.Lorg/biojava/utils/lsid/LifeScienceIdentifier;()VCodeLineNumberTableLocalVariableTablethis+Lorg/biojava/bio/program/formats/Swissprot;getParserListenerf(Lorg/biojava/bio/program/tagvalue/TagValueListener;)Lorg/biojava/bio/program/tagvalue/ParserListener;listener3Lorg/biojava/bio/program/tagvalue/TagValueListener;semiColonSplitter0Lorg/biojava/bio/program/tagvalue/RegexSplitter;semiColonChanger/Lorg/biojava/bio/program/tagvalue/ValueChanger;ftParser2Lorg/biojava/bio/program/tagvalue/LineSplitParser; 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Experimental parsers using the tagvalue framework.

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startDocument(Ljava/lang/String;)VlocatorLjava/lang/String; endDocument()V commentLinecomment recordLine*(Lorg/biojava/bio/program/gff/GFFRecord;)Vrecord'Lorg/biojava/bio/program/gff/GFFRecord;2W(Lorg/biojava/bio/program/gff/GFFEntrySet;Lorg/biojava/bio/program/gff/GFFEntrySet$1;)Vx0x1+Lorg/biojava/bio/program/gff/GFFEntrySet$1; SourceFileGFFEntrySet.java 3 456 787org/biojava/bio/program/gff/GFFEntrySet$EntrySetBuilderjava/lang/Object.org/biojava/bio/program/gff/GFFDocumentHandler)org/biojava/bio/program/gff/GFFEntrySet$1'org/biojava/bio/program/gff/GFFEntrySet access$100;(Lorg/biojava/bio/program/gff/GFFEntrySet;)Ljava/util/List;java/util/Listadd(Ljava/lang/Object;)Z    4 *+*   5 +  G*+W  G*+W  " D*+ # $%&'+ PK .*?:H -org/biojava/bio/program/gff/GFFEntrySet.class2 R ST S UV UW UX YZ \] S ^ _` _ab cd ef g[ hij hk hl hmnEntrySetBuilder InnerClassesPROPERTY_GFF_SCORELjava/lang/String; ConstantValueolinesLjava/util/List;()VCodeLineNumberTableLocalVariableTablethis)Lorg/biojava/bio/program/gff/GFFEntrySet; 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EK; EIJ LVN7***** * * ****O2  "',16P 7QRWXN>*+O PQR:;YZN/*OP QR[XN>*+O PQR<;\ZN/*OP QR]XN>*+O PQR=;^ZN/*OP QR_`N>* O PQR>?abN/* OP QRc`N>* O PQR@?dbN/* OP QRefN>*' O PQRABghN/* OP QRijN>*+O PQRCGklN/*OP QRm`N{1'YY *O+0P1QR1H?nobN/*OP QRpqN>*+O PQRrJstNR**Y!*OP QRnuXN>*+O !"PQRK;vZN/*O%P QR wxN"Y#L*$%M,&,'(N+-)W*-*+:,:&T'(:-$+Y./)W+Y0)W,& +1)Wg+2OB4567'8-99:L;X<`=?ABCEFPHXBy;B[z{'|;9t}~J{n'-> N(<*3*4=5 6OR STU R&XP $?(y;nF DEPK /*?:y@(org/biojava/bio/program/gff/package.html GFF manipulation.

GFF is a text-file format for specifying features within sequences. For up-to-date information, go to the GFF home page. Using this package, you can load GFF from a stream, create Features on Sequences, generate GFF from Features and write GFF to file.

Nearly all of the API uses the concept of a GFF stream that 'pushes' GFF from some source to a recipient. Recipients implement the GFFDocumentHandler interface.

There should be some demonstration programs in the biojava-live/demos/gff directory. PK /*?:Y##'org/biojava/bio/program/gff/package.inf!!BioJavaBuildTool1 External Tools PK .*?:ʽ::6org/biojava/bio/program/gff3/GFF3DocumentHandler.class2   startDocument(Ljava/lang/String;)V endDocument()V commentLine recordLine,(Lorg/biojava/bio/program/gff3/GFF3Record;)V SourceFileGFF3DocumentHandler.java0org/biojava/bio/program/gff3/GFF3DocumentHandlerjava/lang/Object   PK .*?:V%%-org/biojava/bio/program/gff3/GFF3Parser.class2 d c c          0 0 0       0 0 c   -  -    6  - -   -  - 0  -    - ! 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SourceFileGFF3Parser.java gh@ Af efunknown: r|B CDjava/lang/StringBuilder Unknown in EF GHI JK&org/biojava/ontology/OntologyException!org/biojava/utils/ParserException!Couldn't create fallback ontology gL< MNjava/util/ArrayList; OH Ph# QR ST UN VWjava/util/StringTokenizer gX YZ [W \H ]^ \_ java/util/NoSuchElementException `a Sb cd ge1org/biojava/bio/program/gff/IgnoreRecordException fhg,org/biojava/bio/program/gff3/GFF3Record$Impl= hijava/lang/String jN: kR lm no+org/biojava/ontology/AlreadyExistsExceptionorg/biojava/bio/BioError,Assertion Failure: Term should not yet exist%org/biojava/utils/ChangeVetoException(Assertion Failure: Unable to create term pq rqs tajava/lang/NumberFormatException ua vw xa yw z^.0{ | }~    + -    w a  org/biojava/bio/BioExceptionUnable to populate annotations; H=" ` ,/Assertion Failure: Term should not be there yet? 'org/biojava/bio/program/gff3/GFF3Parserjava/lang/Objectjava/io/IOExceptionorg/biojava/ontology/Ontologyjava/io/BufferedReader0org/biojava/bio/program/gff3/GFF3DocumentHandlerjava/util/Listorg/biojava/ontology/Termorg/biojava/bio/Annotation+org/biojava/bio/program/gff/GFFErrorHandler ABORT_PARSINGorg/biojava/ontology/OntoToolsgetDefaultFactory(()Lorg/biojava/ontology/OntologyFactory;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;$org/biojava/ontology/OntologyFactorycreateOntologyE(Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/ontology/Ontology;*(Ljava/lang/String;Ljava/lang/Throwable;)V startDocument(Ljava/lang/String;)VreadLineclear startsWith(Ljava/lang/String;)Z substring(I)Ljava/lang/String; commentLinelength()I((Ljava/lang/String;Ljava/lang/String;Z)V hasMoreTokens()Zsize nextTokenadd(Ljava/lang/Object;)Z&(Ljava/lang/String;)Ljava/lang/String;indexOf(Ljava/lang/String;)I(II)Ljava/lang/String; recordLine,(Lorg/biojava/bio/program/gff3/GFF3Record;)VO(Ljava/lang/Throwable;Ljava/lang/String;Ljava/lang/String;ILjava/lang/String;)V endDocument'org/biojava/bio/program/gff3/GFF3Recordget(I)Ljava/lang/Object; setSequenceID containsTermgetTerm/(Ljava/lang/String;)Lorg/biojava/ontology/Term; createTermA(Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/ontology/Term; setSource(Lorg/biojava/ontology/Term;)VsetTypejava/lang/IntegerparseInt invalidStartsetStart(I)V invalidEndsetEndequals$org/biojava/bio/program/gff/GFFToolsNO_SCOREsetScore(D)Vjava/lang/Double parseDouble(Ljava/lang/String;)D invalidScore#org/biojava/bio/seq/StrandedFeatureUNKNOWNStrand,Lorg/biojava/bio/seq/StrandedFeature$Strand; setStrand/(Lorg/biojava/bio/seq/StrandedFeature$Strand;)VPOSITIVENEGATIVE invalidStrand@(Ljava/lang/String;)Lorg/biojava/bio/seq/StrandedFeature$Strand;NO_FRAMEsetPhase invalidFrame getAnnotation()Lorg/biojava/bio/Annotation;trim(Ljava/lang/String;I)IcharAt(I)C setProperty'(Ljava/lang/Object;Ljava/lang/Object;)V*org/biojava/bio/seq/StrandedFeature$Strand!cdefghi: **j 78k  lmnoi>*+j ?@klmefpqi/*jGk lmrsiV *+,-j b ck* lm tu vw xyz{Vr|i& 2Y   ::Y,Y:6+:ބ,Y:    !:  "W: :   #$: :  % &6    :   ': *,  -(: , ): Y  *: +:#,, #%S  S  +j&~ #%19BEPSXbq|   "+1k% }~   X U  } "} K2lm2tu2vw2xy2 yBE\c % # &BSz{Vi-Y.:,/01,/0:  2 3:I 2 3:/  4:: 6Y7 8: 6Y: 8;,/0:  2 3:I 2 3:/  4:: 6Y7 8: 6Y: 8<6,/0=6: *,/0?6@6 ,/0=6 : *,/0A6  B,/0:  !  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T zV+ir aY+Y:N!Z:Y:[&6   : ': `ZL++\X6 +\ ]6  + d^\ !+ '_W+ `ZL+_W L+`&6  +_W L+ '_W+ `ZLc-2-3: I23: / 4: : 6Ya 8: 6Y: 8, b'475'4E9j)N OPR(S1T7U>WHXUY\Ze\h^k_u`abcefhijklnoqvw xy'|47}9~EGS]`k;hO 0   $ 9 G >H(51, 4) almaaayay T 0  " OM  z9-PK .*?:֜C 2org/biojava/bio/program/gff3/GFF3Record$Impl.class2 Z [ \] ^ _ ` a bc d ef g bh i j k l m n o p q rs Ztuv sequenceIDLjava/lang/String;sourceLorg/biojava/ontology/Term;typestartIendscoreDstrandwStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;phase annotationLorg/biojava/bio/Annotation;()VCodeLineNumberTableLocalVariableTablethisImpl.Lorg/biojava/bio/program/gff3/GFF3Record$Impl;,(Lorg/biojava/bio/program/gff3/GFF3Record;)Vrec)Lorg/biojava/bio/program/gff3/GFF3Record; getSequenceID()Ljava/lang/String; setSequenceID(Ljava/lang/String;)V getSource()Lorg/biojava/ontology/Term; setSource(Lorg/biojava/ontology/Term;)VgetTypesetTypegetStart()IsetStart(I)VgetEndsetEndgetScore()DsetScore(D)V getStrand.()Lorg/biojava/bio/seq/StrandedFeature$Strand; setStrand/(Lorg/biojava/bio/seq/StrandedFeature$Strand;)VgetPhasesetPhase getAnnotation()Lorg/biojava/bio/Annotation; StackMapTable SourceFileGFF3Record.java 01 x y! ! "! #$ %$z {' &'| }, (, ~$ -$ ;< ?@ C@ EF IF KL OP SF ./org/biojava/bio/SmallAnnotation,org/biojava/bio/program/gff3/GFF3Record$Impl$org/biojava/utils/AbstractChangeable'org/biojava/bio/program/gff3/GFF3Record*org/biojava/bio/seq/StrandedFeature$Strandorg/biojava/ontology/OntoToolsANY$org/biojava/bio/program/gff/GFFToolsNO_SCORE#org/biojava/bio/seq/StrandedFeatureUNKNOWNNO_FRAME1  !"!#$%$&'(,-$./0129****** * * *3* 13 4567#8*91:8;4 957082U**+*+*+*+*+ *+ *+ *+3* =>?@"A,B6C@DJETF4U57U9:;<2/*3I4 57=>2>*+3 MN457?@2/*3Q4 57AB2>*+3 UV457 !C@2/*3Y4 57DB2>*+3 ]^457"!EF2/*3a4 57GH2>*3 ef457#$IF2/* 3i4 57JH2>* 3 mn457%$KL2/* 3q4 57MN2>*' 3 uv457&'OP2/* 3y4 57QR2>*+ 3 }~457(,SF2/*34 57TH2>*3 457-$UV2R**Y*34 57WXY+)e*6PK .*?:Uww-org/biojava/bio/program/gff3/GFF3Record.class2Impl InnerClasses getSequenceID()Ljava/lang/String; getSource()Lorg/biojava/ontology/Term;getTypegetStart()IgetEndgetScore()D getStrandStrand.()Lorg/biojava/bio/seq/StrandedFeature$Strand;getPhase SourceFileGFF3Record.java'org/biojava/bio/program/gff3/GFF3Recordjava/lang/Objectorg/biojava/bio/Annotatable,org/biojava/bio/program/gff3/GFF3Record$Impl*org/biojava/bio/seq/StrandedFeature$Strand#org/biojava/bio/seq/StrandedFeature     PK /*?:ׄoo)org/biojava/bio/program/gff3/package.html

Support for reading and writing GFF3. This is a new, ontology-aware, version of GFF.

PK .*?: 7org/biojava/bio/program/hmmer/FullHmmerProfileHMM.class2n 89 8: ;< = 8> ?@A B CD EF G H I J K L M NOPj"Lorg/biojava/bio/dp/EmissionState;cnhmmState!Lorg/biojava/bio/dp/ModelInState;advance[I2(Lorg/biojava/bio/program/hmmer/HmmerProfileHMM;)VCodeLineNumberTableLocalVariableTablethis3Lorg/biojava/bio/program/hmmer/FullHmmerProfileHMM;hmm/Lorg/biojava/bio/program/hmmer/HmmerProfileHMM;nullDist#Lorg/biojava/bio/dist/Distribution; ExceptionsQRSTjState$()Lorg/biojava/bio/dp/EmissionState;cStatenState#()Lorg/biojava/bio/dp/ModelInState;()V SourceFileFullHmmerProfileHMM.javaU VW XYZ [\ ] ^_` ab%org/biojava/bio/dp/SimpleModelInState c &org/biojava/bio/dp/SimpleEmissionStated ef  g    hi jk lm1org/biojava/bio/program/hmmer/FullHmmerProfileHMM$org/biojava/bio/dp/SimpleMarkovModel-org/biojava/bio/symbol/IllegalSymbolException-org/biojava/bio/dp/IllegalTransitionException/org/biojava/bio/symbol/IllegalAlphabetException%org/biojava/utils/ChangeVetoException-org/biojava/bio/program/hmmer/HmmerProfileHMMemissionAlphabet#()Lorg/biojava/bio/symbol/Alphabet; stateAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;%org/biojava/bio/symbol/FiniteAlphabetgetName()Ljava/lang/String;7(ILorg/biojava/bio/symbol/Alphabet;Ljava/lang/String;)V getInsert%(I)Lorg/biojava/bio/dp/EmissionState; org/biojava/bio/dp/EmissionStategetDistribution%()Lorg/biojava/bio/dist/Distribution;5(Lorg/biojava/bio/dp/MarkovModel;Ljava/lang/String;)Vorg/biojava/bio/AnnotationEMPTY_ANNOTATIONLorg/biojava/bio/Annotation;V(Ljava/lang/String;Lorg/biojava/bio/Annotation;[ILorg/biojava/bio/dist/Distribution;)VaddState(Lorg/biojava/bio/dp/State;)V magicalState#()Lorg/biojava/bio/dp/MagicalState;createTransition7(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)V! !*+++M*Y++ * Y ,* Y ,* Y ,******** ****** ***** *** **** *********"R9;<2>FFZNnTvU~VW\]^_`abcdf# $%&'()* +,-./0!/*"j# $%10!/*"o# $%20!/*"t# $%&3!/* "y# $%45!#  YO "367PK /*?: 3org/biojava/bio/program/hmmer/HmmerProfileHMM.class2{ O P Q R S T U V W XY Z [\@] ^_`(Lorg/biojava/bio/symbol/Alphabet;ILorg/biojava/bio/dist/DistributionFactory;Lorg/biojava/bio/dist/DistributionFactory;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis/Lorg/biojava/bio/program/hmmer/HmmerProfileHMM;alpha!Lorg/biojava/bio/symbol/Alphabet;columnsI matchFactory*Lorg/biojava/bio/dist/DistributionFactory; insertFactorynameLjava/lang/String; Exceptionsabc connectModel()VmN"Lorg/biojava/bio/dp/EmissionState;iNdNLorg/biojava/bio/dp/DotState;imOdOiO StackMapTable_def transScoreu(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;Lorg/biojava/bio/symbol/Symbol;Lorg/biojava/bio/symbol/Symbol;)DfromLorg/biojava/bio/dp/State;tosymFromLorg/biojava/bio/symbol/Symbol;symTolog2(D)DxDmakeNewInsertStatew(Ljava/lang/String;Lorg/biojava/bio/Annotation;[ILorg/biojava/bio/dist/Distribution;)Lorg/biojava/bio/dp/EmissionState;strannLorg/biojava/bio/Annotation;adv[Idis#Lorg/biojava/bio/dist/Distribution;makeNewMatchState SourceFileHmmerProfileHMM.java  gh ih jk l mn op qr stu vw ?@x y@2org/biojava/bio/program/hmmer/ProfileEmissionState z-org/biojava/bio/program/hmmer/HmmerProfileHMMorg/biojava/bio/dp/ProfileHMM-org/biojava/bio/symbol/IllegalSymbolException-org/biojava/bio/dp/IllegalTransitionException/org/biojava/bio/symbol/IllegalAlphabetException org/biojava/bio/dp/EmissionStateorg/biojava/bio/dp/DotState%org/biojava/utils/ChangeVetoExceptiongetMatch%(I)Lorg/biojava/bio/dp/EmissionState; getInsert removeState(Lorg/biojava/bio/dp/State;)V()I getDelete (I)Lorg/biojava/bio/dp/DotState;createTransition7(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)V magicalState#()Lorg/biojava/bio/dp/MagicalState; getWeights?(Lorg/biojava/bio/dp/State;)Lorg/biojava/bio/dist/Distribution;!org/biojava/bio/dist/Distribution getWeight"(Lorg/biojava/bio/symbol/Symbol;)Djava/lang/MathlogV(Ljava/lang/String;Lorg/biojava/bio/Annotation;[ILorg/biojava/bio/dist/Distribution;)V!l *+- 8 9>      !"#$%&'(*L*****MN6**:*:*:*+* **+* **,*,*-LNM ****n*,*r@ABCDE+F3G;HCKJLSM[NbQkRsVyWXY[\]_`aEdeR3~)*;v+*Cn,-"./*0-1*28"345484453454# 6$%&78a*+ ,  h49:;:<=>=#$ ?@6 &  ol  ABCD_ Y+,-p4  E" FG HI JKLD_ Y+,-t4  E" FG HI JKMNPK .*?: oT%%Aorg/biojava/bio/program/hmmer/HmmerProfileParser$HmmerModel.class2_ T U  T TZ T T T T T T      T   T T ?PbM 0 0 0 0 / ? 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T    @@@    nullEmissions[InullTransitions emissions[[IinsertEmissions transitionsbeginTransitionspecialTransitionsalphList [Lorg/biojava/bio/symbol/Symbol;hmm/Lorg/biojava/bio/program/hmmer/HmmerProfileHMM;hmm_full3Lorg/biojava/bio/program/hmmer/FullHmmerProfileHMM;this$02Lorg/biojava/bio/program/hmmer/HmmerProfileParser;6(Lorg/biojava/bio/program/hmmer/HmmerProfileParser;I)VCodeLineNumberTableLocalVariableTablethis HmmerModel InnerClasses=Lorg/biojava/bio/program/hmmer/HmmerProfileParser$HmmerModel;lengthI setAlphList(Ljava/lang/String;)Vilist[Ljava/lang/String; tokenizer+Lorg/biojava/bio/seq/io/SymbolTokenization;tLjava/lang/Throwable;sLjava/lang/String; StackMapTablev  setEmissions(Ljava/lang/String;I)VpossetNullEmissionssetInsertEmissionssetNullTransitionssetTransitionssetBeginTransitionsetSpecialTransitionsinitialiseFullProfileHMM()VvalidateDistributionSum&(Lorg/biojava/bio/dist/Distribution;)VtoLorg/biojava/bio/symbol/Symbol;dist#Lorg/biojava/bio/dist/Distribution;iterLjava/util/Iterator;sumD ExceptionsaddProbabilityA(Lorg/biojava/bio/dist/Distribution;Lorg/biojava/bio/dp/State;D)VcurrentPstateLorg/biojava/bio/dp/State;probcheckTransitionSum validateSum(D)VaddProfileHMMTransitionsmodifyProbabilities setBeginEndmatch"Lorg/biojava/bio/dp/EmissionState; match_distsetFullProfileHMM setProfileHMMinsertdeleteLorg/biojava/bio/dp/DotState; null_probj matchEmissioninsertEmission nullModel convertToProb(I)Dscoreresult(ID)Dnullprob SourceFileHmmerProfileParser.java ef g Constructing base model s VW XW YZ [W ^W \Zorg/biojava/bio/symbol/Symbol _`  ab  token !" #$Ujava/lang/Throwable % &'1org/biojava/bio/program/hmmer/FullHmmerProfileHMM g( cd )*%org/biojava/bio/symbol/FiniteAlphabet +, -. /0 12 3 45 67 8 9: ;< => ?< @AB CDjava/lang/Exceptionjava/lang/StringBuilder)Distribution does not sum to 1. Sums to EF EG HI gs JK LM NO aP QO RO  STU VW XY Z [ \T ]^;org/biojava/bio/program/hmmer/HmmerProfileParser$HmmerModeljava/lang/Object)org/biojava/bio/seq/io/SymbolTokenizationjava/lang/Stringjava/util/Iterator!org/biojava/bio/dist/Distribution org/biojava/bio/dp/EmissionStatejava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln0org/biojava/bio/program/hmmer/HmmerProfileParserinitialiseProfileHMM2(I)Lorg/biojava/bio/program/hmmer/HmmerProfileHMM; parseStringA((Ljava/lang/String;I)[Ljava/lang/String;alph!Lorg/biojava/bio/symbol/Alphabet;org/biojava/bio/symbol/AlphabetgetTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization; parseToken3(Ljava/lang/String;)Lorg/biojava/bio/symbol/Symbol;printStackTrace parseString(Ljava/lang/String;I)[I2(Lorg/biojava/bio/program/hmmer/HmmerProfileHMM;)V getAlphabet#()Lorg/biojava/bio/symbol/Alphabet;iterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object; getWeight"(Lorg/biojava/bio/symbol/Symbol;)Djava/lang/DoubleisNaN(D)Z setWeight#(Lorg/biojava/bio/symbol/Symbol;D)V-org/biojava/bio/program/hmmer/HmmerProfileHMMcolumns()IgetMatch%(I)Lorg/biojava/bio/dp/EmissionState; getWeights?(Lorg/biojava/bio/dp/State;)Lorg/biojava/bio/dist/Distribution; getInsert getDelete (I)Lorg/biojava/bio/dp/DotState;java/lang/Mathabs(D)Dappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(D)Ljava/lang/StringBuilder;toString()Ljava/lang/String; magicalState#()Lorg/biojava/bio/dp/MagicalState;createTransition7(Lorg/biojava/bio/dp/State;Lorg/biojava/bio/dp/State;)VnState$()Lorg/biojava/bio/dp/EmissionState;#()Lorg/biojava/bio/dp/ModelInState;cStatejStategetDistribution%()Lorg/biojava/bio/dist/Distribution;(org/biojava/bio/dist/DistributionFactoryDEFAULT*Lorg/biojava/bio/dist/DistributionFactory;createDistributionF(Lorg/biojava/bio/symbol/Alphabet;)Lorg/biojava/bio/dist/Distribution; setNullModelsetDistribution getNullModelpow(DD)D TU VWXWYZ[W\Z]W^W_`abcdefghi_*+** * * * * *`  * *+* j.  +3;HQ^k_lo_pqrsiO+M*N6,*-,2S*,-SM,FIj*  17FIJNk>tq?uv0wxJyzOloO{|} ~iQ* d+Sj k lo{|qsiC *+j  k lo {|siC *+ j  k lo {|siB *+j  k lo {|iO * + Sj   k  lo {| qsiD * +Sj  k lo {|siC *+ j  k lo {|iq*Y*L+j !kyzlo}Ri9+MJ, ,! :)+"cJ*)#j"%&'(%)0+3-8.k4% 9lo9*(} !/i  l+,"$ +,%+: *! :+"9+)gk%+,+,")c%*+&j. 1 23%4/5;6E7S8V9f:k;kH;Ellolll%G} 0/i\<*'Q***()&4*')****)&***+)&j> ? 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Tools for working with profile Hidden Markov Models from the HMMer package. See the HMMer website for more information.

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The OBDA flat file indexing specification adresses the need to provide a cross-platform indexing scheim for flat files that are reccord based. Typically these files have a primary ID per entry and potentially multiple secondary IDs in potentially multiple namespaces. Different entries will all have different primary IDs, but may shair seccondary IDs in a given namespace.

This package provides an API for managing these ID associations and retrieving blocks of files accordingly. Where ever possible, a sensible choice is made between linear scans and binary searches over ID. All index files use fixed-length reccords to make the binary searches as fast as is feasable.

PK /*?:1΀ZZ$org/biojava/bio/program/package.html

Java wrappers for interacting with external bioinformatics tools.

PK /*?:Y###org/biojava/bio/program/package.inf!!BioJavaBuildTool1 External Tools PK .*?:ߠ/org/biojava/bio/program/phred/PhredFormat.class2; G  F F      F  G F  )  - ) ) ) F  7 F    F    DDEFAULTLjava/lang/String; ConstantValue mListenersLjava/util/Vector;PROPERTY_DESCRIPTIONLINE lineWidthI()VCodeLineNumberTableLocalVariableTablethis+Lorg/biojava/bio/program/phred/PhredFormat; getLineWidth()I setLineWidth(I)Vwidth readSequencel(Ljava/io/BufferedReader;Lorg/biojava/bio/seq/io/SymbolTokenization;Lorg/biojava/bio/seq/io/SeqIOListener;)ZreaderLjava/io/BufferedReader; symParser+Lorg/biojava/bio/seq/io/SymbolTokenization;siol&Lorg/biojava/bio/seq/io/SeqIOListener;line descriptionseenEOFZ StackMapTable ExceptionsreadSequenceDataparseEnd bytesReadbrparserlistenerbuffer[Csparser%Lorg/biojava/bio/seq/io/StreamParser; reachedEndwdescribeSequence2(Lorg/biojava/bio/seq/Sequence;)Ljava/lang/String;ex"Ljava/util/NoSuchElementException;seqLorg/biojava/bio/seq/Sequence; writeSequence6(Lorg/biojava/bio/seq/Sequence;Ljava/io/PrintStream;)VvalsiosLjava/io/PrintStream;Ljava/lang/StringBuffer;seqLenH(Lorg/biojava/bio/seq/Sequence;Ljava/lang/String;Ljava/io/PrintStream;)Vformat DeprecatedgetDefaultFormat()Ljava/lang/String;addParseErrorListener)(Lorg/biojava/utils/ParseErrorListener;)V theListener&Lorg/biojava/utils/ParseErrorListener;removeParseErrorListener BadLineParsed&(Lorg/biojava/utils/ParseErrorEvent;)VtheEvent#Lorg/biojava/utils/ParseErrorEvent;notifyParseErrorEventclientindex listeners SourceFilePhredFormat.java STjava/util/Vector NO QR java/io/IOExceptionPremature stream end S> java/lang/StringBuilder8Stream does not appear to contain Phred formatted data:     T   description_line  p` T  ]   T  (Couldn't reset to start of next sequence T  !" #$ java/util/NoSuchElementException %& ' (java/lang/StringBuffer )[ *+,4org/biojava/bio/symbol/IntegerAlphabet$IntegerSymbol IntegerSymbol InnerClasses -[.    / 0"java/lang/IllegalArgumentExceptionUnknown format '' PHRED 12 34 52 67 8[ 9:$org/biojava/utils/ParseErrorListener )org/biojava/bio/program/phred/PhredFormatjava/lang/Object%org/biojava/bio/seq/io/SequenceFormat"org/biojava/utils/ParseErrorSourcejava/io/Serializablejava/lang/String-org/biojava/bio/symbol/IllegalSymbolException%org/biojava/bio/seq/io/ParseExceptionjava/io/BufferedReader)org/biojava/bio/seq/io/SymbolTokenization$org/biojava/bio/seq/io/SeqIOListener#org/biojava/bio/seq/io/StreamParserorg/biojava/bio/seq/Sequence!org/biojava/utils/ParseErrorEventjava/lang/ThrowablereadLine(Ljava/lang/String;)V startsWith(Ljava/lang/String;)Zappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString startSequence substring(I)Ljava/lang/String;trimaddSequenceProperty'(Ljava/lang/Object;Ljava/lang/Object;)V endSequence parseStreamM(Lorg/biojava/bio/seq/io/SeqIOListener;)Lorg/biojava/bio/seq/io/StreamParser;markread([CII)Ijava/lang/CharacterisDigit(C)Zreset characters([CII)Vskip(J)Jclose getAnnotation()Lorg/biojava/bio/Annotation;org/biojava/bio/Annotation getProperty&(Ljava/lang/Object;)Ljava/lang/Object;getNamejava/io/PrintStreamprintprintlnlengthsymbolAt"(I)Lorg/biojava/bio/symbol/Symbol;&org/biojava/bio/symbol/IntegerAlphabetintValuejava/lang/Integer,(Ljava/lang/String;)Ljava/lang/StringBuffer;equalsIgnoreCasecontains(Ljava/lang/Object;)Z addElement(Ljava/lang/Object;)V removeElementclone()Ljava/lang/Object;size elementAt(I)Ljava/lang/Object;!FGHIDJKLM<NOPLMQR STUH**Y*<V<@LW XYZ[U/*VUW XY\]U>*V bcWXY^R_`Up+: Y  Y Y  -:-*+,-6-V. ij kmn;qAsLtVv_weyWHpXYpabpcdpefjgLL$hL_ijkl%2l@mnop`U :,-:66++6d4'+@`:++6 Y66^6   4>   , 4>"++  Y 6M Vf".<@JQ`enqWf qXqR .rRXYsbtdufvwxyijzjk- {|}~1 8mnU M+!"#M N+%M,$VW* XY hLk{lU<, &,*+'()Y*N++66[+,-.6/:-01`*,-2()Y*N- Y 34WV6 )9@QZb{WR9BR@;L"_RXYkgcRk"?lmU2,*56#7Y Y 8,9:*+-;V +1W*2XY22L2k+mU-<VW XY!UY*+= *+>V WXYk!U[*+= *+?WV   WXYkU>*+@V WXYU>*YN*AM-ç :->,B,CD:+EV""#$&%'/(7&=*W4/ R>XY>/Ok-{{ - PK /*?:[1org/biojava/bio/program/phred/PhredSequence.class2 L M NOPQ RS T UM VWX Y Z[ \] ^ _ ` Na bcde fgh ij Nklmnopf(Lorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/bio/Annotation;)VCodeLineNumberTableLocalVariableTablethis-Lorg/biojava/bio/program/phred/PhredSequence; phredSequence#Lorg/biojava/bio/symbol/SymbolList;nameLjava/lang/String;urnannoLorg/biojava/bio/Annotation; StackMapTablenqrs Exceptions getQuality%()Lorg/biojava/bio/symbol/SymbolList;ise/Lorg/biojava/bio/symbol/IllegalSymbolException;cve'Lorg/biojava/utils/ChangeVetoException;iIqual)Lorg/biojava/bio/symbol/SimpleSymbolList;[cggetDNAdna getQualityAt"(I)Lorg/biojava/bio/symbol/Symbol;indextgetDNAAt SourceFilePhredSequence.java "# uvw xy/org/biojava/bio/symbol/IllegalAlphabetExceptionjava/lang/StringBuilder "z%Cannot build a PhredSequence using a {|q} ~ SymbolList.  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Cy MPhredTools.dnaSymbolFromPhred() has returned a symbol not in the DNA alphabet7Something has gone badly wrong with the Phred Alphabet!+org/biojava/bio/program/phred/PhredSequence'org/biojava/bio/seq/impl/SimpleSequence)org/biojava/bio/program/phred/Qualitative!org/biojava/bio/symbol/SymbolListjava/lang/Stringorg/biojava/bio/Annotation#java/lang/IndexOutOfBoundsException getAlphabet#()Lorg/biojava/bio/symbol/Alphabet;(org/biojava/bio/program/phred/PhredToolsgetPhredAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;()Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;org/biojava/bio/symbol/AlphabetgetName()Ljava/lang/String;toString(Ljava/lang/String;)V&org/biojava/bio/symbol/IntegerAlphabetgetSubAlphabetSubIntegerAlphabet InnerClasses?(II)Lorg/biojava/bio/symbol/IntegerAlphabet$SubIntegerAlphabet;$(Lorg/biojava/bio/symbol/Alphabet;)Vlength()IsymbolAtintegerSymbolFromPhred IntegerSymbolW(Lorg/biojava/bio/symbol/Symbol;)Lorg/biojava/bio/symbol/IntegerAlphabet$IntegerSymbol; addSymbol"(Lorg/biojava/bio/symbol/Symbol;)V*(Ljava/lang/String;Ljava/lang/Throwable;)Vorg/biojava/bio/seq/DNAToolsdnaSymbolFromPhred@(Lorg/biojava/bio/symbol/Symbol;)Lorg/biojava/bio/symbol/Symbol;9org/biojava/bio/symbol/IntegerAlphabet$SubIntegerAlphabet4org/biojava/bio/symbol/IntegerAlphabet$IntegerSymbol! !"#$>*+-,*-YY+    %9 :;=@&4>'(>)*>+,>-,>./0=12334567$IYcL=*`0+*NY-NY-+&)&5%* GHJ&P)K*L5N6OAHGR&4* 896 :;7<=I'(;>?0@XAKB C7$FYL=*`0+*NY-NY-+#&#2%* Y Z\#b&]'^2_3`>ZDd&4' :;3 89 7<=F'( ;D?0 @XBKA EF$o*MY, %i j k&  89'(G=0IA5HIF$o*MY, %q r s&  89'(G=0IA5HJK\ \ PK .*?:^--.org/biojava/bio/program/phred/PhredTools.class2                       !"#$% !& ' ( !)*+ ',. )0 123 - ,45 06 78 29 :; <= <>? 8@A BC B BD :E :FG 'HIJ K L B ,MN O P HQ RS TV XY NZ[  \$ ]^@$ ]_ ` a b 8cd ^ 8e 8f g@ hi hj kl m n= no p ]q krs 8tuvw xy x  z  m x{ | }~ |    H_fastaBuilderFactory/Lorg/biojava/bio/seq/io/SequenceBuilderFactory;()VCodeLineNumberTableLocalVariableTablethis*Lorg/biojava/bio/program/phred/PhredTools;getPhredAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;dnaSymbolFromPhred@(Lorg/biojava/bio/symbol/Symbol;)Lorg/biojava/bio/symbol/Symbol;phredSymLorg/biojava/bio/symbol/Symbol;lLjava/util/List; ExceptionsintegerSymbolFromPhred IntegerSymbol InnerClassesW(Lorg/biojava/bio/symbol/Symbol;)Lorg/biojava/bio/symbol/IntegerAlphabet$IntegerSymbol; createPhredk(Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/SymbolList;)Lorg/biojava/bio/symbol/SymbolList;e'Lorg/biojava/utils/ChangeVetoException;dqiIdna#Lorg/biojava/bio/symbol/SymbolList;qualitysubint!Lorg/biojava/bio/symbol/Alphabet;sl)Lorg/biojava/bio/symbol/SimpleSymbolList; StackMapTable% *getPhredSymbol_(Lorg/biojava/bio/symbol/Symbol;Lorg/biojava/bio/symbol/Symbol;)Lorg/biojava/bio/symbol/Symbol;integerwritePhredQualityR(Ljava/io/OutputStream;Ljava/io/OutputStream;Lorg/biojava/bio/seq/db/SequenceDB;)Vcveps-Lorg/biojava/bio/program/phred/PhredSequence;qlpLorg/biojava/bio/seq/Sequence;&Lorg/biojava/bio/seq/SequenceIterator;qualLjava/io/OutputStream;seqdb#Lorg/biojava/bio/seq/db/SequenceDB;qualw%Lorg/biojava/bio/seq/io/StreamWriter;seqwqualDB2?readPhredQuality?(Ljava/io/BufferedReader;)Lorg/biojava/bio/seq/io/StreamReader;brLjava/io/BufferedReader;readPhredSequencegetFastaBuilderFactory1()Lorg/biojava/bio/seq/io/SequenceBuilderFactory;getQualityParser-()Lorg/biojava/bio/seq/io/SymbolTokenization; qualityFromP(D)D probOfErrorD pFromQuality(I)D9(Lorg/biojava/bio/symbol/IntegerAlphabet$IntegerSymbol;)D6Lorg/biojava/bio/symbol/IntegerAlphabet$IntegerSymbol;phredToDistArrayS(Lorg/biojava/bio/program/phred/PhredSequence;)[Lorg/biojava/bio/dist/Distribution;symiterLjava/util/Iterator;iae1Lorg/biojava/bio/symbol/IllegalAlphabetException;ise/Lorg/biojava/bio/symbol/IllegalSymbolException;basepBasepOthersspos$[Lorg/biojava/bio/dist/Distribution;dtc1Lorg/biojava/bio/dist/DistributionTrainerContext;vphredAlignmentToDistArrayH(Lorg/biojava/bio/symbol/Alignment;)[Lorg/biojava/bio/dist/Distribution;ya"Lorg/biojava/bio/symbol/Alignment;labelsaveragematrix%[[Lorg/biojava/bio/dist/Distribution; SourceFilePhredTools.java PHRED %org/biojava/bio/symbol/FiniteAlphabet "org/biojava/bio/symbol/BasisSymbol  org/biojava/bio/symbol/Symbol4org/biojava/bio/symbol/IntegerAlphabet$IntegerSymbol "java/lang/IllegalArgumentExceptionjava/lang/StringBuilder$SymbolLists must be of equal length   :    /org/biojava/bio/symbol/IllegalAlphabetException9Expecting SymbolList 'dna' to use the DNA alphabet, uses    (Expecting SymbolList quality to use the  alphabet or IntegerAlphabet instead uses 'org/biojava/bio/symbol/SimpleSymbolList   %org/biojava/utils/ChangeVetoException"org/biojava/utils/AssertionFailure #org/biojava/utils/ListTools$DoubletDoublet  #org/biojava/bio/seq/io/StreamWriter)org/biojava/bio/program/phred/PhredFormat "org/biojava/bio/seq/io/FastaFormat%org/biojava/bio/seq/db/HashSequenceDB     +org/biojava/bio/program/phred/PhredSequence 'org/biojava/bio/seq/impl/SimpleSequence    (Cannot Add Quality Sequences to Database org/biojava/bio/BioExceptionExpecting PhredSequence, got  #org/biojava/bio/seq/io/StreamReader   9org/biojava/bio/seq/io/FastaDescriptionLineParser$FactoryFactory  token     !org/biojava/bio/dist/Distribution5org/biojava/bio/dist/SimpleDistributionTrainerContext            Sequence  contains an illegal alphabet"The Distribution has become locked-org/biojava/bio/symbol/IllegalSymbolException contains an illegal symbol     java/util/ArrayList   org/biojava/bio/BioError#Could not create the Phred alphabet(org/biojava/bio/program/phred/PhredToolsjava/lang/Objectorg/biojava/bio/symbol/Alphabet!org/biojava/bio/symbol/SymbolListjava/io/OutputStream!org/biojava/bio/seq/db/SequenceDB$org/biojava/bio/seq/SequenceIteratororg/biojava/bio/seq/Sequencejava/io/IOException/org/biojava/bio/dist/DistributionTrainerContextjava/util/Iterator org/biojava/bio/symbol/Alignmentjava/util/List&org/biojava/bio/symbol/AlphabetManageralphabetForName5(Ljava/lang/String;)Lorg/biojava/bio/symbol/Alphabet;validate"(Lorg/biojava/bio/symbol/Symbol;)V getSymbols()Ljava/util/List;get(I)Ljava/lang/Object;&org/biojava/bio/symbol/IntegerAlphabetlength()Iappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/String;)V getAlphabet#()Lorg/biojava/bio/symbol/Alphabet;org/biojava/bio/seq/DNAToolsgetDNAgetNamegetSubAlphabetSubIntegerAlphabet?(II)Lorg/biojava/bio/symbol/IntegerAlphabet$SubIntegerAlphabet; 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isSupported()Z StackMapTableisStartOfDataSet(Ljava/lang/String;)ZpoLine getProgram()I getVersiongetProgramString()Ljava/lang/String;getVersionStringassignProgramAndVersion tFormatFoundZoStLjava/util/StringTokenizer;setMode(I)VpiModegetMode SourceFileBlastLikeVersionSupport.java kl e3 f3 yBLAST vTBLAST!! gh ihjava/util/StringTokenizer k | | jhblast washugcg- ncbi-wu-hmmer ncbi-blastn  ncbi-blastx ncbi-blastp ncbi-tblastn ncbi-tblastx2.0.112.2.22.2.32.2.15 wu-blastn wu-blastx wu-blastp wu-tblastn wu-tblastx2.0a19mp-washu2.02.1.1 gcg-blastn2.0.102.1.2 d3unknown3org/biojava/bio/program/sax/BlastLikeVersionSupportjava/lang/Objectjava/lang/String startsWith(Ljava/lang/String;)V nextToken toLowerCaseindexOf(Ljava/lang/String;)Iconcat&(Ljava/lang/String;)Ljava/lang/String;equals(Ljava/lang/Object;)Z001234563478349:34;<34=>34?@34AB34CD34EF34GH34IJ34KL34MN34OP34QR34ST34UV34WX34YZ34[\34]^34_`34ab345c347 d3 e3 f3 gh ih jh klm3*n gho pqrsm 8def g** #   Ƞ, - * ****nfy#CELNVXo pqt# '   uvm6+++ + + n$-24o6pq6wht$ xym.no pqzym.no pq{|m. no pq}|m. no pq~vmz= Y+ N-- > '      =  =  =  =  = d  e !f "g #  = $  = %  = & = ' = ( ȳ=  = ) ,= * ,= +  = ,  - n"H +7?M[ frx !"$%&()+,./12 678:*;/<1><?A@CBNCSDUF`GeHgJrKxLzPQRTUVXYZ^_aefijmnpo*pqwh t"M m=.n z{opq3ym..no pqlm?./ / n`ab cdPK .*?:%-{$)$)0org/biojava/bio/program/sax/BlastSAXParser.class2                             &     ! ," #$% & '( ) * +,- ./ : :0 :12 3 4 567 89:  ;< =>?@A B CD E CF G H I JKLMN O PQ RS `T `U VW XY `Z[ \ ] ^ _` abcdef g h i j k lm no g p qr stu vwxyz{| C}~        oContentsLjava/io/BufferedReader;oAtts$Lorg/xml/sax/helpers/AttributesImpl; oAttQName#Lorg/biojava/bio/program/sax/QName;oBufferLjava/util/ArrayList;aoChars[CaoLineSeparatoraoKeys[Ljava/lang/String; aoArrayTypeoMapLjava/util/HashMap;iVerIoVersion5Lorg/biojava/bio/program/sax/BlastLikeVersionSupport;oHits1Lorg/biojava/bio/program/sax/HitSectionSAXParser;oSummaryLineHelper1Lorg/biojava/bio/program/sax/SummaryLineHelperIF;oQueryIdLjava/lang/String; oDatabaseId oQueryLengthSTARTUP ConstantValue IN_TRAILERAT_END IN_HEADER IN_SUMMARY FINISHED_HITS tDoneSummaryZJ(Lorg/biojava/bio/program/sax/BlastLikeVersionSupport;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis,Lorg/biojava/bio/program/sax/BlastSAXParser; poVersionpoNamespacePrefix Exceptionsparse>(Ljava/io/BufferedReader;Ljava/lang/String;)Ljava/lang/String;xLjava/io/IOException; poContentspoLineoLine StackMapTable  interpret(Ljava/lang/String;)VstLjava/util/StringTokenizer;iiProgramonNewBlastDataSet emitRawOutput(Ljava/util/ArrayList;)VpoList iTmpListSizeparseSummaryLine emitHeaderIds()VhitsSectionReachedcheckNewBlastLikeDataSet(Ljava/lang/String;)ZchoosePartImplementations SourceFileBlastSAXParser.java "org/xml/sax/helpers/AttributesImpl !org/biojava/bio/program/sax/QName  java/util/ArrayList java/lang/String java/util/HashMap biojavahttp://www.biojava.org /org/biojava/bio/program/sax/HitSectionSAXParser  line.separator      org/xml/sax/SAXExceptionAunexpected poLine parameter, expecting start of BLAST like record   java/io/IOException   File read interrupted  Trailer   BlastLikeDataSetQuery= java/util/StringTokenizer  ^\s+\(\d+\sletters\)\s*$    Database::  Searching Results of Gthis looks like a PSI-blast file, this is currently not supported, yet! *Sequences producing significant alignments.Sequences producing High-scoring Segment Pairs ***** No hits found ****** -------- Header Summary    Parsed for domains:[no more scores\> Detail java/lang/StringBuilderProgram   Version = is not supported by the biojava blast-like parsing framework program    CDATA version xml:spaceNMTOKENpreserve RawOutput      GCG File read interrupted   hitIdhitDescription  HitSummaryidmetaDatanoneHitIdHitDescription queryLengthQueryId DatabaseId    Parameters:BLASTTBLAST6org/biojava/bio/program/sax/NcbiBlastSummaryLineHelper4org/biojava/bio/program/sax/WuBlastSummaryLineHelper2org/biojava/bio/program/sax/HmmerSummaryLineHelper5org/biojava/bio/program/sax/GCGBlastSummaryLineHelper2Could not choose a suitable implementation of the  SummaryLineHelperIF for program  version *org/biojava/bio/program/sax/BlastSAXParser6org/biojava/bio/program/sax/AbstractNativeAppSAXParser9(Lorg/biojava/bio/program/sax/NamespaceConfigurationIF;)VsetNamespacePrefixaddPrefixMapping'(Ljava/lang/String;Ljava/lang/String;)VgetNamespacePrefix()Ljava/lang/String; 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"1?Sbtx yzf  0,vh"+89:+;< +=<w x"yz"fvn*'*>?**@*A*BC+D*Y**E#$*(*,FG**G*GH*Y**E#$%w"/EM[mx nyznfnfAv:*+IwMxyzfAv/*JwMx yzAv:*+KwMxyzfAv:*+LwMxyzfAvE*+,MwMx yzffAv/*NwMx yzAv/*OwMx yzAv/*PwMx yzAv:*+QwMxyzAv/*RwMx yzAv:*+SwMxyzAv/*TwMx yzAv:*+UwMxyzAvE*+,VwMx yzfAv:*+WwMxyzfAvE*+XwMx yzfAv:*+YwMxyzfA{v:*+ZwMxyzfAv/*[wMx yzAv:*+\wMxyzPK .*?:wHe8org/biojava/bio/program/sax/DomainSectionSAXParser.class2 <ab a ;cd e ;f ;ghi ;j ;k ;lm no pq nrs ntuv w xy z { | }~    n ;  ; ; 6  oContentsLjava/io/BufferedReader;oAtts$Lorg/xml/sax/helpers/AttributesImpl; oAttQName#Lorg/biojava/bio/program/sax/QName;oLineLjava/lang/String;J(Lorg/biojava/bio/program/sax/BlastLikeVersionSupport;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis4Lorg/biojava/bio/program/sax/DomainSectionSAXParser; poVersion5Lorg/biojava/bio/program/sax/BlastLikeVersionSupport;poNamespacePrefixparse-(Ljava/io/BufferedReader;Ljava/lang/String;)VstLjava/util/StringTokenizer;st2oTempxLjava/io/IOException; poContentspoLine StackMapTablev Exceptions SourceFileDomainSectionSAXParser.java E"org/xml/sax/helpers/AttributesImpl ?@!org/biojava/bio/program/sax/QName E AB biojavahttp://www.biojava.org => CD----  [no hits above thresholds] java/util/StringTokenizer E modelId CDATA / EdomainPosition sequenceFrom sequenceTostartPositionOfSequence NMTOKENinternalendendPositionOfSequencehmmFromhmmTostartPositionOfModelendPositionOfModelscore expectValue DomainHit E java/io/IOException  File read interupted2org/biojava/bio/program/sax/DomainSectionSAXParser6org/biojava/bio/program/sax/AbstractNativeAppSAXParserjava/lang/Stringorg/xml/sax/SAXException()V9(Lorg/biojava/bio/program/sax/NamespaceConfigurationIF;)VsetNamespacePrefix(Ljava/lang/String;)VaddPrefixMapping'(Ljava/lang/String;Ljava/lang/String;)V startsWith(Ljava/lang/String;)Zjava/io/BufferedReaderreadLine()Ljava/lang/String;trimequals(Ljava/lang/Object;)ZclearsetQNamegetURI getLocalNamegetQName nextToken addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)VcharAt(I)Cprefix&(Ljava/lang/String;)Ljava/lang/String;K(Lorg/biojava/bio/program/sax/NamespaceConfigurationIF;Ljava/lang/String;)V startElement>(Lorg/biojava/bio/program/sax/QName;Lorg/xml/sax/Attributes;)V endElement&(Lorg/biojava/bio/program/sax/QName;)Vjava/lang/SystemoutLjava/io/PrintStream; getMessagejava/io/PrintStreamprintln ;<=>?@ABCDEFG{)**Y*Y**,*  HD9:E G(II )JK)LM)NDOPG*+ *, * **  **  * **  * Y* N******-Y- !:*"*****#****-*$****--:*%&.&****'(#****')**&.&****'(#****')*+****-*,****--:*-&.&****'(#****')*.&.&****'(#****')*/****-*0****-*Y**123*4*Y**1235**  ۧN7-897:9Iu6Jru6H7VY [\$^/`>aIbJeYiejlkulqtuz{(.7Be28ALo<RdoruvIHe QRSR.ATDvUVJKW>XDY" %ZZ[66B\]^_`PK .*?:13!3!3org/biojava/bio/program/sax/FastaSearchParser.class2    L               *           L L L L L L ! 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N/ N012 L3456789 :;<=>?@AB LCDEFGHIJKLMN p OPQRSTUVWXYZ[\]^_`abcNODATAI ConstantValueINHEADERINHITINQUERY INSUBJECTINALIGNresultAnnoTokensLjava/util/HashSet;resultSearchParmTokens hitAnnoTokens hitDataTokens searchStatus searchParsedZhandler-Lorg/biojava/bio/search/SearchContentHandler;lineLjava/lang/String; lineNumberquerySeqTokensLjava/lang/StringBuffer;subjectSeqTokens matchTokens()VCodeLineNumberTableLocalVariableTablethis/Lorg/biojava/bio/program/sax/FastaSearchParser; parseSearchH(Ljava/io/BufferedReader;Lorg/biojava/bio/search/SearchContentHandler;)VreaderLjava/io/BufferedReader; StackMapTable ExceptionsdefillSet3([Ljava/lang/String;Ljava/util/Set;)Ljava/util/Set;i tokenArray[Ljava/lang/String;setLjava/util/Set;parseID&(Ljava/lang/String;)Ljava/lang/String;trimmed firstSpace+ parseDesc parseQueryID firstCommaparseDatabaseIDstLjava/util/StringTokenizer;idcountb!parseHeaderLine$(Ljava/lang/String;Ljava/util/Set;)ZtokenSetdata parseHitLine parseLine6(Ljava/lang/String;Ljava/util/Set;)[Ljava/lang/String; idTokenStart idTokenEndidTokenidValuefparseQuerySequence(Ljava/lang/String;)VparseSubjectSequence parseSequence'(Ljava/lang/String;)[Ljava/lang/String; parseCoordsepIndex SourceFileFastaSearchParser.java java/lang/StringBuffer g h ij >>><<< klm n o pq rs t>>> u v w x yz>> { |g }sdesc !org/biojava/utils/ParserException*Fasta parser failed to recognise line type ~>    ; al_cons: f  j  .Fasta parser encountered a sequence with no Id pNo description, 'Fasta parser failed to parse a query IDjava/util/StringTokenizer  j*Fasta parser failed to parse a database ID s;: java/lang/String java/lang/StringBuilderquery  jsubject ; sq_type: p _sq_typeprotein ; sq_type: Ddna ; al_start: _al_start  ; al_stop:_al_stop; al_display_start:_al_display_start ; sq_len:_sq_len ; sq_offset: _sq_offset mp_namemp_vermp_argv mp_extrapmp_statsmp_KSpg_namepg_ver pg_optcutpg_cgapjava/util/HashSet  pg_matrixpg_ktup pg_gap-penfa_framefa_initnfa_init1fa_optfa_bitssw_scoresw_ident sw_gident sw_overlapfa_ident fa_gident fa_overlapfa_score fa_expect fa_z-score-org/biojava/bio/program/sax/FastaSearchParserjava/lang/Objectjava/io/IOExceptionorg/biojava/bio/BioException java/util/Set(I)Vjava/io/BufferedReaderreadLine()Ljava/lang/String; startsWith(Ljava/lang/String;)Z+org/biojava/bio/search/SearchContentHandler endHeader endSearch substring(I)Ljava/lang/String;addSubHitProperty'(Ljava/lang/Object;Ljava/lang/Object;)V endSubHit setQueryID setDatabaseID startSearch startHeadersetMoreSearches(Z)VstartHit setLengthaddHitProperty:(Ljava/lang/String;Ljava/lang/String;ILjava/lang/String;)VendHit startSubHitappend,(Ljava/lang/String;)Ljava/lang/StringBuffer;add(Ljava/lang/Object;)ZtrimindexOf(I)Ilength()I(II)Ljava/lang/String;(Ljava/lang/String;)I countTokens nextTokenaddSearchPropertycontains-(Ljava/lang/String;)Ljava/lang/StringBuilder;toStringequals lastIndexOf  w9****Y*Y*Y5] ^de*f 9* *, *+ Z *Y ` *  m*,,**,*,*,*,,**w*&sIh* A*,** ,** ,,* *,* O*,, *!*!*!,"** #$,%** &$** '(** )(*Y+* * ,* -*,.,/Y** 01K** 21=*Y+* * ,* - *** 3 * 4 ** *,*,*,*,, *!*!*!,"** #$,%** &$o** 5d* *,*,*,*,, *!*!*!,"** #$,%** &$*  S*,*,*,*,,*,** 6Wqn,`}~  ,4:@EJM]m}  $*2:BRes "'7GW!]"c$k%s&{()-/24789;<>?@BC1E=GBJRKbLrNxO~QRTXZ]bc " BH)LW..  [* s=*+*27W+pqps  i+8M, 9>,-,:*Y;* +, ,<,=,:*Y;* +, ,<,=6  -28?GW\b*iid ] -  *+8M, 9>>,`< *  |&+?@=*YA* +,+=8  &&*>BY+CMN,D66d,EN-*YF* +,-&   "(,<>>> 5 3-**+,GN-* -2-2H ***+,GN-* -2-2$  **Q+I@>+J@6+`=:8:+`<:8:,KLYSYSL& !+2=LHQQQJB7+&L*9*+MM,'* NYOPQ,2QR,2 *+6W#% (/-8/ 993 /9*+MM,'* NYOSQ,2QR,2 *+6W35 8/=8? 993 /D+I+TULYVSYWS+XULYVSYYS+ZLY[SY*+\S+]LY^SY*+\S+_LY`SY*+\S+aLYbSY*+\S+cLYdSY*+\SLBC FH!J*L9PBRTT]VoXxZ\^`bf !T+Je=+`<8 st   LYfSYgSYhSYiSYjSYkSYlSYmSYnSY oSpYqrp'LYsSYtSYuSpYqrp) LYvSYwSYxSYySYzSY{SY|SY}SY~SY SY SY SY SpYqrp0LYSYSpYqrp2?KHnNYPK .*?:B"C<C<6org/biojava/bio/program/sax/FastaSearchSAXParser.class2_ W X YZ [\ ]^ W _` W ab c def g hi j k lm no p q rst g uv w x y z{| }~           8W   n          XW X X       E E    B   E E   E E E      [  ]                 fastaParser/Lorg/biojava/bio/program/sax/FastaSearchParser;searchPropertiesLjava/util/Map; hitPropertiesqueryIDLjava/lang/String; databaseID attributes$Lorg/xml/sax/helpers/AttributesImpl;qName#Lorg/biojava/bio/program/sax/QName;firstHitZmoreSearchesAvailablenFormatLjava/text/NumberFormat;nlpropsLjava/lang/StringBuffer; seqTokens stringOutcharOut[C()VCodeLineNumberTableLocalVariableTablethis2Lorg/biojava/bio/program/sax/FastaSearchSAXParser;parse(Lorg/xml/sax/InputSource;)VbeLorg/biojava/bio/BioException;pe#Lorg/biojava/utils/ParserException;sourceLorg/xml/sax/InputSource;contentLjava/io/BufferedReader; StackMapTable ExceptionsgetMoreSearches()ZsetMoreSearches(Z)Vvalue setQuerySeq(Ljava/lang/String;)V identifier Deprecated setQueryID setSubjectDB setDatabaseID startSearchaddSearchProperty'(Ljava/lang/Object;Ljava/lang/Object;)VkeyLjava/lang/Object; endSearchseLorg/xml/sax/SAXException;s startHeader endHeaderiIspKeysLjava/util/Set;searchPropKeys[Ljava/lang/String;startHitaddHitPropertyendHit startSubHitaddSubHitProperty endSubHitscoreoverlap percentIdFseqTypestrandhpKeys hitPropKeysalStartalStop alDispStart countTokens'(CLjava/lang/String;)Ljava/lang/String;tokenCstringcount prepSeqTokens/(Ljava/lang/StringBuffer;III)Ljava/lang/String;gapCountprefix&(Ljava/lang/String;)Ljava/lang/String;x0getNamespacePrefix()Ljava/lang/String;setNamespacePrefixgetURIFromPrefixaddPrefixMapping'(Ljava/lang/String;Ljava/lang/String;)Vx1getNamespacePrefixes getNamespacesgetErrorHandler()Lorg/xml/sax/ErrorHandler;setErrorHandler(Lorg/xml/sax/ErrorHandler;)VLorg/xml/sax/ErrorHandler; getDTDHandler()Lorg/xml/sax/DTDHandler; setDTDHandler(Lorg/xml/sax/DTDHandler;)VLorg/xml/sax/DTDHandler;getEntityResolver()Lorg/xml/sax/EntityResolver;setEntityResolver(Lorg/xml/sax/EntityResolver;)VLorg/xml/sax/EntityResolver; setProperty'(Ljava/lang/String;Ljava/lang/Object;)V getProperty&(Ljava/lang/String;)Ljava/lang/Object; setFeature(Ljava/lang/String;Z)V getFeature(Ljava/lang/String;)ZgetContentHandler()Lorg/xml/sax/ContentHandler;setContentHandler(Lorg/xml/sax/ContentHandler;)VLorg/xml/sax/ContentHandler; SourceFileFastaSearchSAXParser.java biojava 0http://www.biojava.org 23-org/biojava/bio/program/sax/FastaSearchParser "org/xml/sax/helpers/AttributesImpl !org/biojava/bio/program/sax/QName  java/text/DecimalFormat###.0 java/lang/StringBuffer  line.separator J,  Torg/xml/sax/SAXException5Running FastaSearchSAXParser with null ContentHandler xmlns  / /  /CDATA !" xmlns:biojavaBlastLikeDataSetCollection +, # $% &' ()org/biojava/bio/BioException *!org/biojava/utils/ParserException java/util/HashMap + ,-DetailBlastLikeDataSet ./:An error occurred while creating an endElement SAX event: 0 1 2programpg_name 34java/lang/Stringversionpg_verHeaderidmetaDatanoneQueryId DatabaseId xml:spacepreserve RawOutput 56 78 9:; <= > ?@java/lang/StringBuilder ?A: B/ C8 DE FG>An error occurred while creating SAX events from header data: GAn error occurred while creating startElement SAX event from hit data: sequenceLengthsubject_sq_lenHitHitIdHitDescriptiondesc  HSPCollectionHSP fa_z-score HI/Failed to retrieve hit z-score from search data expectValue fa_expectnumberOfIdentities matchTokens "# fa_overlapJ sw_overlap/Failed to retrieve hit overlap from search data alignmentSizefa_identK LMsw_identpercentageIdentityN OP query_sq_typedna QIproteinquerySequenceTypesubject_sq_typehitSequenceType queryStrandplusfa_framefminus hitStrand HSPSummaryTokens ROBlastLikeAlignmentquery_al_start query_al_stopquery_al_display_start startPosition stopPosition QuerySequencequerySeqTokensS TU ()MatchConsensus V/subject_al_startsubject_al_stopsubject_al_display_start HitSequencesubjectSeqTokens;An error occurred while creating SAX events from hit data: WX YZ [\ ]^ ./ 1, 5 6 78 9: <= >? AB CD FG JK LM NO PQ RS0org/biojava/bio/program/sax/FastaSearchSAXParser6org/biojava/bio/program/sax/AbstractNativeAppSAXParser+org/biojava/bio/search/SearchContentHandlerjava/io/BufferedReaderjava/io/IOException java/util/Set%org/xml/sax/SAXNotRecognizedException$org/xml/sax/SAXNotSupportedException9(Lorg/biojava/bio/program/sax/NamespaceConfigurationIF;)V(I)Vjava/lang/SystemgetContentStream3(Lorg/xml/sax/InputSource;)Ljava/io/BufferedReader;oHandlerclearsetQNamegetURI getLocalNamegetQName addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)VK(Lorg/biojava/bio/program/sax/NamespaceConfigurationIF;Ljava/lang/String;)V startElement>(Lorg/biojava/bio/program/sax/QName;Lorg/xml/sax/Attributes;)V parseSearchH(Ljava/io/BufferedReader;Lorg/biojava/bio/search/SearchContentHandler;)V endElement&(Lorg/biojava/bio/program/sax/QName;)V(Ljava/lang/Exception;)V java/util/Mapput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;errLjava/io/PrintStream;java/io/PrintStreamprintlnprintStackTraceget&(Ljava/lang/Object;)Ljava/lang/Object;keySet()Ljava/util/Set;size()ItoArray(([Ljava/lang/Object;)[Ljava/lang/Object;java/util/Arrayssort([Ljava/lang/Object;)V setLengthappend,(Ljava/lang/String;)Ljava/lang/StringBuffer;-(Ljava/lang/String;)Ljava/lang/StringBuilder;toStringlengthgetChars(II[CI)V characters([CII)V containsKey(Ljava/lang/Object;)Zjava/lang/Objectjava/lang/Float parseFloat(Ljava/lang/String;)Fjava/text/NumberFormatformat(D)Ljava/lang/String;equalsendsWithjava/lang/IntegerparseInt(Ljava/lang/String;)ItrimcharAt(I)CvalueOf(I)Ljava/lang/String; deleteCharAt(I)Ljava/lang/StringBuffer; substring(II)Ljava/lang/String;!)q******Y * Y *Y**Y*Y*Y*6 aL Obce'f2g>hKiYjgkpl q*+M* Y * !*"#* *$*%*&'()**#* *$*%*&')*Y**+,-* .** ,*/*Y**+,-0NY-2NY-213Jqs txz'{GPp4  nTI /* >* >*+4 >*+5 >*+6 >*+7 : *8Y9:   O *:+,;W    A**Y**<,-0**Y**=,-0L>?@+A03& 034<@4 AT + * !*B#* *$*%*&'*:CDE)*F#* *$*%*&'*:GDE)*Y**=,-* .* !*Y**H,-* .* !*I#* *$*%*&'*5)*J#* *$*%*&'K)*Y**L,-* .*Y**L,-0* !*I#* *$*%*&'*7)*J#* *$*%*&'K)*Y**M,-* .*Y**M,-0* !*N#* *$*%*&'O)*Y**P,-* .*:QL++RdESTTM,U*V**WW>,Q*XYY,2Z[Z\WW*XYY*:,2DEZ*Z\WW**]^**]*^_**^*^`*Y**P,-0*Y**H,-0L>a@+A-<Eq  $'').+7,Y3b4;>@BCJNPRUW*X2ZO[zX^_behnjlmo4,T      ,TSU E*5** !*Y**<,-* .L>b@+A*8Y9c),* uw x|),-59D- El O *c+,;W     + + O *c+,;W      * !*d#* *$*%*&'*ceDE)*Y**f,-* .* !*I#* *$*%*&'*cIDE)*J#* *$*%*&'K)*Y**g,-* .*Y**g,-0* !*Y**h,-* .**ciDEj**jk^*j*jk*^l**^*^`*Y**h,-0*Y**m,-* .*Y**n,-* .*cop*coDEL Yq *r#* *$*%*&'+)*s#* *$*%*&'*ctDE)*u#* *$*%*&'*:*cvDEw)*cxp*cxDyM-*czp*czDyM Y{ *|#* *$*%*&',)*c}p*c}DE~F*cDE~F*#* *$*%*&'*%j)*cD ::*#* *$*%*&')*cD ::*#* *$*%*&')s*#* *$*%*&')*cD ::*#* *$*%*&')*Y**,-* .* !*Y**P,-* .*cQ:RdESTT:U*V**WW6e2O*XYY2Z[Z\WW*XYY*c2DEZ*Z\WW**]^**]*^_**^*^`*Y**P,-0*Y**,-0*Y**,-* .*cDE:*cDE:*cDE: *#* *$*%*&')*#* *$*%*&')*Y**,-* .*V**cDEWW*** j**jk^*j*jk*^l**^*^`*Y**,-0* !*N#* *$*%*&'O)*Y**,-* .**cvDEj**jk^*j*jk*^l**^*^`*Y**,-0*cDE:*cDE:*cDE: * !*#* *$*%*&')*#* *$*%*&')*Y**,-* .*V**cDEWW*** j**jk^*j*jk*^l**^*^`*Y**,-0*Y**,-0*Y**n,-0*Y**m,-0*Y**f,-0L>@+A<vy<RYb/=Oe{ =K]k} *15>^ q!x#|&'.129:<?@H5K<MRQ]SxU}XYZ]^_`Zc dg-j?mQpgswtuxy8EYgy%5ELUu~.@RdvyzZz.)j 5A] x w z T ! !JL!Bu!(tTKz "#%>,k6, 4 %%$%%&#'  ()G+- +W6+]6+-+dd``# $&($*/+51H GGG G G  1*  A+,:*+?-A.//*? 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ARS:*+?-TUVPK .*?:c()VCodeLineNumberTableLocalVariableTablethis4Lorg/biojava/bio/program/sax/FastaSequenceSAXParser;parse(Lorg/xml/sax/InputSource;)VxLjava/io/IOException;poSourceLorg/xml/sax/InputSource; oContentsLjava/io/BufferedReader;oLineLjava/lang/String; StackMapTable Exceptions interpret-(Ljava/io/BufferedReader;Ljava/lang/String;)V poContentspoLineparseHeaderLine(Ljava/lang/String;)VappendSequenceoStLjava/util/StringTokenizer; emitSequenceprefix&(Ljava/lang/String;)Ljava/lang/String;x0getNamespacePrefix()Ljava/lang/String;setNamespacePrefixgetURIFromPrefixaddPrefixMapping'(Ljava/lang/String;Ljava/lang/String;)Vx1getNamespacePrefixes()Z getNamespacesgetErrorHandler()Lorg/xml/sax/ErrorHandler;setErrorHandler(Lorg/xml/sax/ErrorHandler;)VLorg/xml/sax/ErrorHandler; getDTDHandler()Lorg/xml/sax/DTDHandler; setDTDHandler(Lorg/xml/sax/DTDHandler;)VLorg/xml/sax/DTDHandler;getEntityResolver()Lorg/xml/sax/EntityResolver;setEntityResolver(Lorg/xml/sax/EntityResolver;)VLorg/xml/sax/EntityResolver; 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getMessagejava/io/PrintStreamprintlnK(Lorg/biojava/bio/program/sax/NamespaceConfigurationIF;Ljava/lang/String;)V endElement&(Lorg/biojava/bio/program/sax/QName;)Vcloseclear startElement>(Lorg/biojava/bio/program/sax/QName;Lorg/xml/sax/Attributes;)V changeState(I)V startsWith setLength substring(I)Ljava/lang/String;append,(Ljava/lang/String;)Ljava/lang/StringBuffer; hasMoreTokens nextTokensetQNamegetURI getLocalNamegetQName addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V toCharArray()[C characters([CII)V!MNOPQRSTUVWVXYZ[\]^[\_`abB**Y*Y**Y *Y * * *c& UEFI&J1K6V;WAXd BefghbRN*+M,N-*,-,N:**Y**,"c:cfk lnot"q$r/s7x;zM|Q~d4$ijRefRklJmnPopq rsBtuvwxbY* %**Y**** * *,!"* **,#* $*,%c6 $)1:AEJRSXd YefYynYzpq) uv{|b[* $* +&'W* cdefzp}|b{"(Y+)*M,+* ,,'Wc !d "ef"zp ~q  ab|**-.**/*0*12* 34*Y**5*** 367**7*78*Y**5c"6L[i{d |efuvAb:*+9cAdefpAb/*:cAd efA|b:*+;cAdefpAb:*+<cAdefpAbE*+,=cAd efppAb/*>cAd efAb/*?cAd efAb/*@cAd efAb:*+AcAdefAb/*BcAd efAb:*+CcAdefAb/*DcAd efAb:*+EcAdefAbE*+,FcAd efpuAb:*+GcAdefpuAbE*+HcAd efpYuAb:*+IcAdefpuAg|b:*+JcAdefpuvAb/*KcAd efAb:*+LcAdefPK .*?:x~ ;org/biojava/bio/program/sax/GCGBlastSummaryLineHelper.class2 !JK LMN J OP Q R ST UV WXY Z [ L\ ]^_ J` ab c def gh i jklmoHitDescriptionLjava/lang/StringBuffer; previousHitIDLjava/lang/String; previousScorepreviousEValue()VCodeLineNumberTableLocalVariableTablethis7Lorg/biojava/bio/program/sax/GCGBlastSummaryLineHelper;parse](Ljava/lang/String;Ljava/util/HashMap;Lorg/biojava/bio/program/sax/BlastLikeVersionSupport;)V firstLineZiIhitIDiCountpoLinepoMapLjava/util/HashMap; poVersion5Lorg/biojava/bio/program/sax/BlastLikeVersionSupport;iGraboStLjava/util/StringTokenizer; StackMapTableknopP Exceptionsq SourceFileGCGBlastSummaryLineHelper.java )*!n rsjava/lang/StringBuffer #$java/util/StringTokenizer )t uv wxhitIdo yz {| hitDescription }~ %&  java/lang/StringBuildercurr: { prev: x tscore '& expectValue (& 5org/biojava/bio/program/sax/GCGBlastSummaryLineHelperjava/lang/Object/org/biojava/bio/program/sax/SummaryLineHelperIFjava/lang/Stringjava/util/HashMap3org/biojava/bio/program/sax/BlastLikeVersionSupportorg/xml/sax/SAXException startsWith(Ljava/lang/String;)Z(Ljava/lang/String;)V countTokens()I nextToken()Ljava/lang/String;put8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;append,(Ljava/lang/String;)Ljava/lang/StringBuffer; substring(I)Ljava/lang/String;equals(Ljava/lang/Object;)Zjava/lang/SystemoutLjava/io/PrintStream;-(Ljava/lang/String;)Ljava/lang/StringBuilder;toStringjava/io/PrintStreamprintln setLength(I)V0 !"#$%&'&(&)*+3*, <=- ./01+l 6+ 66*YY+: dd6 :,  W6   * W* W ,* W*BY*,* W,* W1** * ,* W,* W"** W* W,v_b cef h*r/t;vBwKzU{b|lzr~-p 23N$45 B6&;75./8&9:;<=523*>?@K - ABCDEB#Y-ABCDEFGHIPK .*?:A 6org/biojava/bio/program/sax/GenericSAXParserTest.class2u BC DEF GH IJK ILMNOP GQ RS RTUV WX WY WZ B [ \]^_()VCodeLineNumberTableLocalVariableTablethis2Lorg/biojava/bio/program/sax/GenericSAXParserTest;main([Ljava/lang/String;)Vie"Ljava/lang/InstantiationException;iae"Ljava/lang/IllegalAccessException;cnfe"Ljava/lang/ClassNotFoundException;args[Ljava/lang/String;oInputLjava/lang/String; oClassNameoChosenSAXParserLorg/xml/sax/XMLReader;oParseroHandlerLorg/xml/sax/ContentHandler; StackMapTable`.UVXY Exceptionsa SourceFileGenericSAXParserTest.java -help` bc-hd efg h>Given the name of a SAXParser (i.e. the name of the class, and hi:and the pathname of an example file you wish to parse, the5application outputs an XML representation of the data7Usage: java GenericSAXParserTest oFor example java org.biojava.bio.program.sax.GenericSAxParserTestorg.biojava.bio.program.sax.BlastLikeSAXParser jkl mn oporg/xml/sax/XMLReader java/lang/InstantiationException q java/lang/IllegalAccessException java/lang/ClassNotFoundException6org/biojava/bio/program/sax/SimpleXMLEmitterTestHelper rs ti*---------------------END------------------0org/biojava/bio/program/sax/GenericSAXParserTestjava/lang/Objectjava/lang/Stringjava/lang/Exceptionequals(Ljava/lang/Object;)Zjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln(Ljava/lang/String;)Vexit(I)Vjava/lang/ClassforName%(Ljava/lang/String;)Ljava/lang/Class; newInstance()Ljava/lang/Object;printStackTracesetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse  /*!3" #$ %& 'LM**2*2S     * *2M*2LN,N:: :-:Y:+!$=>B F&G,H4J<LDNJORRXS`WfXlZp]v^z_~fjsmnsopsqrx"\ '()*+,-./010U23)43 567. 88O 988:;I?@APK .*?:`##2org/biojava/bio/program/sax/HSPSummaryHelper.class2 3] ^_ 2` 2abc ^d efg hi ] jkl emn o p q er hs et juv ewxyz{|}~ e   ()VCodeLineNumberTableLocalVariableTablethis.Lorg/biojava/bio/program/sax/HSPSummaryHelper;parse](Ljava/lang/String;Ljava/util/HashMap;Lorg/biojava/bio/program/sax/BlastLikeVersionSupport;)VpoLineLjava/lang/String;poMapLjava/util/HashMap; poVersion5Lorg/biojava/bio/program/sax/BlastLikeVersionSupport;iProgramI StackMapTable ExceptionsparseNCBIBlastoKeyoValueoTmpLjava/util/StringTokenizer; aoTmpArray[CoTokenoToken2oSt2oSt oTmpBufferLjava/lang/StringBuffer;liM parseWUBlast SourceFileHSPSummaryHelper.java 45 G< Z<org/xml/sax/SAXException:Failed attempting to parse an HSP Summary because program   is not supported. 4java/lang/StringBuffer 5java/util/StringTokenizer , 4 score expect  expectValue identities/numberOfIdentities alignmentSize(%)percentageIdentity positivesnumberOfPositivespercentagePositivesstrand queryStrand hitStrandframe queryFrame plus minus hitFrame,org/biojava/bio/program/sax/HSPSummaryHelperjava/lang/Objectjava/lang/Stringjava/util/HashMap3org/biojava/bio/program/sax/BlastLikeVersionSupport getProgram()IgetProgramString()Ljava/lang/String;concat&(Ljava/lang/String;)Ljava/lang/String;(Ljava/lang/String;)Vclear toLowerCase'(Ljava/lang/String;Ljava/lang/String;)V hasMoreTokens()Z nextTokentrimequals(Ljava/lang/Object;)Zput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object; 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getMessagejava/io/PrintStreamprintln startsWithresetoHandler(Ljava/io/Reader;)Vclose!/0123452367289:F***;GB HI< =>?@:N*+M,N,N:   :- *-**3'Y:Y:,:*Y,,;fTWY[]a^_&`.h1j:k?nHoMslvuwxz{<HAB=>CDEFGH1zIJKJL#MNOPQR  STAUV::*+;<<=>WHAXY:/*;<< =>AZ[::*+;<<=>WHA\V::*+;<<=>WHA]^:E*+,;<< =>WH_HA`a:/* ;<< =>Aba:/*!;<< =>Acd:/*";<< =>Aef::*+#;<<=>WgAhi:/*$;<< =>Ajk::*+%;<<=>WlAmn:/*&;<< =>Aop::*+';<<=>WqArs:E*+,(;<< =>WH_tSuvAwx::*+);<<=>WHSuvAyz:E*+*;<< =>WH_{SuvA|}::*++;<<=>WHSuvA?[::*+,;<<=>WHSTA~:/*-;<< =>A::*+.;<<=>WPK .*?:כ<org/biojava/bio/program/sax/SimpleXMLEmitterTestHelper.class2d => = ? @ AB C DE FG H I DJ K L M NO P QRS oXMLWriter5Lorg/biojava/bio/program/sax/BaseXMLWriterTestHelper; tEmitQNamesZoNameLjava/lang/String;()VCodeLineNumberTableLocalVariableTablethis8Lorg/biojava/bio/program/sax/SimpleXMLEmitterTestHelper;(Z)Vflag characters([CII)Vach[CiIj ExceptionsT endElement9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)Vstring1string2string3 isEmitQNames()Z setEmitQNames startElementQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)V attributesLorg/xml/sax/Attributes; StackMapTable SourceFileSimpleXMLEmitterTestHelper.java 3org/biojava/bio/program/sax/BaseXMLWriterTestHelper  U VW XYZ [\ 5#java/lang/String & ]^ _\ .Y 34 ` ab 6c 6^6org/biojava/bio/program/sax/SimpleXMLEmitterTestHelper"org/xml/sax/helpers/DefaultHandlerorg/xml/sax/SAXExceptionjava/lang/SystemoutLjava/io/PrintStream; writeHeader()Ljava/lang/String;java/io/PrintStreamprintln(Ljava/lang/String;)V writePCData&(Ljava/lang/String;)Ljava/lang/String;printorg/xml/sax/Attributes getLength()I>(Ljava/lang/String;Lorg/xml/sax/Attributes;)Ljava/lang/String; \"**Y**<=>?!A "!"#o'**Y** *DEFGH&J '!"'$%&d* Y+  OP *!"'()*+*,-./Z*  T U *!"01234/*Y !"5#>* ^_ !"$67F* *-*,** ** cdfgh4jEk 4F!"F0F1F2F89:;885org/biojava/bio/program/sax/SummaryLineHelperIF.class2   parse](Ljava/lang/String;Ljava/util/HashMap;Lorg/biojava/bio/program/sax/BlastLikeVersionSupport;)V Exceptions  SourceFileSummaryLineHelperIF.java/org/biojava/bio/program/sax/SummaryLineHelperIFjava/lang/Objectorg/xml/sax/SAXExceptionPK .*?:Ay:org/biojava/bio/program/sax/WuBlastSummaryLineHelper.class2b 9: 9; < => ?@ A BC D EFG HIJKLMNO()VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/program/sax/WuBlastSummaryLineHelper;parse](Ljava/lang/String;Ljava/util/HashMap;Lorg/biojava/bio/program/sax/BlastLikeVersionSupport;)ViGrabIipoLineLjava/lang/String;poMapLjava/util/HashMap; poVersion5Lorg/biojava/bio/program/sax/BlastLikeVersionSupport;iCountoHitDescriptionLjava/lang/StringBuffer;oStLjava/util/StringTokenizer; StackMapTableMPQR:; ExceptionsS SourceFileWuBlastSummaryLineHelper.java java/lang/StringBufferjava/util/StringTokenizer TR UV WVhitId XYQ Z[ \] ^_ hitDescription `a readingFramescoresmallestSumProbabilitynumberOfContributingHSPs4org/biojava/bio/program/sax/WuBlastSummaryLineHelperjava/lang/Object/org/biojava/bio/program/sax/SummaryLineHelperIFjava/lang/Stringjava/util/HashMap3org/biojava/bio/program/sax/BlastLikeVersionSupportorg/xml/sax/SAXException(Ljava/lang/String;)V getProgram()I countTokens nextToken()Ljava/lang/String;put8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object; setLength(I)Vappend,(Ljava/lang/String;)Ljava/lang/StringBuffer; substring(I)Ljava/lang/String;03* :;  Y:Y+:- - 66dd6, W 6 W W, W, W, W, W, WNY [b%d+g.k:mFnLpVqaripot|wxz{|~f ( !O "!#$%&'(:y)!. ! *+,-.Y%/01234/01234 /012345678PK /*?:}E55<org/biojava/bio/program/sax/blastxml/BlastAggregator$1.class2%    !this$06Lorg/biojava/bio/program/sax/blastxml/BlastAggregator;9(Lorg/biojava/bio/program/sax/blastxml/BlastAggregator;)VCodeLineNumberTableLocalVariableTablethis InnerClasses8Lorg/biojava/bio/program/sax/blastxml/BlastAggregator$1; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileBlastAggregator.javaEnclosingMethod" #  $7org/biojava/bio/program/sax/blastxml/BlastOutputHandler6org/biojava/bio/program/sax/blastxml/BlastAggregator$1java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory4org/biojava/bio/program/sax/blastxml/BlastAggregator<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V    4 *+* .   = Y+ 0   PK /*?:(  :org/biojava/bio/program/sax/blastxml/BlastAggregator.class2'     !<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/program/sax/blastxml/BlastAggregator;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileBlastAggregator.java "9org/biojava/bio/seq/io/game/ElementRecognizer$ByLocalName ByLocalName InnerClasses BlastOutput #6org/biojava/bio/program/sax/blastxml/BlastAggregator$1 $ %&4org/biojava/bio/program/sax/blastxml/BlastAggregator7org/biojava/bio/program/sax/blastxml/StAXFeatureHandler-org/biojava/bio/seq/io/game/ElementRecognizer(Ljava/lang/String;)V9(Lorg/biojava/bio/program/sax/blastxml/BlastAggregator;)V addHandlerk(Lorg/biojava/bio/seq/io/game/ElementRecognizer;Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;)V    W*+*YY* *-4 PK /*?:+oo?org/biojava/bio/program/sax/blastxml/BlastOutputHandler$1.class2  ()VCodeLineNumberTableLocalVariableTablethis InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$1; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileBlastOutputHandler.javaEnclosingMethod 7org/biojava/bio/program/sax/blastxml/BlastOutputHandler 9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$1java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V0 /* J   = Y+ L    PK /*?:TAorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$2$1.class2W , - . /0 12 134 /56 78 79:;<=>?@ ABCthis$1D InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$2;>(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$2;)VCodeLineNumberTableLocalVariableTablethis=Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$2$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; StackMapTable Exceptions SourceFileBlastOutputHandler.javaEnclosingMethod EF  G HIJ KLM NO PQblastn RSdnaT U% V%blastpproteinblastxtblastntblastxorg/xml/sax/SAXExceptionunknown BLAST program. #;org/biojava/bio/program/sax/blastxml/BlastOutputHandler$2$1/org/biojava/utils/stax/StringElementHandlerBase9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$2 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$09Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;java/lang/Stringtrim()Ljava/lang/String;7org/biojava/bio/program/sax/blastxml/BlastOutputHandler access$002_(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;Ljava/lang/String;)Ljava/lang/String; access$000M(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;)Ljava/lang/String;equals(Ljava/lang/Object;)Z7org/biojava/bio/program/sax/blastxml/StAXFeatureHandlerquerySequenceTypehitSequenceType 4 *+*t  !"#;*+W*  *   j*  K*  ,*  YJv|!}&~.@EM_dl~ !$%&. '()*+PK /*?:&ckk?org/biojava/bio/program/sax/blastxml/BlastOutputHandler$2.class2'    !"this$09Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;<(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$2; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileBlastOutputHandler.javaEnclosingMethod# $%  %;org/biojava/bio/program/sax/blastxml/BlastOutputHandler$2$1 &9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$2java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory7org/biojava/bio/program/sax/blastxml/BlastOutputHandlerinitDelegation()V>(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$2;)V    4 *+* r   = Y* t  PK /*?: W W Aorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$3$1.class2z F G H IJ KL M KN OP G KQ KRSTU VWXY Z[\]^_ Z`abthis$1c InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$3;>(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$3;)VCodeLineNumberTableLocalVariableTablethis=Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$3$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; Exceptionsd startElement{(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;Lorg/biojava/utils/stax/DelegationManager;)VnsURI localNameqNameattrsLorg/xml/sax/Attributes;dm*Lorg/biojava/utils/stax/DelegationManager; endElementd(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/utils/stax/StAXContentHandler;)Vhandler+Lorg/biojava/utils/stax/StAXContentHandler;listenerLorg/xml/sax/ContentHandler; bldsAttrs$Lorg/xml/sax/helpers/AttributesImpl; StackMapTableeP SourceFileBlastOutputHandler.javaEnclosingMethod fg  !h ijk lmn op ./ qr 78"org/xml/sax/helpers/AttributesImpl st uthttp://www.biojava.orgprogramCDATA vwversionBlastLikeDataSet'http://www.biojava.org:BlastLikeDataSete .xHeaderhttp://www.biojava.org:Header RawOutput http://www.biojava.org:RawOutput 7y;org/biojava/bio/program/sax/blastxml/BlastOutputHandler$3$1/org/biojava/utils/stax/StringElementHandlerBase9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$3org/xml/sax/SAXExceptionorg/xml/sax/ContentHandler getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$09Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;java/lang/Stringtrim()Ljava/lang/String;7org/biojava/bio/program/sax/blastxml/BlastOutputHandler access$102_(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;Ljava/lang/String;)Ljava/lang/String; getListener()Lorg/xml/sax/ContentHandler; access$000M(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;)Ljava/lang/String; access$100 addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)VQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)V9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V  !"#4 *+*$%  &'()#H*+W$ %&'*+,-./#l *+,-$  %> &' 0+ 1+ 2+ 34 56,-78#J*:*+,- Y :* >* 1 *  *    Y   Y  $. 8Ofu%H&'0+1+2+9: ;<=>? f@A,-BCDEPK /*?:kk?org/biojava/bio/program/sax/blastxml/BlastOutputHandler$3.class2'    !"this$09Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;<(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$3; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileBlastOutputHandler.javaEnclosingMethod# $%  %;org/biojava/bio/program/sax/blastxml/BlastOutputHandler$3$1 &9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$3java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory7org/biojava/bio/program/sax/blastxml/BlastOutputHandlerinitDelegation()V>(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$3;)V    4 *+*    = Y*   PK /*?:kl77Aorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$4$1.class24   !" #$%&this$1' InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$4;>(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$4;)VCodeLineNumberTableLocalVariableTablethis=Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$4$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; Exceptions( SourceFileBlastOutputHandler.javaEnclosingMethod )*  + ,-. /01 23;org/biojava/bio/program/sax/blastxml/BlastOutputHandler$4$1/org/biojava/utils/stax/StringElementHandlerBase9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$4org/xml/sax/SAXException getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$09Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;java/lang/Stringtrim()Ljava/lang/String;7org/biojava/bio/program/sax/blastxml/BlastOutputHandler access$202_(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;Ljava/lang/String;)Ljava/lang/String;   4 *+*  H*+W    PK /*?:5kk?org/biojava/bio/program/sax/blastxml/BlastOutputHandler$4.class2'    !"this$09Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;<(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$4; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileBlastOutputHandler.javaEnclosingMethod# $%  %;org/biojava/bio/program/sax/blastxml/BlastOutputHandler$4$1 &9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$4java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory7org/biojava/bio/program/sax/blastxml/BlastOutputHandlerinitDelegation()V>(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$4;)V    4 *+*    = Y*   PK /*?:477Aorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$5$1.class24   !" #$%&this$1' InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$5;>(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$5;)VCodeLineNumberTableLocalVariableTablethis=Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$5$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; Exceptions( SourceFileBlastOutputHandler.javaEnclosingMethod )*  + ,-. /01 23;org/biojava/bio/program/sax/blastxml/BlastOutputHandler$5$1/org/biojava/utils/stax/StringElementHandlerBase9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$5org/xml/sax/SAXException getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$09Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;java/lang/Stringtrim()Ljava/lang/String;7org/biojava/bio/program/sax/blastxml/BlastOutputHandler access$302_(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;Ljava/lang/String;)Ljava/lang/String;   4 *+*  H*+W    PK /*?:7kk?org/biojava/bio/program/sax/blastxml/BlastOutputHandler$5.class2'    !"this$09Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;<(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$5; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileBlastOutputHandler.javaEnclosingMethod# $%  %;org/biojava/bio/program/sax/blastxml/BlastOutputHandler$5$1 &9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$5java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory7org/biojava/bio/program/sax/blastxml/BlastOutputHandlerinitDelegation()V>(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$5;)V    4 *+*    = Y*   PK /*?:877Aorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$6$1.class24   !" #$%&this$1' InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$6;>(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$6;)VCodeLineNumberTableLocalVariableTablethis=Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$6$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; Exceptions( SourceFileBlastOutputHandler.javaEnclosingMethod )*  + ,-. /01 23;org/biojava/bio/program/sax/blastxml/BlastOutputHandler$6$1/org/biojava/utils/stax/StringElementHandlerBase9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$6org/xml/sax/SAXException getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$09Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;java/lang/Stringtrim()Ljava/lang/String;7org/biojava/bio/program/sax/blastxml/BlastOutputHandler access$402_(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;Ljava/lang/String;)Ljava/lang/String;   4 *+*  H*+W    PK /*?:3^kk?org/biojava/bio/program/sax/blastxml/BlastOutputHandler$6.class2'    !"this$09Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;<(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$6; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileBlastOutputHandler.javaEnclosingMethod# $%  %;org/biojava/bio/program/sax/blastxml/BlastOutputHandler$6$1 &9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$6java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory7org/biojava/bio/program/sax/blastxml/BlastOutputHandlerinitDelegation()V>(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$6;)V    4 *+*    = Y*   PK /*?:m{ Aorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$7$1.class2 C D E !F GHI JKLM NOPQR ST SU GVWX YZ Y[ S\ G]^_`a bcdthis$1e InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$7;w(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$7;Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)VCodeLineNumberTableLocalVariableTablethis=Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$7$1;x09Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;startElementHandlerQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)V queryAttrs$Lorg/xml/sax/helpers/AttributesImpl;dbAttrsnsURILjava/lang/String; localNameqNameattrsLorg/xml/sax/Attributes;listenerLorg/xml/sax/ContentHandler; StackMapTablef Exceptionsg SourceFileBlastOutputHandler.javaEnclosingMethod hi $ %j kl mno pq"org/xml/sax/helpers/AttributesImpl %rhttp://www.biojava.orgidCDATA stmetadatanoneQueryIdhttp://www.biojava.org:QueryIdf u/ vw xqQueryDescription'http://www.biojava.org:QueryDescriptiony z{ |} ~ q DatabaseId!http://www.biojava.org:DatabaseIdHeaderhttp://www.biojava.org:Header ./;org/biojava/bio/program/sax/blastxml/BlastOutputHandler$7$1Aorg/biojava/bio/program/sax/blastxml/BlastOutputIterationsHandler9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$7org/xml/sax/ContentHandlerorg/xml/sax/SAXException getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V getListener()Lorg/xml/sax/ContentHandler;this$09Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;7org/biojava/bio/program/sax/blastxml/BlastOutputHandler access$300M(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;)Ljava/lang/String;()V addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V startElement endElement9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V access$400java/lang/String toCharArray()[Clength()I characters([CII)V access$200  $%&'? *+*,() *+ ,-./'*:*NY:   *     *FY***NY:   *     *+,-(R!"$3%B&Q'^+k,-.124567;>?)RB01B21*+345464789:;^<OW=>?@A!B#!PK /*?:T?org/biojava/bio/program/sax/blastxml/BlastOutputHandler$7.class2'    !"this$09Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;<(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses;Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$7; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileBlastOutputHandler.javaEnclosingMethod# $%  %;org/biojava/bio/program/sax/blastxml/BlastOutputHandler$7$1 &9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$7java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory7org/biojava/bio/program/sax/blastxml/BlastOutputHandlerinitDelegation()Vw(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler$7;Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V    4 *+*    > Y*+   PK /*?:8RR=org/biojava/bio/program/sax/blastxml/BlastOutputHandler.class2 'X 'Y 'Z '[ '\ (] '^ '_ad ef h (ijk hlm hno hpq hrs h 't (uvwx yz{ $| '}~BLASTOUTPUT_HANDLER_FACTORY9Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;programLjava/lang/String;version databaseIdqueryIdqueryDefwrapZ<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)VCodeLineNumberTableLocalVariableTablethis9Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;initDelegation()VendElementHandlerd(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/utils/stax/StAXContentHandler;)VnsURI localNameqNamehandler+Lorg/biojava/utils/stax/StAXContentHandler; Exceptions access$002_(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;Ljava/lang/String;)Ljava/lang/String;x0x1 access$000M(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;)Ljava/lang/String; access$102 access$100 access$202 access$302 access$402 access$300 access$400 access$200 SourceFileBlastOutputHandler.java 0, /, ., -, +, 34 12 <=9org/biojava/bio/seq/io/game/ElementRecognizer$ByLocalName ByLocalName InnerClassesBlastOutput_program 39org/biojava/bio/program/sax/blastxml/BlastOutputHandler$2 3 BlastOutput_version9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$3BlastOutput_db9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$4BlastOutput_query-ID9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$5BlastOutput_query-def9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$6BlastOutput_iterations9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$7 :; http://www.biojava.orgBlastLikeDataSet'http://www.biojava.org:BlastLikeDataSet 9org/biojava/bio/program/sax/blastxml/BlastOutputHandler$1 3= )*7org/biojava/bio/program/sax/blastxml/BlastOutputHandler7org/biojava/bio/program/sax/blastxml/StAXFeatureHandlerorg/xml/sax/SAXException-org/biojava/bio/seq/io/game/ElementRecognizer(Ljava/lang/String;)V<(Lorg/biojava/bio/program/sax/blastxml/BlastOutputHandler;)V addHandlerk(Lorg/biojava/bio/seq/io/game/ElementRecognizer;Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;)VlistenerLorg/xml/sax/ContentHandler;org/xml/sax/ContentHandler endElement9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V '()*+,-,.,/,0,12345|(*+*******6& cQ RSTU^#f'g7(89(:;<=5* Y Y* * Y Y** Y Y** Y Y** Y Y** Y Y*6q*?Ti ~D7 89>?5i* !"#6 NO7489@,A,B,CDEFGH5;*+Z6C7I9J,KL5/*6C7 I9MH5;*+Z6C7I9J,NL5/*6C7 I9OH5;*+Z6C7I9J,PH5;*+Z6C7I9J,QH5;*+Z6C7I9J,RL5/*6C7 I9SL5/*6C7 I9TL5/*6C7 I9U=5# $Y%&6HVWcB `b $PK .*?:H(Iorg/biojava/bio/program/sax/blastxml/BlastOutputIterationsHandler$1.class2  ()VCodeLineNumberTableLocalVariableTablethis InnerClassesELorg/biojava/bio/program/sax/blastxml/BlastOutputIterationsHandler$1; 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getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHitHandler.javaEnclosingMethod# $  %3org/biojava/bio/program/sax/blastxml/HitHandler$2$1 &1org/biojava/bio/program/sax/blastxml/HitHandler$2java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HitHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V6(Lorg/biojava/bio/program/sax/blastxml/HitHandler$2;)V    4 *+* A   = Y* C  PK /*?:89org/biojava/bio/program/sax/blastxml/HitHandler$3$1.class23   !" #$%&this$1' InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HitHandler$3;6(Lorg/biojava/bio/program/sax/blastxml/HitHandler$3;)VCodeLineNumberTableLocalVariableTablethis5Lorg/biojava/bio/program/sax/blastxml/HitHandler$3$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; Exceptions( SourceFileHitHandler.javaEnclosingMethod )*  + ,-. /01 23org/biojava/bio/program/sax/blastxml/HitHandler$3$1/org/biojava/utils/stax/StringElementHandlerBase1org/biojava/bio/program/sax/blastxml/HitHandler$3org/xml/sax/SAXException getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HitHandler;java/lang/Stringtrim()Ljava/lang/String;/org/biojava/bio/program/sax/blastxml/HitHandlersHit_def   4 *+*a  G*+ de   PK /*?:IYY7org/biojava/bio/program/sax/blastxml/HitHandler$3.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HitHandler;4(Lorg/biojava/bio/program/sax/blastxml/HitHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HitHandler$3; 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localNameqNameattrsLorg/xml/sax/Attributes; Exceptions( SourceFileHitHandler.javaEnclosingMethod )*  + 3org/biojava/bio/program/sax/blastxml/HitHandler$5$13org/biojava/bio/program/sax/blastxml/HitHspsHandler1org/biojava/bio/program/sax/blastxml/HitHandler$5org/xml/sax/SAXException getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V    ? *+*,   ` *+,-  4      ! PK /*?:@S7org/biojava/bio/program/sax/blastxml/HitHandler$5.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HitHandler;4(Lorg/biojava/bio/program/sax/blastxml/HitHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HitHandler$5; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHitHandler.javaEnclosingMethod# $  %3org/biojava/bio/program/sax/blastxml/HitHandler$5$1 &1org/biojava/bio/program/sax/blastxml/HitHandler$5java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HitHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()Vo(Lorg/biojava/bio/program/sax/blastxml/HitHandler$5;Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V    4 *+*    > Y*+   PK /*?:8n; ; 5org/biojava/bio/program/sax/blastxml/HitHandler.class2g < = > ?AD EF H IJK HLM HNO H P QRST UVW X YZ[HIT_HANDLER_FACTORY9Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;hitAttrs$Lorg/xml/sax/helpers/AttributesImpl; hitIdAttrssHit_defLjava/lang/String;<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)VCodeLineNumberTableLocalVariableTablethis1Lorg/biojava/bio/program/sax/blastxml/HitHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;endElementHandlerd(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/utils/stax/StAXContentHandler;)VnsURI localNameqNamehandler+Lorg/biojava/utils/stax/StAXContentHandler; Exceptions\()V SourceFileHitHandler.java &' !" #" $%]9org/biojava/bio/seq/io/game/ElementRecognizer$ByLocalName ByLocalName InnerClassesHit_id &^1org/biojava/bio/program/sax/blastxml/HitHandler$2 &_ `aHit_def1org/biojava/bio/program/sax/blastxml/HitHandler$3Hit_len1org/biojava/bio/program/sax/blastxml/HitHandler$4Hit_hsps1org/biojava/bio/program/sax/blastxml/HitHandler$5 -. bchttp://www.biojava.orgHithttp://www.biojava.org:Hitd ef1org/biojava/bio/program/sax/blastxml/HitHandler$1 &9  /org/biojava/bio/program/sax/blastxml/HitHandler7org/biojava/bio/program/sax/blastxml/StAXFeatureHandlerorg/xml/sax/SAXException-org/biojava/bio/seq/io/game/ElementRecognizer(Ljava/lang/String;)V4(Lorg/biojava/bio/program/sax/blastxml/HitHandler;)V addHandlerk(Lorg/biojava/bio/seq/io/game/ElementRecognizer;Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;)VlistenerLorg/xml/sax/ContentHandler;org/xml/sax/ContentHandler endElement9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V  !"#"$%&'(i*+****YY* *Y  Y* *YY* *YY* )& 92 34@)]>lSh*i+,i-./0(i*) *4+,1%2%3%456789(# Y)):;C2@B  PK .*?:bZW__;org/biojava/bio/program/sax/blastxml/HitHspsHandler$1.class2  ()VCodeLineNumberTableLocalVariableTablethis InnerClasses7Lorg/biojava/bio/program/sax/blastxml/HitHspsHandler$1; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHitHspsHandler.javaEnclosingMethod 3org/biojava/bio/program/sax/blastxml/HitHspsHandler 5org/biojava/bio/program/sax/blastxml/HitHspsHandler$1java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V0 /*    = Y+     PK .*?:(ʹ9org/biojava/bio/program/sax/blastxml/HitHspsHandler.class2X 247 8 9: ; < =>?@A B CD CEF B HIJHIT_HSPS_HANDLER_FACTORY9Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)VCodeLineNumberTableLocalVariableTablethis5Lorg/biojava/bio/program/sax/blastxml/HitHspsHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;startElementHandlerQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)VnsURILjava/lang/String; localNameqNameattrsLorg/xml/sax/Attributes; ExceptionsKendElementHandlerd(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/utils/stax/StAXContentHandler;)Vhandler+Lorg/biojava/utils/stax/StAXContentHandler;()V SourceFileHitHspsHandler.java L9org/biojava/bio/seq/io/game/ElementRecognizer$ByLocalName ByLocalName InnerClassesHsp MN O PQ  RShttp://www.biojava.org HSPCollection$http://www.biojava.org:HSPCollection"org/xml/sax/helpers/AttributesImpl /T U! VW5org/biojava/bio/program/sax/blastxml/HitHspsHandler$1 3org/biojava/bio/program/sax/blastxml/HitHspsHandler7org/biojava/bio/program/sax/blastxml/StAXFeatureHandlerorg/xml/sax/SAXException-org/biojava/bio/seq/io/game/ElementRecognizer(Ljava/lang/String;)V/org/biojava/bio/program/sax/blastxml/HspHandlerHSP_HANDLER_FACTORY addHandlerk(Lorg/biojava/bio/seq/io/game/ElementRecognizer;Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;)VlistenerLorg/xml/sax/ContentHandler;org/xml/sax/ContentHandler startElement endElement9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V R*+*Y'*, !p*   Y  674"#$#%#&'()*+i*    AB4"#$#%#,-()./# Y01635 PK /*?:OO7org/biojava/bio/program/sax/blastxml/HspHandler$1.class2  ()VCodeLineNumberTableLocalVariableTablethis InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$1; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod /org/biojava/bio/program/sax/blastxml/HspHandler 1org/biojava/bio/program/sax/blastxml/HspHandler$1java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V0 /* (   = Y+ *    PK /*?:fJ8:org/biojava/bio/program/sax/blastxml/HspHandler$10$1.class2c / 0 12 34 567 18 9 :;<=> :? @ABC :DEF GHIthis$1J InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$10;7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$10;)VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/program/sax/blastxml/HspHandler$10$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String;frameNoI StackMapTable Exceptions SourceFileHspHandler.javaEnclosingMethod KL  MN OPQ RST U&protein VW XYZ [\http://www.biojava.orghitFrameCDATA ]^_ `adna queryStrand b^org/xml/sax/SAXExceptionillegal sequence type $4org/biojava/bio/program/sax/blastxml/HspHandler$10$1/org/biojava/utils/stax/StringElementHandlerBase2org/biojava/bio/program/sax/blastxml/HspHandler$10 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vjava/lang/Stringtrim()Ljava/lang/String;java/lang/IntegerparseInt(Ljava/lang/String;)I7org/biojava/bio/program/sax/blastxml/StAXFeatureHandlerhitSequenceTypeequals(Ljava/lang/Object;)Zthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;/org/biojava/bio/program/sax/blastxml/HspHandlerhspAttrs$Lorg/xml/sax/helpers/AttributesImpl; access$000F(Lorg/biojava/bio/program/sax/blastxml/HspHandler;I)Ljava/lang/String;"org/xml/sax/helpers/AttributesImpl addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V access$100 4 *+*  !"#$o+=&*     * ;&*   * Y6Adn o!"o%&g'()6- *+,-.PK /*?:$ ]]8org/biojava/bio/program/sax/blastxml/HspHandler$10.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$10; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %4org/biojava/bio/program/sax/blastxml/HspHandler$10$1 &2org/biojava/bio/program/sax/blastxml/HspHandler$10java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$10;)V    4 *+*    = Y*   PK /*?:<:org/biojava/bio/program/sax/blastxml/HspHandler$11$1.class2G " # $ %& '( )* )+,-. /012this$13 InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$11;7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$11;)VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/program/sax/blastxml/HspHandler$11$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod 45  6 789 :;< =>? @A BChttp://www.biojava.orgnumberOfIdentitiesCDATAD EF4org/biojava/bio/program/sax/blastxml/HspHandler$11$1/org/biojava/utils/stax/StringElementHandlerBase2org/biojava/bio/program/sax/blastxml/HspHandler$11 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;java/lang/Stringtrim()Ljava/lang/String;java/lang/IntegerparseInt(Ljava/lang/String;)I/org/biojava/bio/program/sax/blastxml/HspHandleriNumberOfIdentitiesIhspAttrs$Lorg/xml/sax/helpers/AttributesImpl;"org/xml/sax/helpers/AttributesImpl addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V 4 *+*  d(*+*   + '(( ! PK /*?:AT]]8org/biojava/bio/program/sax/blastxml/HspHandler$11.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$11; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %4org/biojava/bio/program/sax/blastxml/HspHandler$11$1 &2org/biojava/bio/program/sax/blastxml/HspHandler$11java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$11;)V    4 *+*    = Y*   PK /*?:;22:org/biojava/bio/program/sax/blastxml/HspHandler$12$1.class27  ! "#$%& '()*this$1+ InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$12;7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$12;)VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/program/sax/blastxml/HspHandler$12$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod ,-  . /01 23http://www.biojava.orgnumberOfPositivesCDATA4 564org/biojava/bio/program/sax/blastxml/HspHandler$12$1/org/biojava/utils/stax/StringElementHandlerBase2org/biojava/bio/program/sax/blastxml/HspHandler$12 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;/org/biojava/bio/program/sax/blastxml/HspHandlerhspAttrs$Lorg/xml/sax/helpers/AttributesImpl;"org/xml/sax/helpers/AttributesImpl addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V  4 *+*  O*+   PK /*?:T\']]8org/biojava/bio/program/sax/blastxml/HspHandler$12.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$12; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %4org/biojava/bio/program/sax/blastxml/HspHandler$12$1 &2org/biojava/bio/program/sax/blastxml/HspHandler$12java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$12;)V    4 *+*    = Y*   PK /*?:'6:org/biojava/bio/program/sax/blastxml/HspHandler$13$1.class2G " # $ %& '( )* )+,-. /012this$13 InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$13;7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$13;)VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/program/sax/blastxml/HspHandler$13$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod 45  6 789 :;< =>? @A BChttp://www.biojava.org alignmentSizeCDATAD EF4org/biojava/bio/program/sax/blastxml/HspHandler$13$1/org/biojava/utils/stax/StringElementHandlerBase2org/biojava/bio/program/sax/blastxml/HspHandler$13 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;java/lang/Stringtrim()Ljava/lang/String;java/lang/IntegerparseInt(Ljava/lang/String;)I/org/biojava/bio/program/sax/blastxml/HspHandleriAlignmentSizeIhspAttrs$Lorg/xml/sax/helpers/AttributesImpl;"org/xml/sax/helpers/AttributesImpl addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V 4 *+*  d(*+*   +   ' (( ! PK /*?:]]8org/biojava/bio/program/sax/blastxml/HspHandler$13.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$13; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %4org/biojava/bio/program/sax/blastxml/HspHandler$13$1 &2org/biojava/bio/program/sax/blastxml/HspHandler$13java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$13;)V    4 *+*    = Y*   PK /*?:MO!"":org/biojava/bio/program/sax/blastxml/HspHandler$14$1.class2*     !this$1" InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$14;7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$14;)VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/program/sax/blastxml/HspHandler$14$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod #$  % &'( )4org/biojava/bio/program/sax/blastxml/HspHandler$14$1/org/biojava/utils/stax/StringElementHandlerBase2org/biojava/bio/program/sax/blastxml/HspHandler$14 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;/org/biojava/bio/program/sax/blastxml/HspHandler sHsp_qseq   4 *+*  D *+     PK /*?:@E]]8org/biojava/bio/program/sax/blastxml/HspHandler$14.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$14; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %4org/biojava/bio/program/sax/blastxml/HspHandler$14$1 &2org/biojava/bio/program/sax/blastxml/HspHandler$14java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$14;)V    4 *+*    = Y*   PK /*?:G"":org/biojava/bio/program/sax/blastxml/HspHandler$15$1.class2*     !this$1" InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$15;7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$15;)VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/program/sax/blastxml/HspHandler$15$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod #$  % &'( )4org/biojava/bio/program/sax/blastxml/HspHandler$15$1/org/biojava/utils/stax/StringElementHandlerBase2org/biojava/bio/program/sax/blastxml/HspHandler$15 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;/org/biojava/bio/program/sax/blastxml/HspHandler sHsp_hseq   4 *+*"  D *+ $ %   PK /*?:7j]]8org/biojava/bio/program/sax/blastxml/HspHandler$15.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$15; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %4org/biojava/bio/program/sax/blastxml/HspHandler$15$1 &2org/biojava/bio/program/sax/blastxml/HspHandler$15java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$15;)V    4 *+*     = Y* "  PK /*?:B@%%:org/biojava/bio/program/sax/blastxml/HspHandler$16$1.class2*     !this$1" InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$16;7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$16;)VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/program/sax/blastxml/HspHandler$16$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod #$  % &'( )4org/biojava/bio/program/sax/blastxml/HspHandler$16$1/org/biojava/utils/stax/StringElementHandlerBase2org/biojava/bio/program/sax/blastxml/HspHandler$16 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;/org/biojava/bio/program/sax/blastxml/HspHandler sHsp_midline   4 *+*/  D *+ 1 2   PK /*?:~CUI]]8org/biojava/bio/program/sax/blastxml/HspHandler$16.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses4Lorg/biojava/bio/program/sax/blastxml/HspHandler$16; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %4org/biojava/bio/program/sax/blastxml/HspHandler$16$1 &2org/biojava/bio/program/sax/blastxml/HspHandler$16java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V7(Lorg/biojava/bio/program/sax/blastxml/HspHandler$16;)V    4 *+* -   = Y* /  PK /*?:0$$9org/biojava/bio/program/sax/blastxml/HspHandler$2$1.class27  ! "#$%& '()*this$1+ InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$2;6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$2;)VCodeLineNumberTableLocalVariableTablethis5Lorg/biojava/bio/program/sax/blastxml/HspHandler$2$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod ,-  . /01 23http://www.biojava.orgbitScoreCDATA4 563org/biojava/bio/program/sax/blastxml/HspHandler$2$1/org/biojava/utils/stax/StringElementHandlerBase1org/biojava/bio/program/sax/blastxml/HspHandler$2 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;/org/biojava/bio/program/sax/blastxml/HspHandlerhspAttrs$Lorg/xml/sax/helpers/AttributesImpl;"org/xml/sax/helpers/AttributesImpl addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V  4 *+*X  O*+ Z[  PK /*?:YY7org/biojava/bio/program/sax/blastxml/HspHandler$2.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$2; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %3org/biojava/bio/program/sax/blastxml/HspHandler$2$1 &1org/biojava/bio/program/sax/blastxml/HspHandler$2java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$2;)V    4 *+* V   = Y* X  PK /*?: cg!!9org/biojava/bio/program/sax/blastxml/HspHandler$3$1.class27  ! "#$%& '()*this$1+ InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$3;6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$3;)VCodeLineNumberTableLocalVariableTablethis5Lorg/biojava/bio/program/sax/blastxml/HspHandler$3$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod ,-  . /01 23http://www.biojava.orgscoreCDATA4 563org/biojava/bio/program/sax/blastxml/HspHandler$3$1/org/biojava/utils/stax/StringElementHandlerBase1org/biojava/bio/program/sax/blastxml/HspHandler$3 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;/org/biojava/bio/program/sax/blastxml/HspHandlerhspAttrs$Lorg/xml/sax/helpers/AttributesImpl;"org/xml/sax/helpers/AttributesImpl addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V  4 *+*e  O*+ gh  PK /*?:uYY7org/biojava/bio/program/sax/blastxml/HspHandler$3.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$3; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %3org/biojava/bio/program/sax/blastxml/HspHandler$3$1 &1org/biojava/bio/program/sax/blastxml/HspHandler$3java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$3;)V    4 *+* c   = Y* e  PK /*?:{ ''9org/biojava/bio/program/sax/blastxml/HspHandler$4$1.class27  ! "#$%& '()*this$1+ InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$4;6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$4;)VCodeLineNumberTableLocalVariableTablethis5Lorg/biojava/bio/program/sax/blastxml/HspHandler$4$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod ,-  . /01 23http://www.biojava.org expectValueCDATA4 563org/biojava/bio/program/sax/blastxml/HspHandler$4$1/org/biojava/utils/stax/StringElementHandlerBase1org/biojava/bio/program/sax/blastxml/HspHandler$4 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;/org/biojava/bio/program/sax/blastxml/HspHandlerhspAttrs$Lorg/xml/sax/helpers/AttributesImpl;"org/xml/sax/helpers/AttributesImpl addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V  4 *+*r  O*+ tu  PK /*?:eYY7org/biojava/bio/program/sax/blastxml/HspHandler$4.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$4; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %3org/biojava/bio/program/sax/blastxml/HspHandler$4$1 &1org/biojava/bio/program/sax/blastxml/HspHandler$4java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$4;)V    4 *+* p   = Y* r  PK /*?::dd9org/biojava/bio/program/sax/blastxml/HspHandler$5$1.class20     !"#$this$1% InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$5;6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$5;)VCodeLineNumberTableLocalVariableTablethis5Lorg/biojava/bio/program/sax/blastxml/HspHandler$5$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod &'  ( )*+ ,-. /3org/biojava/bio/program/sax/blastxml/HspHandler$5$1/org/biojava/utils/stax/StringElementHandlerBase1org/biojava/bio/program/sax/blastxml/HspHandler$5 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;java/lang/Stringtrim()Ljava/lang/String;/org/biojava/bio/program/sax/blastxml/HspHandlersHsp_query_from   4 *+*  G*+    PK /*?::YY7org/biojava/bio/program/sax/blastxml/HspHandler$5.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$5; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %3org/biojava/bio/program/sax/blastxml/HspHandler$5$1 &1org/biojava/bio/program/sax/blastxml/HspHandler$5java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$5;)V    4 *+* }   = Y*   PK /*?:~bb9org/biojava/bio/program/sax/blastxml/HspHandler$6$1.class20     !"#$this$1% InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$6;6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$6;)VCodeLineNumberTableLocalVariableTablethis5Lorg/biojava/bio/program/sax/blastxml/HspHandler$6$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod &'  ( )*+ ,-. /3org/biojava/bio/program/sax/blastxml/HspHandler$6$1/org/biojava/utils/stax/StringElementHandlerBase1org/biojava/bio/program/sax/blastxml/HspHandler$6 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;java/lang/Stringtrim()Ljava/lang/String;/org/biojava/bio/program/sax/blastxml/HspHandler sHsp_query_to   4 *+*  G*+    PK /*?:-D/YY7org/biojava/bio/program/sax/blastxml/HspHandler$6.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$6; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %3org/biojava/bio/program/sax/blastxml/HspHandler$6$1 &1org/biojava/bio/program/sax/blastxml/HspHandler$6java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$6;)V    4 *+*    = Y*   PK /*?:Hvbb9org/biojava/bio/program/sax/blastxml/HspHandler$7$1.class20     !"#$this$1% InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$7;6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$7;)VCodeLineNumberTableLocalVariableTablethis5Lorg/biojava/bio/program/sax/blastxml/HspHandler$7$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod &'  ( )*+ ,-. /3org/biojava/bio/program/sax/blastxml/HspHandler$7$1/org/biojava/utils/stax/StringElementHandlerBase1org/biojava/bio/program/sax/blastxml/HspHandler$7 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;java/lang/Stringtrim()Ljava/lang/String;/org/biojava/bio/program/sax/blastxml/HspHandler sHsp_hit_from   4 *+*  G*+    PK /*?:{$YY7org/biojava/bio/program/sax/blastxml/HspHandler$7.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$7; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %3org/biojava/bio/program/sax/blastxml/HspHandler$7$1 &1org/biojava/bio/program/sax/blastxml/HspHandler$7java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$7;)V    4 *+*    = Y*   PK /*?:K8``9org/biojava/bio/program/sax/blastxml/HspHandler$8$1.class20     !"#$this$1% InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$8;6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$8;)VCodeLineNumberTableLocalVariableTablethis5Lorg/biojava/bio/program/sax/blastxml/HspHandler$8$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileHspHandler.javaEnclosingMethod &'  ( )*+ ,-. /3org/biojava/bio/program/sax/blastxml/HspHandler$8$1/org/biojava/utils/stax/StringElementHandlerBase1org/biojava/bio/program/sax/blastxml/HspHandler$8 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;java/lang/Stringtrim()Ljava/lang/String;/org/biojava/bio/program/sax/blastxml/HspHandler sHsp_hit_to   4 *+*  G*+    PK /*?:MZYY7org/biojava/bio/program/sax/blastxml/HspHandler$8.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$8; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %3org/biojava/bio/program/sax/blastxml/HspHandler$8$1 &1org/biojava/bio/program/sax/blastxml/HspHandler$8java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$8;)V    4 *+*    = Y*   PK /*?:ҕ9org/biojava/bio/program/sax/blastxml/HspHandler$9$1.class2c / 0 12 34 567 18 9 :;<=> :? @ABC :DEF GHIthis$1J InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$9;6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$9;)VCodeLineNumberTableLocalVariableTablethis5Lorg/biojava/bio/program/sax/blastxml/HspHandler$9$1;setStringValue(Ljava/lang/String;)VsLjava/lang/String;frameNoI StackMapTable Exceptions SourceFileHspHandler.javaEnclosingMethod KL  MN OPQ RST U&protein VW XYZ [\http://www.biojava.org queryFrameCDATA ]^_ `adna hitStrand b^org/xml/sax/SAXExceptionillegal sequence type $3org/biojava/bio/program/sax/blastxml/HspHandler$9$1/org/biojava/utils/stax/StringElementHandlerBase1org/biojava/bio/program/sax/blastxml/HspHandler$9 getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;()Vjava/lang/Stringtrim()Ljava/lang/String;java/lang/IntegerparseInt(Ljava/lang/String;)I7org/biojava/bio/program/sax/blastxml/StAXFeatureHandlerhitSequenceTypeequals(Ljava/lang/Object;)Zthis$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;/org/biojava/bio/program/sax/blastxml/HspHandlerhspAttrs$Lorg/xml/sax/helpers/AttributesImpl; access$000F(Lorg/biojava/bio/program/sax/blastxml/HspHandler;I)Ljava/lang/String;"org/xml/sax/helpers/AttributesImpl addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V access$100 4 *+*  !"#$o+=&*     * ;&*   * Y6Adn o!"o%&g'()6- *+,-.PK /*?:64VYY7org/biojava/bio/program/sax/blastxml/HspHandler$9.class2'    !"this$01Lorg/biojava/bio/program/sax/blastxml/HspHandler;4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses3Lorg/biojava/bio/program/sax/blastxml/HspHandler$9; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileHspHandler.javaEnclosingMethod# $  %3org/biojava/bio/program/sax/blastxml/HspHandler$9$1 &1org/biojava/bio/program/sax/blastxml/HspHandler$9java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory/org/biojava/bio/program/sax/blastxml/HspHandler<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V()V6(Lorg/biojava/bio/program/sax/blastxml/HspHandler$9;)V    4 *+*    = Y*   PK /*?:{5org/biojava/bio/program/sax/blastxml/HspHandler.class2I u u v u u u u u u u u u   v     ! $ ' * - 0 3 6 9 < E E E E D P u     P u v     !"#$%&'()* r u+,-HSP_HANDLER_FACTORY9Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;bitScoreLjava/lang/String; ConstantValueyscore} expectValuenumberOfIdentitiesnumberOfPositives alignmentSize queryFramehitFrame queryStrand hitStrandpercentageIdentityhspAttrs$Lorg/xml/sax/helpers/AttributesImpl; alignAttrsiNumberOfIdentitiesIiAlignmentSize sHsp_qseq sHsp_hseq sHsp_midline sHsp_hit_from sHsp_hit_tosHsp_query_from sHsp_query_to<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)VCodeLineNumberTableLocalVariableTablethis1Lorg/biojava/bio/program/sax/blastxml/HspHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;stringifyFrame(I)Ljava/lang/String;frame StackMapTable ExceptionsstringifyStrandstrandstartElementHandlerQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)VnsURI localNameqNameattrsLorg/xml/sax/Attributes;endElementHandlerd(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/utils/stax/StAXContentHandler;)Vhandler+Lorg/biojava/utils/stax/StAXContentHandler; queryAttrs matchAttrshitAttrs access$000F(Lorg/biojava/bio/program/sax/blastxml/HspHandler;I)Ljava/lang/String;x0x1 access$100()V SourceFileHspHandler.java z z z z z z z.9org/biojava/bio/seq/io/game/ElementRecognizer$ByLocalName ByLocalName InnerClasses Hsp_bit-score /1org/biojava/bio/program/sax/blastxml/HspHandler$2 0 12 Hsp_score1org/biojava/bio/program/sax/blastxml/HspHandler$3 Hsp_evalue1org/biojava/bio/program/sax/blastxml/HspHandler$4Hsp_query-from1org/biojava/bio/program/sax/blastxml/HspHandler$5 Hsp_query-to1org/biojava/bio/program/sax/blastxml/HspHandler$6 Hsp_hit-from1org/biojava/bio/program/sax/blastxml/HspHandler$7 Hsp_hit-to1org/biojava/bio/program/sax/blastxml/HspHandler$8Hsp_query-frame1org/biojava/bio/program/sax/blastxml/HspHandler$9 Hsp_hit-frame2org/biojava/bio/program/sax/blastxml/HspHandler$10 Hsp_identity2org/biojava/bio/program/sax/blastxml/HspHandler$11 Hsp_positive2org/biojava/bio/program/sax/blastxml/HspHandler$12 Hsp_align-len2org/biojava/bio/program/sax/blastxml/HspHandler$13Hsp_qseq2org/biojava/bio/program/sax/blastxml/HspHandler$14Hsp_hseq2org/biojava/bio/program/sax/blastxml/HspHandler$15 Hsp_midline2org/biojava/bio/program/sax/blastxml/HspHandler$16minus3minus2minus1plus1plus2plus3org/xml/sax/SAXExceptionjava/lang/StringBuilder #illegal frame number encountered. ( 34 35) 67plusminus"illegal strand number encountered."org/xml/sax/helpers/AttributesImpl  is non-compliant.http://www.biojava.orgCDATA8 69 :; <=HSPhttp://www.biojava.org:HSP> ? HSPSummary!http://www.biojava.org:HSPSummary @ABlastLikeAlignment)http://www.biojava.org:BlastLikeAlignment startPosition stopPosition QuerySequence$http://www.biojava.org:QuerySequenceB CD EF GHxmlspace xml:spacepreserveMatchConsensus%http://www.biojava.org:MatchConsensus HitSequence"http://www.biojava.org:HitSequence1org/biojava/bio/program/sax/blastxml/HspHandler$1 wx/org/biojava/bio/program/sax/blastxml/HspHandler7org/biojava/bio/program/sax/blastxml/StAXFeatureHandler-org/biojava/bio/seq/io/game/ElementRecognizer(Ljava/lang/String;)V4(Lorg/biojava/bio/program/sax/blastxml/HspHandler;)V addHandlerk(Lorg/biojava/bio/seq/io/game/ElementRecognizer;Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;)Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/lang/Float(F)Ljava/lang/String; addAttribute](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)VlistenerLorg/xml/sax/ContentHandler;org/xml/sax/ContentHandler startElement endElement9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)Vjava/lang/String toCharArray()[Clength()I characters([CII)V uvwxyz{|}z{~z{z{z{z{z{z{z{z{z{Uzzzzzzzp*+***** * * * * *YY**YY**YY**YY**YY**Y !Y*"*Y#$Y*%*Y&'Y*(*Y)*Y*+*Y,-Y*.*Y/0Y*1*Y23Y*4*Y56Y*7*Y89Y*:*Y;?@ABCDYEYFGHIJHKL"<,=/>2?5@8A;B>C^^ ,D^MNDYOLHIJDb *PYQR U V4 z z z D*=*4*-*&* * * * * DYSL*RTUUVd*h*nWX*YZT[\PYQ]*YZT^_*R]*YZT^_`*YZTabPYQ]PYQ:TccV* XTddV* X*YZTef]*YZ*g*hi*YZTef`PYQ:jklVmX*YZTno]*YZ* g* hi*YZTno`PYQ:TccV* XTddV* X*YZTpp]*YZ*g*hi*YZTpq`*YZTab`*YZT[\`naCjMnmvyz}!3<K_z RzzzM<C D:*!D:*!D# rYst& !$'*-0369<rPK .*?:J[~gg=org/biojava/bio/program/sax/blastxml/IterationHandler$1.class2  ()VCodeLineNumberTableLocalVariableTablethis InnerClasses9Lorg/biojava/bio/program/sax/blastxml/IterationHandler$1; 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localNameqNamehandler+Lorg/biojava/utils/stax/StAXContentHandler; Exceptions5()V SourceFileIterationHandler.java 69org/biojava/bio/seq/io/game/ElementRecognizer$ByLocalName ByLocalName InnerClassesIteration_hits 78 9 :;7org/biojava/bio/program/sax/blastxml/IterationHandler$1 " 5org/biojava/bio/program/sax/blastxml/IterationHandler7org/biojava/bio/program/sax/blastxml/StAXFeatureHandlerorg/xml/sax/SAXException-org/biojava/bio/seq/io/game/ElementRecognizer(Ljava/lang/String;)V9org/biojava/bio/program/sax/blastxml/IterationHitsHandlerITERATION_HITS_HANDLER_FACTORY addHandlerk(Lorg/biojava/bio/seq/io/game/ElementRecognizer;Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;)V  R*+*Y%(.S74 !"# Y #$)&( PK .*?:w-=wwAorg/biojava/bio/program/sax/blastxml/IterationHitsHandler$1.class2  ()VCodeLineNumberTableLocalVariableTablethis InnerClasses=Lorg/biojava/bio/program/sax/blastxml/IterationHitsHandler$1; getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler; SourceFileIterationHitsHandler.javaEnclosingMethod 9org/biojava/bio/program/sax/blastxml/IterationHitsHandler ;org/biojava/bio/program/sax/blastxml/IterationHitsHandler$1java/lang/Object7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V0 /*    = Y+     PK .*?:&C?org/biojava/bio/program/sax/blastxml/IterationHitsHandler.class2X 247 8 9: ; < =>?@A B CD CEF B HIJITERATION_HITS_HANDLER_FACTORY9Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)VCodeLineNumberTableLocalVariableTablethis;Lorg/biojava/bio/program/sax/blastxml/IterationHitsHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;startElementHandlerQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)VnsURILjava/lang/String; localNameqNameattrsLorg/xml/sax/Attributes; ExceptionsKendElementHandlerd(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/utils/stax/StAXContentHandler;)Vhandler+Lorg/biojava/utils/stax/StAXContentHandler;()V SourceFileIterationHitsHandler.java L9org/biojava/bio/seq/io/game/ElementRecognizer$ByLocalName ByLocalName InnerClassesHit MN O PQ  RShttp://www.biojava.orgDetailhttp://www.biojava.org:Detail"org/xml/sax/helpers/AttributesImpl /T U! VW;org/biojava/bio/program/sax/blastxml/IterationHitsHandler$1 9org/biojava/bio/program/sax/blastxml/IterationHitsHandler7org/biojava/bio/program/sax/blastxml/StAXFeatureHandlerorg/xml/sax/SAXException-org/biojava/bio/seq/io/game/ElementRecognizer(Ljava/lang/String;)V/org/biojava/bio/program/sax/blastxml/HitHandlerHIT_HANDLER_FACTORY addHandlerk(Lorg/biojava/bio/seq/io/game/ElementRecognizer;Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;)VlistenerLorg/xml/sax/ContentHandler;org/xml/sax/ContentHandler startElement endElement9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V R*+*Y$') !p*   Y  344"#$#%#&'()*+i*    >?4"#$#%#,-()./# Y01635 PK .*?:.CEorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler$Binding.class2#      recognizer/Lorg/biojava/bio/seq/io/game/ElementRecognizer;handlerFactory9Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;this$09Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;Lorg/biojava/bio/seq/io/game/ElementRecognizer;Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;)VCodeLineNumberTableLocalVariableTablethisBinding InnerClassesALorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler$Binding;erhf SourceFileStAXFeatureHandler.java !  "?org/biojava/bio/program/sax/blastxml/StAXFeatureHandler$Bindingjava/lang/Object()V7org/biojava/bio/program/sax/blastxml/StAXFeatureHandler    ^*+**,*-q rst   PK .*?:d=org/biojava/bio/program/sax/blastxml/StAXFeatureHandler.class2 S TU S V WX Y Z[ \ Z] Z^ _ `a b cd ef g h i jklBinding InnerClasses biojavaUriLjava/lang/String; ConstantValuemCDATAPCDATA querySequenceTypehitSequenceTypelistenerLorg/xml/sax/ContentHandler;staxenv9Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;handlersLjava/util/List;levelI()VCodeLineNumberTableLocalVariableTablethis<(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)V addHandlerk(Lorg/biojava/bio/seq/io/game/ElementRecognizer;Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;)Vrec/Lorg/biojava/bio/seq/io/game/ElementRecognizer;handler9Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory; getListener()Lorg/xml/sax/ContentHandler;startElementHandlerQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)VnsURI localNameqNameattrsLorg/xml/sax/Attributes; Exceptionsn startElement{(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;Lorg/biojava/utils/stax/DelegationManager;)VbALorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler$Binding;idm*Lorg/biojava/utils/stax/DelegationManager; StackMapTableendElementHandlerd(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/utils/stax/StAXContentHandler;)V+Lorg/biojava/utils/stax/StAXContentHandler; endElement SourceFileStAXFeatureHandler.java ,- *+java/util/ArrayList () &'?org/biojava/bio/program/sax/blastxml/StAXFeatureHandler$Binding ,op qr $% st uv w6x yz {8| }~ ;< LM " #7org/biojava/bio/program/sax/blastxml/StAXFeatureHandler-org/biojava/utils/stax/StAXContentHandlerBasehttp://www.biojava.orgorg/xml/sax/SAXException(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;Lorg/biojava/bio/seq/io/game/ElementRecognizer;Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;)Vjava/util/Listadd(Ljava/lang/Object;)Zsize()Iget(I)Ljava/lang/Object; recognizer-org/biojava/bio/seq/io/game/ElementRecognizerfilterStartElementQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)ZhandlerFactory7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;(org/biojava/utils/stax/DelegationManagerdelegate.(Lorg/biojava/utils/stax/StAXContentHandler;)V   !"#$%&'()*+ ,-.K***Y/PC QR0 1',2.^***Y*+/ZC [\]01'&'34.W*Y*+, W/ 0 1'56789:.2* /0 1';<.S/041'=>?@ABCDE.t*Y`*S* d6A* : +,-** *+,-/. $4F[\bjs0R4(FGCH+t1't=t>t?t@AtIJK <BCLM.S/041'=>?7NBCOM.{*YdZ *+,-/041'=>?7NKBCP-.% / /0QR PK .*?:0+GG@org/biojava/bio/program/sax/blastxml/StAXFeatureHandlerMod.class2U + , - ./ .01 2 34 5 67 89 :;<()VCodeLineNumberTableLocalVariableTablethis ?@A BC DE?org/biojava/bio/program/sax/blastxml/StAXFeatureHandler$Binding FGH IJ KLM NOP QR ST:org/biojava/bio/program/sax/blastxml/StAXFeatureHandlerMod7org/biojava/bio/program/sax/blastxml/StAXFeatureHandlerorg/xml/sax/SAXExceptionlevelhandlersLjava/util/List;java/util/Listsize()Iget(I)Ljava/lang/Object; recognizer/Lorg/biojava/bio/seq/io/game/ElementRecognizer;-org/biojava/bio/seq/io/game/ElementRecognizerfilterStartElementQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)ZhandlerFactory9Lorg/biojava/bio/program/sax/blastxml/StAXHandlerFactory;7org/biojava/bio/program/sax/blastxml/StAXHandlerFactory getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler;(org/biojava/utils/stax/DelegationManagerdelegate.(Lorg/biojava/utils/stax/StAXContentHandler;)VstartElementHandlerQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)V /* q*Y`*P*d6>*:+,- *  * *+,- . ' -/$041F2X3Y/_:g;p=R4%@qqq q!q"#q$%& 9'()* PK .*?:s=org/biojava/bio/program/sax/blastxml/StAXHandlerFactory.class2  getHandlerf(Lorg/biojava/bio/program/sax/blastxml/StAXFeatureHandler;)Lorg/biojava/utils/stax/StAXContentHandler; SourceFileStAXHandlerFactory.java7org/biojava/bio/program/sax/blastxml/StAXHandlerFactoryjava/lang/ObjectPK /*?:z0~DD1org/biojava/bio/program/sax/blastxml/package.html

Parsers for the XML output from NCBI blast.

PK /*?:(Cff(org/biojava/bio/program/sax/package.html Parsers which offer XML representations of the output from common bioinformatics tools. PK /*?:Y##'org/biojava/bio/program/sax/package.inf!!BioJavaBuildTool1 External Tools PK .*?:gWoo@org/biojava/bio/program/scf/SCF$BaseCallUncertaintyDecoder.class2  decode"(B)Lorg/biojava/bio/symbol/Symbol; Exceptions SourceFileSCF.java:org/biojava/bio/program/scf/SCF$BaseCallUncertaintyDecoderBaseCallUncertaintyDecoder InnerClassesjava/lang/Object-org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/program/scf/SCF  PK .*?:F|?org/biojava/bio/program/scf/SCF$DefaultUncertaintyDecoder.class2O ' () (* (+ (, (- (. /012 '3 4 5 6 79:;()VCodeLineNumberTableLocalVariableTablethisDefaultUncertaintyDecoder InnerClasses;Lorg/biojava/bio/program/scf/SCF$DefaultUncertaintyDecoder;decode"(B)Lorg/biojava/bio/symbol/Symbol;callBcC StackMapTable Exceptions SourceFileSCF.java = >? !? @? A? BC DEF GC-org/biojava/bio/symbol/IllegalSymbolExceptionjava/lang/StringBuilderNo Symbol for HI HJ KL MN9org/biojava/bio/program/scf/SCF$DefaultUncertaintyDecoderjava/lang/Object:org/biojava/bio/program/scf/SCF$BaseCallUncertaintyDecoderBaseCallUncertaintyDecoderorg/biojava/bio/seq/DNAToolsa'()Lorg/biojava/bio/symbol/AtomicSymbol;gtn!()Lorg/biojava/bio/symbol/Symbol;getDNA)()Lorg/biojava/bio/symbol/FiniteAlphabet;%org/biojava/bio/symbol/FiniteAlphabet getGapSymbolappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(C)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/String;)Vorg/biojava/bio/program/scf/SCF /* = -xAdChGlNtTpadchglnttp Y Y  & hlpt x |  !"# h$ %&88<PK .*?:+GGV  9org/biojava/bio/program/scf/SCF$Parser$HeaderStruct.class2n J K LM JNO P QR S QT U V W X Y Z [ \ Q] ^ _ ` ab HEADER_LENGTHI ConstantValue magic_numberJsamplessamples_offsetbasesbases_left_clipbases_right_clip bases_offset comments_sizecomments_offsetversion[C sample_sizecode_set private_sizeprivate_offsetspare[J()VCodeLineNumberTableLocalVariableTablethisdParser InnerClasses HeaderStruct5Lorg/biojava/bio/program/scf/SCF$Parser$HeaderStruct;createQ(Ljava/io/DataInputStream;J)Lorg/biojava/bio/program/scf/SCF$Parser$HeaderStruct;idinLjava/io/DataInputStream; initOffseths StackMapTableM Exceptionse SourceFileSCF.java 23 *+ 013org/biojava/bio/program/scf/SCF$Parser$HeaderStructjava/lang/IllegalStateExceptionICan't skip more than four bytes and still have enough info to read header 2fg hi ! ji "! #! $! %! &! 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" # $% & ' ( ) * + , - . / 0 1 2 3 4 5 6 789: j;<=>?Parser InnerClasses@ HeaderStructoffsetJdinLjava/io/DataInputStream;header5Lorg/biojava/bio/program/scf/SCF$Parser$HeaderStruct;decoderABaseCallUncertaintyDecoders(Ljava/io/DataInputStream;Lorg/biojava/bio/program/scf/SCF;Lorg/biojava/bio/program/scf/SCF$Parser$HeaderStruct;J)VCodeLineNumberTableLocalVariableTablethis(Lorg/biojava/bio/program/scf/SCF$Parser; initOffset StackMapTable>B@ Exceptions createDecoder?(J)Lorg/biojava/bio/program/scf/SCF$BaseCallUncertaintyDecoder;codeSet getParsed#()Lorg/biojava/bio/program/scf/SCF;parse()VsectLjava/lang/Integer;itLjava/util/Iterator;SAMPLESBASESCOMMENTSPRIVATE sectionOrderLjava/util/TreeMap;CD parseSamples parseBases parseCommentskeyLjava/lang/String;valueraw[BrLjava/io/BufferedReader;lineeqIdxIE parsePrivateprivReadthisReadskipTo(J)V actualSkip newOffsetskipcreateAndSetBaseCallAlignment4(Ljava/util/List;Ljava/util/List;[Ljava/util/List;)V baseCallsLjava/util/Map;ise/Lorg/biojava/bio/symbol/IllegalSymbolException;iae1Lorg/biojava/bio/symbol/IllegalAlphabetException;dnaLjava/util/List;offsetsprobs[Ljava/util/List;8< SourceFileSCF.java uv wx  "java/lang/IllegalArgumentExceptionCan't parse a null inputstream Forg/biojava/bio/program/scf/SCF GvCorg/biojava/bio/chromatogram/UnsupportedChromatogramFormatException:Can't parse an SCF with more than 2147483647 trace samples Hv9Can't parse an SCF with more than 2147483647 called bases yz Iv {~J KLjava/lang/StringBuilderWarning: the code set ( MN MO>) is not specifically supported. 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PQR SF9org/biojava/bio/program/scf/SCF$DefaultUncertaintyDecoderDefaultUncertaintyDecoderjava/lang/Integer Tjava/util/TreeMapjava/lang/Long Uv VW Xv Yv Zv [\] ^_C `a bc de fvB ghjava/io/BufferedReaderjava/io/InputStreamReaderjava/io/ByteArrayInputStream i ISO-8859-1 j k lQE mn op oq rst uv wv xy z{"Can't skip backwards: (newOffset== ) < (offset==) |norg/biojava/utils/SmallMap} ~                      -org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/BioError?@AM6,BYN9-=C6-D:-`E:*FGWı6 l mn$o=v@wIxQzW{Z~cmHcmh=CF:@@-@$k*H **.8**HIW<=*J3/**J*Jd:=*Ya`<DZ*  *,.>Xcj k,?.=  ;c*/YYKL*M *eB! #*!N6*Ya!eBݱ&  5<BMY_b*Mccv<'v5%OY P:Q*R+STWU*V,WTWX*Y-2ZTW[*Y-2\TW]*Y-2^TW_*Y-2`TWa*Y-2bTWc*Y-2dTWe*Y-2fTW**gh:jYkl:jYnlimF !7OgH    M r*o qsot | }" $ PK .*?:%L 3org/biojava/bio/program/scf/SCF$ParserFactory.class2 LM N O 4P ?Q ?R STU ?V W XYZ[\ L] ^_ ` a@@b de dghi()VCodeLineNumberTableLocalVariableTablethis ParserFactory InnerClasses/Lorg/biojava/bio/program/scf/SCF$ParserFactory;parse:(Ljava/io/InputStream;Lorg/biojava/bio/program/scf/SCF;J)VinLjava/io/InputStream;out!Lorg/biojava/bio/program/scf/SCF; initOffsetJdinLjava/io/DataInputStream;parserjParser(Lorg/biojava/bio/program/scf/SCF$Parser; Exceptionsk createParsere(Ljava/io/DataInputStream;Lorg/biojava/bio/program/scf/SCF;J)Lorg/biojava/bio/program/scf/SCF$Parser;e!Ljava/lang/NumberFormatException;offsetheaderl HeaderStruct5Lorg/biojava/bio/program/scf/SCF$Parser$HeaderStruct;versionF StackMapTableMmlZj SourceFileSCF.java !java/io/DataInputStream n 9: )! op q0m rsjava/lang/String Bt uv wxjava/lang/NumberFormatExceptionCorg/biojava/bio/chromatogram/UnsupportedChromatogramFormatExceptionjava/lang/StringBuilderThe SCF's version ( yz) is not a number {| }(org/biojava/bio/program/scf/SCF$V2ParserV2Parser ~(org/biojava/bio/program/scf/SCF$V3ParserV3Parser5Only version 2 and version 3 SCFs are supported (not -org/biojava/bio/program/scf/SCF$ParserFactoryjava/lang/Object&org/biojava/bio/program/scf/SCF$Parserjava/io/IOException3org/biojava/bio/program/scf/SCF$Parser$HeaderStructorg/biojava/bio/program/scf/SCF(Ljava/io/InputStream;)VcreateQ(Ljava/io/DataInputStream;J)Lorg/biojava/bio/program/scf/SCF$Parser$HeaderStruct; sample_size access$000%(Lorg/biojava/bio/program/scf/SCF;I)V[C([C)Vjava/lang/Float parseFloat(Ljava/lang/String;)Fappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/String;)Vs(Ljava/io/DataInputStream;Lorg/biojava/bio/program/scf/SCF;Lorg/biojava/bio/program/scf/SCF$Parser$HeaderStruct;J)V  !"/*#$ %( )*"wY*:+ :# $4+,-./0 123678 9:" 7* :7+ h Y 80: YY Y  Y*+:CY*+:)YY Y -0#: -02]l~$f 2+;< {363612-./0=0 >A36-BCD40EFGH, %EFGI78JK'*S& 4S5?4@ Sc Sf PK .*?:B;rr.org/biojava/bio/program/scf/SCF$V2Parser.class2 8p 7q <rX <s 7t uv wx 7y uz 7{ |} ~ | ~ | ~ | ~  < 7 <  u % u 7 u  % ~  7Parser InnerClasses HeaderStructs(Ljava/io/DataInputStream;Lorg/biojava/bio/program/scf/SCF;Lorg/biojava/bio/program/scf/SCF$Parser$HeaderStruct;J)VCodeLineNumberTableLocalVariableTablethisV2Parser*Lorg/biojava/bio/program/scf/SCF$V2Parser;dinLjava/io/DataInputStream;out!Lorg/biojava/bio/program/scf/SCF;header5Lorg/biojava/bio/program/scf/SCF$Parser$HeaderStruct; initOffsetJ Exceptions parseSamples()VnIiise/Lorg/biojava/bio/symbol/IllegalSymbolException;counttrace[[ImaxVal[I StackMapTableZ parseBasesueELorg/biojava/bio/chromatogram/UnsupportedChromatogramFormatException;ptmpprobs[Ljava/util/List;dnaLjava/util/List;offsetsprobTmp[Bej SourceFileSCF.java 9> IJ L L EF  L GH  -org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/BioError Can't happen 9 L Ljava/util/ArrayList 9 Corg/biojava/bio/chromatogram/UnsupportedChromatogramFormatException1SCF contains a base with peak offset > 2147483647 9   Base call decoding failure ACan't happen unless getProbabilityAlphabet() has been misdefined. 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Support for the SCF chromatogram format.

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SourceFileDataStoreFactory.java.org/biojava/bio/program/ssaha/DataStoreFactoryjava/lang/Objectjava/io/IOException/org/biojava/bio/symbol/IllegalAlphabetExceptionorg/biojava/bio/BioException    PK .*?:왋K1org/biojava/bio/program/ssaha/HitMerger$Hit.class2> + , - . /12 + 34 5 678hitIDI queryOffset hitOffset hitLength(IIII)VCodeLineNumberTableLocalVariableTablethisHit InnerClasses-Lorg/biojava/bio/program/ssaha/HitMerger$Hit;equals(Ljava/lang/Object;)ZroLjava/lang/Object; StackMapTable1 compareTo(Ljava/lang/Object;)IrelDisttoString()Ljava/lang/String; SourceFileHitMerger.java 9    :+org/biojava/bio/program/ssaha/HitMerger$Hitjava/lang/StringBuilder ;< ;= '(java/lang/Objectjava/lang/Comparable()V'org/biojava/bio/program/ssaha/HitMergerappend(I)Ljava/lang/StringBuilder;-(Ljava/lang/String;)Ljava/lang/StringBuilder;  *****mn opqr4@+:+M*,(*,*,*,uv w>}  2@@ !" <#@$%u+M*,*,**`,,`d>*,*,*,*,N379=?JLWYdfqs*uu !p3B&"#  '(`6Y*  *  *  *  6)* 0 PK .*?:>Qj -org/biojava/bio/program/ssaha/HitMerger.class2z JK J L M N OP QR S OT UV OW OX Y Z [ \ ] O^ _ ` a bc bdefgHit InnerClasseshitListLjava/util/List; minLengthIdelegate.Lorg/biojava/bio/program/ssaha/SearchListener;2(Lorg/biojava/bio/program/ssaha/SearchListener;I)VCodeLineNumberTableLocalVariableTablethis)Lorg/biojava/bio/program/ssaha/HitMerger; startSearch(Ljava/lang/String;)VseqIDLjava/lang/String;hit(IIII)VhitID queryOffset hitOffset hitLength-Lorg/biojava/bio/program/ssaha/HitMerger$Hit; endSearchhighjlowuboundi StackMapTableRmerge(Lorg/biojava/bio/program/ssaha/HitMerger$Hit;Lorg/biojava/bio/program/ssaha/HitMerger$Hit;)Lorg/biojava/bio/program/ssaha/HitMerger$Hit;abqoholen doOverlap](Lorg/biojava/bio/program/ssaha/HitMerger$Hit;Lorg/biojava/bio/program/ssaha/HitMerger$Hit;)Z SourceFileHitMerger.java %hjava/util/ArrayList  #$ !"i jh ,-+org/biojava/bio/program/ssaha/HitMerger$Hit %1 klm no pq rs 3" 4" 5" FG ?@ tu 2" 01 7-v wx yx'org/biojava/bio/program/ssaha/HitMergerjava/lang/Object,org/biojava/bio/program/ssaha/SearchListener()Vjava/util/Listclearadd(Ljava/lang/Object;)Zjava/util/Collectionssort(Ljava/util/List;)Vsize()Iget(I)Ljava/lang/Object;set'(ILjava/lang/Object;)Ljava/lang/Object;java/lang/Mathmin(II)Imax! !"#$%&'h**Y*+*() *+#$!",-'P**+( !")*+./01' Y :* W(*+,)>*+2"3"4"5" 067-'* =* * N--`-h`6`6* L* :`)*-**-W--**----P*+(F/23$466I7Y9i:l=v>?6CD2HI)HY386;W9"$:66;" <"*+./=  1>0>#?@'C+,>+,6++`,,`d6 Y+ (L MN2S)>C*+CA6CB6 7C"*D"2E"FG'F+,<++`,,+,,`+,d+,d(W) F*+FA6FB6=D@HI   PK .*?:E##3org/biojava/bio/program/ssaha/MappedDataStore.class2 =    <     <  < < < <  <  '  + + +  2 2 2 2  packing Lorg/biojava/bio/symbol/Packing; wordLengthI hashTableLjava/nio/IntBuffer;hitTableLjava/nio/MappedByteBuffer; nameArray nameTable(Ljava/io/File;)VCodeLineNumberTableLocalVariableTablecnfe"Ljava/lang/ClassNotFoundException;this/Lorg/biojava/bio/program/ssaha/MappedDataStore; dataStoreFileLjava/io/File;channelLjava/nio/channels/FileChannel; rootBuffer hashTablePos hitTablePos nameArrayPos nameTablePospackingStreamLength packingBuffer[B packingStreamLjava/io/ByteArrayInputStream;packingSerializerLjava/io/ObjectInputStream; hashTable_MB hashTableSize hitTable_MB hitTableSize nameArray_MB nameArraySize nameTable_MB nameTableSize StackMapTable] Exceptions getAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;searchf(Ljava/lang/String;Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/program/ssaha/SearchListener;)Vjwordise/Lorg/biojava/bio/symbol/IllegalSymbolException;seqIDLjava/lang/String;symList#Lorg/biojava/bio/symbol/SymbolList;listener.Lorg/biojava/bio/program/ssaha/SearchListener; seqNameForID(I)Ljava/lang/String;iidoffsetlengthsbuffLjava/lang/StringBuffer;fireHits3(IILorg/biojava/bio/program/ssaha/SearchListener;)Ve$Ljava/lang/IllegalArgumentException;hits hitOffset SourceFileMappedDataStore.java Ijava/io/FileInputStream IJ    AB java/io/ByteArrayInputStream Ijava/io/ObjectInputStream I org/biojava/bio/symbol/Packing ?@ java/lang/ClassNotFoundExceptionjava/lang/ErrorCan't restore packing I CD EF GD HF uv   -org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/BioError%Assertion Failure: Symbol dissapeared I java/lang/StringBuffer I   "java/lang/IllegalArgumentException   java/lang/StringBuilderword:    offset:  hitOffset -org/biojava/bio/program/ssaha/MappedDataStorejava/lang/Object'org/biojava/bio/program/ssaha/DataStore java/io/Filejava/nio/channels/FileChanneljava/nio/MappedByteBufferjava/io/IOExceptionjava/lang/String!org/biojava/bio/symbol/SymbolList,org/biojava/bio/program/ssaha/SearchListener()V getChannel!()Ljava/nio/channels/FileChannel;%java/nio/channels/FileChannel$MapModeMapMode InnerClasses READ_ONLY'Ljava/nio/channels/FileChannel$MapMode;mapF(Ljava/nio/channels/FileChannel$MapMode;JJ)Ljava/nio/MappedByteBuffer;position(I)Ljava/nio/Buffer;getInt()Iget([B)Ljava/nio/ByteBuffer;([B)V(Ljava/io/InputStream;)V readObject()Ljava/lang/Object;*(Ljava/lang/String;Ljava/lang/Throwable;)V asIntBuffer()Ljava/nio/IntBuffer;%org/biojava/bio/symbol/PackingFactory primeWordG(Lorg/biojava/bio/symbol/SymbolList;ILorg/biojava/bio/symbol/Packing;)I startSearch(Ljava/lang/String;)VnextWordI(Lorg/biojava/bio/symbol/SymbolList;IIILorg/biojava/bio/symbol/Packing;)I endSearchjava/nio/IntBuffer(I)I(I)VgetChar()Cappend(C)Ljava/lang/StringBuffer;toString()Ljava/lang/String;java/lang/SystemoutLjava/io/PrintStream;-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;java/io/PrintStreamprintlnhit(IIII)V <=>?@ABCDEFGDHFIJK$m*Y+M, N- W- 6- 6- 6- 6*- - 6, `N- W: - W Y : Y : * : Y ,:   W 6 *,` d,: W 6*,`d,: W 6*,`d,: W 6*,`dL%#$&+"-(../40:1B4H:W?^@dAkBvCFIGHLQRSZ_`ahmn"o:vI{P|W}lM NO mPQmRS]TUQVF(EWB.?XB49YB:3ZBH%[Bd \] v^_ `a bF cB dF}eBYfF"KgBI$hFWiBj' klmnopqr stuvK4 *LM  PQwxK0o,* * 6-+!*-"* `6,#+,* *$6** d`-"-+%:'Y()_b&L2 0BRX_bdnMH%3yBQzBd {|oPQo}~ooj!%2 k KF**=* W* >+Y,:6*-.W/L" $-:@M>'BFPQFB =B,B$"j'kKs**6* WT:12Y34567812Y39567812Y3:5678* 66"-* * * ;ݱ0L: 8QknwMROz&Bw)BPQzBB Bj kP %  PK .*?:i:org/biojava/bio/program/ssaha/MappedDataStoreFactory.class2> A        @  $  ( ( ( (  @  @ ()VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/program/ssaha/MappedDataStoreFactory; getDataStore9(Ljava/io/File;)Lorg/biojava/bio/program/ssaha/DataStore; storeFileLjava/io/File; ExceptionsbuildDataStore~(Ljava/io/File;Lorg/biojava/bio/seq/db/SequenceDB;Lorg/biojava/bio/symbol/Packing;II)Lorg/biojava/bio/program/ssaha/DataStore;iIjwordseqLorg/biojava/bio/seq/Sequence;&Lorg/biojava/bio/seq/SequenceIterator;countse%Ljava/lang/IndexOutOfBoundsException;nameLjava/lang/String;"Ljava/nio/BufferOverflowException;seqDB#Lorg/biojava/bio/seq/db/SequenceDB;packing Lorg/biojava/bio/symbol/Packing; wordLength threshold packingStreamLjava/io/ByteArrayOutputStream;packingSerializerLjava/io/ObjectOutputStream;structDataSize hashTablePos hitTablePos nameArrayPos nameTablePosstoreLjava/io/RandomAccessFile;channelLjava/nio/channels/FileChannel;words hashTableSize hashTable_MBLjava/nio/MappedByteBuffer; hashTableLjava/nio/IntBuffer;seqCount nameChars nameArraySize nameArray_MB nameArray nameTableSize nameTable kmersUsedhitCount hitTableSizeJhitTable hitOffset seqNumber rootBuffer StackMapTableaddCount(Ljava/nio/IntBuffer;I)Vbuffercount writeRecord5(Ljava/nio/IntBuffer;Ljava/nio/MappedByteBuffer;III)Vposoffset kmerPointer SourceFileMappedDataStoreFactory.java CD-org/biojava/bio/program/ssaha/MappedDataStore Cjava/io/ByteArrayOutputStreamjava/io/ObjectOutputStream C D S  java/io/RandomAccessFilerw C               ! "# $% &S '( )*#java/lang/IndexOutOfBoundsExceptionHit offset negative C+, -.java/lang/StringBuildercounts: /0 /1 2 3 4+word:  hitOffset:  '5 67 89  java/nio/BufferOverflowExceptionname:  seqNumber: na pos: nt pos: : ;< JK =*4org/biojava/bio/program/ssaha/MappedDataStoreFactoryjava/lang/Object.org/biojava/bio/program/ssaha/DataStoreFactoryjava/io/IOException java/io/File!org/biojava/bio/seq/db/SequenceDBorg/biojava/bio/symbol/Packingjava/nio/channels/FileChanneljava/nio/MappedByteBufferjava/nio/IntBuffer$org/biojava/bio/seq/SequenceIteratororg/biojava/bio/seq/Sequencejava/lang/String/org/biojava/bio/symbol/IllegalAlphabetExceptionorg/biojava/bio/BioException(Ljava/io/File;)V(Ljava/io/OutputStream;)V writeObject(Ljava/lang/Object;)Vflushorg/biojava/utils/Constants BYTES_IN_INT toByteArray()[B createNewFile()Z#(Ljava/io/File;Ljava/lang/String;)V getChannel!()Ljava/nio/channels/FileChannel;wordSize()B%java/nio/channels/FileChannel$MapModeMapMode InnerClasses READ_WRITE'Ljava/nio/channels/FileChannel$MapMode;mapF(Ljava/nio/channels/FileChannel$MapMode;JJ)Ljava/nio/MappedByteBuffer; asIntBuffer()Ljava/nio/IntBuffer;put(II)Ljava/nio/IntBuffer;position(I)Ljava/nio/Buffer;sequenceIterator(()Lorg/biojava/bio/seq/SequenceIterator;hasNext nextSequence ()Lorg/biojava/bio/seq/Sequence;length()IgetName()Ljava/lang/String;%org/biojava/bio/symbol/PackingFactory primeWordG(Lorg/biojava/bio/symbol/SymbolList;ILorg/biojava/bio/symbol/Packing;)InextWordI(Lorg/biojava/bio/symbol/SymbolList;IIILorg/biojava/bio/symbol/Packing;)I BYTES_IN_CHARputInt(II)Ljava/nio/ByteBuffer;get(I)I(Ljava/lang/String;)Vjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toStringjava/io/PrintStreamprintln(I)Ljava/nio/ByteBuffer;charAt(I)CputChar(C)Ljava/nio/ByteBuffer;([B)Ljava/nio/ByteBuffer;force()Ljava/nio/MappedByteBuffer;getInt!@ABCDE/*FGG HIJKE= Y+FKG HI LMNOPQE &Y:Y:-  h `6+ W Y+:  :-hx66  h`6 ::W6`WW66,:m:U`6-6*`6-6*ۧ `6 ` h6 ::W `6  h` h`6 :!W "W666*`#6 `6 `6  `ia ia7 :!W "W66   `#6!!! $Y%& `W `!W ! `h``6a:"'(Y)*+!,-.'(Y)/+ ,-.'(Y)0+,-." `W C6  "W,:!!0!:"" `1 dW":##2W6$$##$34W$"-6$* $5`6%%"*"$%-6$*%d` $5%Ч{:#'(Y)7+"+-.'(Y)8+ ,-.'(Y)9+:,-.'(Y);+1,-.#  :!!"W! 2W! 2W! 2W! 2W!2W! 2W! 6qt$ 6FqY Z[\^.g3h?iFmSsWtcys~z$'.8HOX_r *6;EQ^qtv '2?LR \ i {  #1$8%@&H'P(X)`*l+w-}./013G2RS(TS6US^VWtRXYS.RSvQZ["*YS!RS 5TS$o3TS%'{\]#\FUS$vZ^#!VW"7RX!HILM_`abcSdS efgh.miSWDjS kS .mlS _<mS ?\no FUpqSHrSc8sSs(tuz!vwxSyS8czSHS{uOL|wr)}S~uSSuSS 1ju! H'u'L ,nR H2BwNOEi+`#>+`WF78 9:G*HIwUS SE S+`#6E `6,?6 `h` `6,"W,2W,2W,`!WF* C DEG H3J:KALGMROG\ 2S3SSHISvwSuSSSSSUS ISR  PK .*?:0org/biojava/bio/program/ssaha/NIODataStore.class2: K   J            J " J J ) J  J  4 8  ; ; ;  ) ) packing Lorg/biojava/bio/symbol/Packing; wordLengthI hashTableLjava/nio/LongBuffer;hitTable"Lorg/biojava/utils/io/LargeBuffer; nameTableLjava/nio/MappedByteBuffer;(Ljava/io/File;)VCodeLineNumberTableLocalVariableTablecnfe"Ljava/lang/ClassNotFoundException;this,Lorg/biojava/bio/program/ssaha/NIODataStore; dataStoreFileLjava/io/File;channelLjava/nio/channels/FileChannel; rootBuffer hashTablePosJ hitTablePos nameTablePospackingStreamLength packingBuffer[B packingStreamLjava/io/ByteArrayInputStream;packingSerializerLjava/io/ObjectInputStream; hashTable_MB hashTableSize nameTable_MB nameTableSize hitTable_MB hitTableSize StackMapTablek Exceptions getAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;searchf(Ljava/lang/String;Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/program/ssaha/SearchListener;)Vjwordise/Lorg/biojava/bio/symbol/IllegalSymbolException;ioeLjava/io/IOException;seqIDLjava/lang/String;symList#Lorg/biojava/bio/symbol/SymbolList;listener.Lorg/biojava/bio/program/ssaha/SearchListener; seqNameForID(I)Ljava/lang/String;iidlengthsbuffLjava/lang/StringBuffer;fireHits3(IILorg/biojava/bio/program/ssaha/SearchListener;)Ve$Ljava/lang/IllegalArgumentException;hitsoffset hitOffset SourceFileNIODataStore.java Wjava/io/FileInputStream WX   P P         OP java/lang/StringBuilderhashTablePos:     hitTablePos: nameTablePos: packingStreamLength:  java/io/ByteArrayInputStream Wjava/io/ObjectInputStream W !"org/biojava/bio/symbol/Packing MN java/lang/ClassNotFoundExceptionjava/lang/ErrorCan't restore packing W#hashTableSize: $% QR UV org/biojava/utils/io/LargeBuffer W& ST ' () *   +, --org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/BioError%Assertion Failure: Symbol dissapeared Wjava/io/IOException-org/biojava/bio/program/ssaha/SearchException W. /0java/lang/StringBuffer W1 23 45 6  7"java/lang/IllegalArgumentExceptionword: offset:  hitOffset 89*org/biojava/bio/program/ssaha/NIODataStorejava/lang/Object'org/biojava/bio/program/ssaha/DataStore java/io/Filejava/nio/channels/FileChanneljava/nio/MappedByteBufferjava/lang/String!org/biojava/bio/symbol/SymbolList,org/biojava/bio/program/ssaha/SearchListener()V getChannel!()Ljava/nio/channels/FileChannel;%java/nio/channels/FileChannel$MapModeMapMode InnerClasses READ_ONLY'Ljava/nio/channels/FileChannel$MapMode;org/biojava/utils/Constants BYTES_IN_LONG BYTES_IN_INTmapF(Ljava/nio/channels/FileChannel$MapMode;JJ)Ljava/nio/MappedByteBuffer;position(I)Ljava/nio/Buffer;getLong()JgetInt()Ijava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;(J)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintln(Ljava/lang/String;)V(I)Ljava/lang/StringBuilder;get([B)Ljava/nio/ByteBuffer;([B)V(Ljava/io/InputStream;)V readObject()Ljava/lang/Object;*(Ljava/lang/String;Ljava/lang/Throwable;)V asLongBuffer()Ljava/nio/LongBuffer;K(Ljava/nio/channels/FileChannel;Ljava/nio/channels/FileChannel$MapMode;JJ)V%org/biojava/bio/symbol/PackingFactory primeWordG(Lorg/biojava/bio/symbol/SymbolList;ILorg/biojava/bio/symbol/Packing;)I startSearchnextWordI(Lorg/biojava/bio/symbol/SymbolList;IIILorg/biojava/bio/symbol/Packing;)I endSearch(Ljava/lang/Throwable;)VgetShort()S(I)VgetChar()C(C)Ljava/lang/StringBuffer;java/nio/LongBuffer(I)J(J)Vhit(IIII)V JKLMNOPQRSTUVWXYw *Y+M, hh`N- W- 7- 7- 7*- - 6 Y Y Y Y , hh` `N-hh` W : - WY : Y : *  :"Y#$,: W 7 Y%*,ae&',: W 6*,ad(,: W 7*)Y,ae*+  !Z%$%'%-+/1071=2E5K6e789:ABCDEH K IJN*S1T8URVn]}bcdkpqrx[ \]^_`abc%dV1ef7gf=hfKiP jk lm no *pV8qf}brVTsP,tVufv& wxyz{|}~ 7Y4 * ,Z{[  ^_YXy,* * -6-+.*-/* `6,0),* * 16** d-/-+2:4Y56:8Y9]`3]l7Z:0BPV]`blnx[R%1POPb n y^_yyyv%%0 wK 8Y:*( W*(:=;YW-?Z #/5[4P:^_:P)P v 8Yu*'@7A*+CT: YE YF YG*+H66"-*+H*+H* IݱDZ: !:Smpy[R!O|&Py)P^_PP fv wP %7  PK .*?:eǦ 7org/biojava/bio/program/ssaha/NIODataStoreFactory.class2~ \                  [    : : : ? :         [     : [ : : !"()VCodeLineNumberTableLocalVariableTablethis3Lorg/biojava/bio/program/ssaha/NIODataStoreFactory; getDataStore9(Ljava/io/File;)Lorg/biojava/bio/program/ssaha/DataStore; storeFileLjava/io/File; Exceptions#buildDataStore~(Ljava/io/File;Lorg/biojava/bio/seq/db/SequenceDB;Lorg/biojava/bio/symbol/Packing;II)Lorg/biojava/bio/program/ssaha/DataStore;iIjwordseqLorg/biojava/bio/seq/Sequence;&Lorg/biojava/bio/seq/SequenceIterator;countsJe%Ljava/lang/IndexOutOfBoundsException;namePosnameLjava/lang/String;"Ljava/nio/BufferOverflowException;seqDB#Lorg/biojava/bio/seq/db/SequenceDB;packing Lorg/biojava/bio/symbol/Packing; wordLength threshold packingStreamLjava/io/ByteArrayOutputStream;packingSerializerLjava/io/ObjectOutputStream;structDataSize hashTablePos hitTablePos nameTablePosstoreLjava/io/RandomAccessFile;channelLjava/nio/channels/FileChannel;words hashTableSize hashTable_MBLjava/nio/MappedByteBuffer; hashTableLjava/nio/LongBuffer;seqCount nameChars nameTableSize nameTable kmersUsedhitCount hitTableSizehitTable"Lorg/biojava/utils/io/LargeBuffer; hitOffset seqNumber rootBuffer StackMapTable $%&'()*+,-.addCount(Ljava/nio/LongBuffer;I)Vbuffercount writeRecord=(Ljava/nio/LongBuffer;Lorg/biojava/utils/io/LargeBuffer;III)Vposoffset kmerPointer SourceFileNIODataStoreFactory.java ^_*org/biojava/bio/program/ssaha/NIODataStore ^/java/io/ByteArrayOutputStreamjava/io/ObjectOutputStream ^0 12 3_4 5n 6n 78$ 9:java/io/RandomAccessFilerw ^; <=> ?@java/lang/StringBuilder Word length: AB AC DEF GH& IJWords:  Allocated: AKL OP' QR( ST) UV WXInitialized hash table First parse% YZ* [: \]+ ^E _`,a bc de G_Done fn gnnameTableSize: hi jk hitCount:  kmersUsed: hitTableSize:  hitTablePos:  org/biojava/utils/io/LargeBuffer ^l Wm nm"Writing pointers from hash to hits#java/lang/IndexOutOfBoundsExceptionHit offset negative ^H hocounts: word:  hitOffset:  2nd parse W` pq rs tu  java/nio/BufferOverflowExceptionname:  seqNumber: nt pos: nv hw Ux yz y_ Committed ef {| h}1org/biojava/bio/program/ssaha/NIODataStoreFactoryjava/lang/Object.org/biojava/bio/program/ssaha/DataStoreFactoryjava/io/IOException java/io/File!org/biojava/bio/seq/db/SequenceDBorg/biojava/bio/symbol/Packingjava/nio/channels/FileChanneljava/nio/MappedByteBufferjava/nio/LongBuffer$org/biojava/bio/seq/SequenceIteratororg/biojava/bio/seq/Sequencejava/lang/String/org/biojava/bio/symbol/IllegalAlphabetExceptionorg/biojava/bio/BioException(Ljava/io/File;)V(Ljava/io/OutputStream;)V writeObject(Ljava/lang/Object;)Vflushorg/biojava/utils/Constants BYTES_IN_LONG BYTES_IN_INT toByteArray()[B createNewFile()Z#(Ljava/io/File;Ljava/lang/String;)V getChannel!()Ljava/nio/channels/FileChannel;java/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintln(Ljava/lang/String;)VwordSize()B(J)Ljava/lang/StringBuilder;%java/nio/channels/FileChannel$MapModeMapMode InnerClasses READ_WRITE'Ljava/nio/channels/FileChannel$MapMode;mapF(Ljava/nio/channels/FileChannel$MapMode;JJ)Ljava/nio/MappedByteBuffer; 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startSearch(Ljava/lang/String;)VseqIDLjava/lang/String; endSearchhit(IIII)VhitIDI queryOffset hitOffset hitLength SourceFileSearchListener.java < java/lang/StringBuilder startSearch: => ?@A B endSearch:  hit. hitID: =C queryOffset:  hitOffset:  hitLength: 1org/biojava/bio/program/ssaha/SearchListener$Echojava/lang/Object,org/biojava/bio/program/ssaha/SearchListener()Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintln(I)Ljava/lang/StringBuilder;1F **+   S*Y+  !S*Y +  "#7*Y        6477$%7&%7'%7(%)* PK .*?:PDcAorg/biojava/bio/program/ssaha/SearchListener$FilterByLength.class2%    ! minLengthI2(Lorg/biojava/bio/program/ssaha/SearchListener;I)VCodeLineNumberTableLocalVariableTablethisFilterByLength InnerClasses=Lorg/biojava/bio/program/ssaha/SearchListener$FilterByLength;delegate.Lorg/biojava/bio/program/ssaha/SearchListener;hit(IIII)VhitID queryOffset hitOffset hitLength StackMapTable SourceFileSearchListener.java #  $;org/biojava/bio/program/ssaha/SearchListener$FilterByLength4org/biojava/bio/program/ssaha/SearchListener$WrapperWrapper1(Lorg/biojava/bio/program/ssaha/SearchListener;)V,org/biojava/bio/program/ssaha/SearchListener1  Q *+*      v* *   4 " PK .*?:  6org/biojava/bio/program/ssaha/SearchListener$Tee.class2G 012 03 4 56 7 8 9 : ; 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Overview

SSAHA is Sequence Searching Algorithm by Hashing. The idea is to take a sequence database, such as EMBL, walk over all of the sequences using a window size and step size, represent each of these same-sized fragments as a bit-string, and use the bit-string as an index into a hash-table. The hash-table is used to store the location of every window (sequence and position). Search sequences are encoded as bit-patterns in the same manner, and then this is used as an index into the table to fetch all hits. Finaly, these hits are sorted and potentialy merged to produce HSPs.

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"#Failed to build Homology:$ %r &y '( )* abhitSequenceType + ,-java/lang/Stringprogram!Failed to determine sequence type jr. /0token1 234 5 queryStrandminus6 7 8 subjectStrand queryFrame 9: subjectFramequerySequenceStart; <=querySequenceEndsubjectSequenceStartsubjectSequenceEnd subjectId >? @?(org/biojava/bio/seq/homol/SimpleHomologyunknown A querySequence BCD2org/biojava/bio/seq/homol/HomologyFeature$Template EZ Z$org/biojava/bio/symbol/RangeLocation jF GH IJ KL MN O PR'org/biojava/bio/symbol/SimpleSymbolList ST jUsubjectSequence&org/biojava/bio/symbol/SimpleAlignment j* VW%org/biojava/utils/ChangeVetoException Failed to create HomologyFeature jX7org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder2org/biojava/bio/program/ssbind/ViewSequenceFactory+org/biojava/bio/search/SearchContentHandler*org/biojava/bio/seq/StrandedFeature$Strandorg/biojava/bio/seq/Sequence java/util/MapqueryViewCachesubjectViewCache(I)Vclearjava/util/ListaddAll(Ljava/util/Collection;)Zadd(Ljava/lang/Object;)Zjava/lang/SystemerrLjava/io/PrintStream;java/io/PrintStreamprintlnprintStackTraceput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;putAll(Ljava/util/Map;)V containsKeyget&(Ljava/lang/Object;)Ljava/lang/Object;/org/biojava/bio/program/ssbind/AlphabetResolverresolveAlphabet;(Ljava/lang/String;)Lorg/biojava/bio/symbol/FiniteAlphabet;%org/biojava/bio/symbol/FiniteAlphabetgetTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;#org/biojava/bio/seq/StrandedFeaturePOSITIVEjava/lang/ObjectequalsNEGATIVE startsWith(Ljava/lang/String;)Zjava/lang/IntegerparseInt(Ljava/lang/String;)ImakeQueryViewSequence2(Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;makeSubjectViewSequence setLengthappend,(Ljava/lang/String;)Ljava/lang/StringBuffer;)org/biojava/bio/seq/homol/HomologyFeaturetype(II)Vlocation!Lorg/biojava/bio/symbol/Location;strand0org/biojava/bio/program/ssbind/AnnotationFactorymakeAnnotation-(Ljava/util/Map;)Lorg/biojava/bio/Annotation; annotationLorg/biojava/bio/Annotation;$Lorg/biojava/bio/seq/homol/Homology; createFeatureZE(Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature; substring(I)Ljava/lang/String;@(Lorg/biojava/bio/seq/io/SymbolTokenization;Ljava/lang/String;)V setAlignment%(Lorg/biojava/bio/symbol/Alignment;)V*(Ljava/lang/String;Ljava/lang/Throwable;)V[$org/biojava/bio/seq/Feature$Templateorg/biojava/bio/seq/Feature!VWX YZ[A\Z]^_^`^abcdefghifjklT***+*Y*Y*Y*Y *Y * Y m* j^ kmn$o/p:qErSsnTopTifqrl>*+m wxnop\Zstl/*m|n opuvl>*m nopwhxylG* *Ym n opzyl=**Wm n op{yl8 *m  n  op|yl+mn op}ylE**m n op~yl+mn opyl+mn opyl|**WL+mn opQ lO *+,Wm  n  op  wlO *+,Wm  n  op  wlO *+,Wm  n  op  wl *****^** !L-*"*" !L Y#$+%M*,&'(L(M*)*) *+,L*-*- *+,M*.*. !*/,L*0*0 !*/,M*1 !2>*3 !26*4 !26*5 !26+, 6>6,,666*6 !:**7:*8: 9Y:: Y: ;: *"*" !: * <* *= !>W?Y@:  AB  C DYEF +G *HI  J  KLY** MNW* <* *O !>W?Y@:AB CDYEF,G*HI J  KLY** MNWPY Q: R : YT USmA !/AOakp|0CVipsvz   ! "#$'%-&9'@*d-l.1234567:=>@BDn>Z^ZkZp s6Z  p   op0CVilZbZ Q H^ | A ,$''[U  ? QY PK .*?:);*+*+;org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.class2 z y y  y y y y y y y  y     y  y y   y   %  y      y y y   ! " y# 6$ %& 6' 6( 6) 6* 6+ 6, 6- 6. 6/ 01 02 345 678 K9 y:; <=> ?@A BCDE zF 3G 3HIJ JKLM NOPQRS TUVWXYZ i[ k\] ^ k_`a kb qcdef vg uhijk subjectDBs/Lorg/biojava/bio/seq/db/SequenceDBInstallation;querySeqHolder#Lorg/biojava/bio/seq/db/SequenceDB; databaseIDLjava/lang/String;queryIDresultAnnotationLorg/biojava/bio/Annotation;resultPreAnnotationLjava/util/Map;searchParametershitData subHitData tokenParser+Lorg/biojava/bio/seq/io/SymbolTokenization;hitsLjava/util/List;subHitssubs3[Lorg/biojava/bio/search/SeqSimilaritySearchSubHit;moreSearchesAvailableZtarget(Ljava/util/List;)VCodeLineNumberTableLocalVariableTablethis7Lorg/biojava/bio/program/ssbind/BlastLikeSearchBuilder;e(Ljava/util/List;Lorg/biojava/bio/seq/db/SequenceDB;Lorg/biojava/bio/seq/db/SequenceDBInstallation;)VmakeSearchResult4()Lorg/biojava/bio/search/SeqSimilaritySearchResult;queryLorg/biojava/bio/seq/Sequence; subjectDB StackMapTablel ExceptionssetQuerySeqHolder&(Lorg/biojava/bio/seq/db/SequenceDB;)VsetSubjectDBInstallation2(Lorg/biojava/bio/seq/db/SequenceDBInstallation;)V setQueryID(Ljava/lang/String;)V setDatabaseIDgetMoreSearches()ZsetMoreSearches(Z)Vvalue startSearch()V endSearchbeLorg/biojava/bio/BioException; startHeader endHeaderstartHitendHit startSubHit endSubHitaddSearchProperty'(Ljava/lang/Object;Ljava/lang/Object;)VkeyLjava/lang/Object;addHitPropertyaddSubHitPropertymakeHit1()Lorg/biojava/bio/search/SeqSimilaritySearchHit;qSmStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;sSiIscDevpvmixQueryStrandmixSubjectStrandnullQueryStrandnullSubjectStrandqStrandsStrandqStartqEndsStartsEnd subjectIDim makeSubHit4()Lorg/biojava/bio/search/SeqSimilaritySearchSubHit; identifieralpha'Lorg/biojava/bio/symbol/FiniteAlphabet;swapvallabelMap tokenBufferLjava/lang/StringBuffer;7 SourceFileBlastLikeSearchBuilder.java java/util/HashMap ~ |}org/biojava/bio/BioException9Running BlastLikeSearchBuilder with null query SequenceDB HRunning BlastLikeSearchBuilder with null subject SequenceDB installation nojava/lang/StringBuilder9Failed to retrieve query sequence from queryDB using ID ' pq' (sequence was null) rs t uv!org/biojava/bio/seq/db/SequenceDB8Failed to retrieve database from installation using ID '' (database was null)6org/biojava/bio/search/SimpleSeqSimilaritySearchResult wqueryId  databaseIdjava/util/ArrayListx yz { |}~ *Failed to build SeqSimilaritySearchResult:     0org/biojava/bio/search/SeqSimilaritySearchSubHit                subjectId java/lang/String3org/biojava/bio/search/SimpleSeqSimilaritySearchHit  subjectSequenceType }program!Failed to determine sequence type token  queryStrandplus }   subjectStrand queryFrame  subjectFramequerySequenceStart querySequenceEndsubjectSequenceStartsubjectSequenceEndscore  expectValuee1pValueorg/biojava/utils/SmallMapjava/lang/StringBuffer  querySequence  pQuery'org/biojava/bio/symbol/SimpleSymbolList  subjectSequence6org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit&org/biojava/bio/symbol/SimpleAlignment  5org/biojava/bio/program/ssbind/BlastLikeSearchBuilderjava/lang/Object$org/biojava/bio/search/SearchBuilderorg/biojava/bio/seq/Sequence*org/biojava/bio/seq/StrandedFeature$Strand getSequence2(Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;-org/biojava/bio/seq/db/SequenceDBInstallation getSequenceDB;(Ljava/lang/String;)Lorg/biojava/bio/seq/db/SequenceDBLite;(Lorg/biojava/bio/seq/Sequence;Lorg/biojava/bio/seq/db/SequenceDB;Ljava/util/Map;Ljava/util/List;Lorg/biojava/bio/Annotation;)V0org/biojava/bio/program/ssbind/AnnotationFactorymakeAnnotation-(Ljava/util/Map;)Lorg/biojava/bio/Annotation;java/util/Listadd(Ljava/lang/Object;)Zjava/lang/SystemerrLjava/io/PrintStream;java/io/PrintStreamprintlnprintStackTrace java/util/Mapclearput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;size()ItoArray(([Ljava/lang/Object;)[Ljava/lang/Object;byScoreByScoreComparatorDLorg/biojava/bio/search/SeqSimilaritySearchSubHit$ByScoreComparator;java/util/Arrayssort,([Ljava/lang/Object;Ljava/util/Comparator;)VgetScore()D getEValue getPValuegetQueryStrand.()Lorg/biojava/bio/seq/StrandedFeature$Strand;getSubjectStrand getQueryStart getQueryEndgetSubjectStart getSubjectEndjava/lang/Mathmin(II)Imax#org/biojava/bio/seq/StrandedFeatureUNKNOWNget&(Ljava/lang/Object;)Ljava/lang/Object;(DDDIILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;Ljava/lang/String;Lorg/biojava/bio/Annotation;Ljava/util/List;)V containsKey/org/biojava/bio/program/ssbind/AlphabetResolverresolveAlphabet;(Ljava/lang/String;)Lorg/biojava/bio/symbol/FiniteAlphabet;%org/biojava/bio/symbol/FiniteAlphabetgetTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;equalsPOSITIVENEGATIVE startsWith(Ljava/lang/String;)Zjava/lang/IntegerparseInt(Ljava/lang/String;)Ijava/lang/Double parseDouble(Ljava/lang/String;)D(I)Vremove,(Ljava/lang/String;)Ljava/lang/StringBuffer; substring(I)Ljava/lang/String;@(Lorg/biojava/bio/seq/io/SymbolTokenization;Ljava/lang/String;)V(Ljava/util/Map;)V(DDDIILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;Lorg/biojava/bio/symbol/Alignment;Lorg/biojava/bio/Annotation;)VBorg/biojava/bio/search/SeqSimilaritySearchSubHit$ByScoreComparator!yz{|}~;***+*Y*Y*Y*Y " $/:;;d*+ *, *-  *~|}!* Y* Y* *L+& YY** *M,& YY*Y+,*** !. "04Whl 0uh=47 >*+  ~>*+  |}I *+*"+#!" # I *+*$+#'( ) /*- >* 23: *%Y& 7 8  ***' **()WL*+,+- > ?EAC%D)F *\ E*.*.J KL +N G*.*%Y&/R ST =**0)W XY 8 * . ] ^  p*/*1)WL+- difhjQO *+,2W n o   O *+,2W s t   O * +,2W x y   3H3J39**/*/5d67889*9:;*9*9d2<H*9*9d2=J*9*9d2>9666 6 *92?: *92@: *92A6 *92B6*92C6*92D6 6  6 *96*92?:*92@:6 6  6 6 *92AE6 *92BF6*92CE6*92DF6lG: G:  :  : *HIJ:KY')   *'*/L0 .8J\orux{  %(;Natw|~p r^u[xX {U H ; . !%5 + N *M^* NO* NIJL-*PO*PIJL YQ+RM*,STMLM* UO!* UIVW XLYL* ZO!* ZIVW XMYM* [O$* [IJV\ XLYL* ]O$* ]IJV\ XMYM* ^IJ_>* `IJ_6* aIJ_6* bIJ_6+Y 6>6,Y6663939 39 * cO* cIJd9* eO@* eIJ:  f\Yg d9  d9 * hO* hIJd9 iYj: kYl:* mnJoW pqY*Mrs2WkYl:* tnJoW *HIqY*Mrs2WuY  +,vY w* 'x:'5GQVbdft   .ATgnqtx"$%&*+,./13679<='?0B<CPDkGwHIL$DQV q- drfp.ATgoFA < 0 <B' +'**[/C  36PK .*?:$apII5org/biojava/bio/program/ssbind/HSPStAXHandler$1.class2  ()VCodeLineNumberTableLocalVariableTablethis InnerClasses1Lorg/biojava/bio/program/ssbind/HSPStAXHandler$1; getHandlerf(Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;)Lorg/biojava/utils/stax/StAXContentHandler; ssContext9Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter; SourceFileHSPStAXHandler.javaEnclosingMethod -org/biojava/bio/program/ssbind/HSPStAXHandler /org/biojava/bio/program/ssbind/HSPStAXHandler$1java/lang/Object1org/biojava/bio/program/ssbind/StAXHandlerFactory<(Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;)V0 /* (   = Y+ +    PK .*?:_L3org/biojava/bio/program/ssbind/HSPStAXHandler.class2W .034 5 67 89 :; < => ?@ ?AB D EFGHSP_HANDLER_FACTORY3Lorg/biojava/bio/program/ssbind/StAXHandlerFactory;<(Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;)VCodeLineNumberTableLocalVariableTablethis/Lorg/biojava/bio/program/ssbind/HSPStAXHandler; ssContext9Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;handleStartElementQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)VnsURILjava/lang/String; localNameqNameattrsLorg/xml/sax/Attributes; ExceptionsHhandleEndElement9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V()V SourceFileHSPStAXHandler.java I6org/biojava/bio/program/xff/ElementRecognizer$ByNSNameByNSName InnerClasseshttp://www.biojava.org HSPSummary JK L MNBlastLikeAlignmentO P Q RST U+ V+/org/biojava/bio/program/ssbind/HSPStAXHandler$1 + -org/biojava/bio/program/ssbind/HSPStAXHandler7org/biojava/bio/program/ssbind/SeqSimilarityStAXHandlerorg/xml/sax/SAXException-org/biojava/bio/program/xff/ElementRecognizer'(Ljava/lang/String;Ljava/lang/String;)V4org/biojava/bio/program/ssbind/HSPSummaryStAXHandlerHSPSUMMARY_HANDLER_FACTORY addHandlere(Lorg/biojava/bio/program/xff/ElementRecognizer;Lorg/biojava/bio/program/ssbind/StAXHandlerFactory;)V3org/biojava/bio/program/ssbind/AlignmentStAXHandlerALIGNMENT_HANDLER_FACTORY7org/biojava/bio/program/ssbind/SeqSimilarityStAXAdaptergetSearchContentHandler/()Lorg/biojava/bio/search/SearchContentHandler;+org/biojava/bio/search/SearchContentHandler startSubHit endSubHit!j**+*Y*Y 78<)?**c *  G H4  ! "! #! $%&'()Y *  O P*  ! "! #!&'*+# Y&,-2/1 PK .*?:E5mee<org/biojava/bio/program/ssbind/HSPSummaryStAXHandler$1.class2  ()VCodeLineNumberTableLocalVariableTablethis InnerClasses8Lorg/biojava/bio/program/ssbind/HSPSummaryStAXHandler$1; getHandlerf(Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;)Lorg/biojava/utils/stax/StAXContentHandler; ssContext9Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter; SourceFileHSPSummaryStAXHandler.javaEnclosingMethod 4org/biojava/bio/program/ssbind/HSPSummaryStAXHandler 6org/biojava/bio/program/ssbind/HSPSummaryStAXHandler$1java/lang/Object1org/biojava/bio/program/ssbind/StAXHandlerFactory<(Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;)V0 /* (   = Y+ +    PK .*?:T, :org/biojava/bio/program/ssbind/HSPSummaryStAXHandler.class2f ; < =>? @A BCDEFGHIJKLMNOPQRST W XYZHSPSUMMARY_HANDLER_FACTORY3Lorg/biojava/bio/program/ssbind/StAXHandlerFactory;<(Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;)VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/program/ssbind/HSPSummaryStAXHandler; ssContext9Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;handleStartElementQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)VnsURILjava/lang/String; localNameqNameattrsLorg/xml/sax/Attributes;sch-Lorg/biojava/bio/search/SearchContentHandler;attr StackMapTable[\ Exceptions]()V SourceFileHSPSummaryStAXHandler.java  %&^ _`scorea bc[ de expectValuenumberOfIdentities alignmentSizepercentageIdentitybitScorepValuenumberOfPositivesquerySequenceTypehitSequenceTypesubjectSequenceType queryStrand hitStrand subjectStrand queryFramehitFrame subjectFrame6org/biojava/bio/program/ssbind/HSPSummaryStAXHandler$1 InnerClasses 8 4org/biojava/bio/program/ssbind/HSPSummaryStAXHandler7org/biojava/bio/program/ssbind/SeqSimilarityStAXHandler+org/biojava/bio/search/SearchContentHandlerjava/lang/Stringorg/xml/sax/SAXException7org/biojava/bio/program/ssbind/SeqSimilarityStAXAdaptergetSearchContentHandler/()Lorg/biojava/bio/search/SearchContentHandler;org/xml/sax/AttributesgetValue&(Ljava/lang/String;)Ljava/lang/String;addSubHitProperty'(Ljava/lang/Object;Ljava/lang/Object;)V! >*+! 12"#$%&'( r*:     :  : : : ::::::!%: >?-@?BQDcHnIsJ~LMNPQRTUVXYZ\]^abc e+f0g;iFjKkVmanfoqp"Hr#$r)*r+*r,*r-. i/0n1*2 ~345678 # Y!&9:V PK .*?:Fv&UU8org/biojava/bio/program/ssbind/HeaderStAXHandler$1.class2  ()VCodeLineNumberTableLocalVariableTablethis InnerClasses4Lorg/biojava/bio/program/ssbind/HeaderStAXHandler$1; getHandlerf(Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;)Lorg/biojava/utils/stax/StAXContentHandler; ssContext9Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter; SourceFileHeaderStAXHandler.javaEnclosingMethod 0org/biojava/bio/program/ssbind/HeaderStAXHandler 2org/biojava/bio/program/ssbind/HeaderStAXHandler$1java/lang/Object1org/biojava/bio/program/ssbind/StAXHandlerFactory<(Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;)V0 /* ,   = Y+ /    PK .*?:Mq8org/biojava/bio/program/ssbind/HeaderStAXHandler$2.class2*    !"#this$02Lorg/biojava/bio/program/ssbind/HeaderStAXHandler;5(Lorg/biojava/bio/program/ssbind/HeaderStAXHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses4Lorg/biojava/bio/program/ssbind/HeaderStAXHandler$2; getHandlerf(Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;)Lorg/biojava/utils/stax/StAXContentHandler; ssContext9Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter; SourceFileHeaderStAXHandler.javaEnclosingMethod$ %  &Corg/biojava/bio/program/ssbind/HeaderStAXHandler$QueryIDStAXHandlerQueryIDStAXHandler (2org/biojava/bio/program/ssbind/HeaderStAXHandler$2java/lang/Object1org/biojava/bio/program/ssbind/StAXHandlerFactory0org/biojava/bio/program/ssbind/HeaderStAXHandler<(Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;)V()V)i(Lorg/biojava/bio/program/ssbind/HeaderStAXHandler;Lorg/biojava/bio/program/ssbind/HeaderStAXHandler$1;)V2org/biojava/bio/program/ssbind/HeaderStAXHandler$1    4 *+* @   A Y* C  'PK .*?:rT8org/biojava/bio/program/ssbind/HeaderStAXHandler$3.class2*    !"#this$02Lorg/biojava/bio/program/ssbind/HeaderStAXHandler;5(Lorg/biojava/bio/program/ssbind/HeaderStAXHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses4Lorg/biojava/bio/program/ssbind/HeaderStAXHandler$3; getHandlerf(Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;)Lorg/biojava/utils/stax/StAXContentHandler; ssContext9Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter; SourceFileHeaderStAXHandler.javaEnclosingMethod$ %  &Lorg/biojava/bio/program/ssbind/HeaderStAXHandler$QueryDescriptionStAXHandlerQueryDescriptionStAXHandler (2org/biojava/bio/program/ssbind/HeaderStAXHandler$3java/lang/Object1org/biojava/bio/program/ssbind/StAXHandlerFactory0org/biojava/bio/program/ssbind/HeaderStAXHandler<(Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;)V()V)i(Lorg/biojava/bio/program/ssbind/HeaderStAXHandler;Lorg/biojava/bio/program/ssbind/HeaderStAXHandler$1;)V2org/biojava/bio/program/ssbind/HeaderStAXHandler$1    4 *+* J   A Y* M  'PK .*?:{8org/biojava/bio/program/ssbind/HeaderStAXHandler$4.class2*    !"#this$02Lorg/biojava/bio/program/ssbind/HeaderStAXHandler;5(Lorg/biojava/bio/program/ssbind/HeaderStAXHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses4Lorg/biojava/bio/program/ssbind/HeaderStAXHandler$4; 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getAnnotation()Lorg/biojava/bio/Annotation;org/biojava/bio/Annotationkeys()Ljava/util/Set; java/util/Set assertTrue(Z)VgetHits()Ljava/util/List;getScore()D(DDD)V getSubjectID'(Ljava/lang/String;Ljava/lang/String;)V getQueryStart getQueryEndgetQueryStrand.()Lorg/biojava/bio/seq/StrandedFeature$Strand; assertSamegetSubjectStart getSubjectEndgetSubjectStrand#org/biojava/bio/seq/StrandedFeature!EFGHIJKLMNOPQRSTUVWVX\]V^V_\`RaTbVcVd\eVfVg\ hij>*+k JKlmnoTpqjc**Y * Y * YY*L+* +* *Y*+k* OPQ(R3U?YGZO]Z`balcmn?$rstuvwqj;**** * ****k* efhi!j&k+l0m5n:ol ;mntuvxqjY**kstul mntyqj|3**L*  !+"#kyz}2~l3mnz{tuv|qj|3**L*  $+%#k2l3mnz{t}qjK**L+&'(=))k/<Jl Kmn-z{/~Vt'@ @qj **L+*+M*,,-.*,/0*1,2*3,4*5,67*8,9*:,;*<,=7k2 .<IVcp}l mnzz{.jtqj"**L+*M,,d+N*>--.*-/0*?-2*@-4*A-67*B-9*C-;*D-=7k6 %7ER_lyl*mnz{%|P7jtj ?**',*-*1*3*5*8*:* <k*  &,28>l\ ?mn?R?T?V?V?\?V?V?\ tj ?**'>*-*?*@*A*B*C* Dk*  &,28>l\ ?mn?R?T?V?V?\?V?V?\ t[ YZPK /*?:ٻ/^ ^ :org/biojava/bio/program/ssbind/SSBindFasta3_3t08Test.class2 ,J ,K@L *M@33333N *OP QR ST UV *WXY Z[ \] ^ _`a b b *cd Z *e fgh !b fi *j klm &n ko *pq Srs$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis6Lorg/biojava/bio/program/ssbind/SSBindFasta3_3t08Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTabletu ExceptionsvtestResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindFasta3_3t08Test.java /0 89 CISY_ECOLI w{ CISY_RICCN |{2org/biojava/bio/program/ssbind/fasta_3.3t08.out.gz} ~  -.java/lang/AssertionErrorjava/lang/StringBuilder /9 Resource  could not be located /java/util/zip/GZIPInputStreamjava/io/BufferedInputStream / <0org/biojava/bio/program/sax/FastaSearchSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 4org/biojava/bio/program/ssbind/SSBindFasta3_3t08Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/ExceptionsetTopHitValuesStrand InnerClassesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand#org/biojava/bio/seq/StrandedFeature!*,-./01>*+2 ,-34567891 ***    L* +M',#YY+*YY,YN-* -!Y*"#2. 137,;/<;?e@xDFGH3*45/m:7;a;<=>? e@ABCD91[*$%&L+'()2LOP345EFG915*+2(? @HIz xyPK /*?:2k ?org/biojava/bio/program/ssbind/SSBindNCBIblastn2_0_11Test.class2 0N 0O@P QR QS .T@F U  .VW XY Z[ \] .^_` ab cd e fgh i i .jk !a .l mno %i mp .q rst *u rv .wx Zyz$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis;Lorg/biojava/bio/program/ssbind/SSBindNCBIblastn2_0_11Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTable{| Exceptions}testBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindNCBIblastn2_0_11Test.java 34 <=ECGLTA01~  AC068733 8org/biojava/bio/program/ssbind/ncbi_blastn_2.0.11.out.gz   12java/lang/AssertionErrorjava/lang/StringBuilder 3= Resource  could not be located 3java/util/zip/GZIPInputStreamjava/io/BufferedInputStream 3 @.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 9org/biojava/bio/program/ssbind/SSBindNCBIblastn2_0_11Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/Exception#org/biojava/bio/seq/StrandedFeaturePOSITIVEStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;NEGATIVEsetTopHitValuesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand!.012345>*+6 -.789:;<=5' **C F*    L*+M',#YY+*YY, !Y"N-*#$-%Y* &'6. 2486<9=E@oAEGHI7*899m>;Ea?@ABC oDEFGH=5[*()*L++,-6MPQ789IJK=55./6)C @LM QPK /*?:Z >org/biojava/bio/program/ssbind/SSBindNCBIblastn2_2_3Test.class2 0N 0O@P QR QS .T@F U  .VW XY Z[ \] .^_` ab cd e fgh i i .jk !a .l mno %i mp .q rst *u rv .wx Zyz$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis:Lorg/biojava/bio/program/ssbind/SSBindNCBIblastn2_2_3Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTable{| Exceptions}testBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindNCBIblastn2_2_3Test.java 34 <=ECGLTA01~  AC068733 7org/biojava/bio/program/ssbind/ncbi_blastn_2.2.3.out.gz   12java/lang/AssertionErrorjava/lang/StringBuilder 3= Resource  could not be located 3java/util/zip/GZIPInputStreamjava/io/BufferedInputStream 3 @.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 8org/biojava/bio/program/ssbind/SSBindNCBIblastn2_2_3Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/Exception#org/biojava/bio/seq/StrandedFeaturePOSITIVEStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;NEGATIVEsetTopHitValuesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand!.012345>*+6 -.789:;<=5' **C F*    L*+M',#YY+*YY, !Y"N-*#$-%Y* &'6. 2486<9=E@oAEGHI7*899m>;Ea?@ABC oDEFGH=5[*()*L~++,-6MPQ789IJK=55./6)C @LM QPK /*?:Dp p ?org/biojava/bio/program/ssbind/SSBindNCBIblastp2_0_11Test.class2 ,J ,K@xL *M@LN *OP QR ST UV *WXY Z[ \] ^ _`a b b *cd Z *e fgh !b fi *j klm &n ko *pq Srs$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis;Lorg/biojava/bio/program/ssbind/SSBindNCBIblastp2_0_11Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTabletu ExceptionsvtestBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindNCBIblastp2_0_11Test.java /0 89 CISY_ECOLI w{Q9R655 |{8org/biojava/bio/program/ssbind/ncbi_blastp_2.0.11.out.gz} ~  -.java/lang/AssertionErrorjava/lang/StringBuilder /9 Resource  could not be located /java/util/zip/GZIPInputStreamjava/io/BufferedInputStream / <.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 9org/biojava/bio/program/ssbind/SSBindNCBIblastp2_0_11Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/ExceptionsetTopHitValuesStrand InnerClassesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand#org/biojava/bio/seq/StrandedFeature!*,-./01>*+2 ,-34567891 *** s[  L* +M',#YY+*YY,YN-* -!Y*"#2. 137);,<8?b@uD}FGH3*45,m:78a;<}=>? b@ABCD91\ *$%&L+'()2LOP3 45EFG915*+2(? @HIz xyPK /*?:in n >org/biojava/bio/program/ssbind/SSBindNCBIblastp2_2_3Test.class2 ,J ,K@0L *M@f N *OP QR ST UV *WXY Z[ \] ^ _`a b b *cd Z *e fgh !b fi *j klm &n ko *pq Srs$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis:Lorg/biojava/bio/program/ssbind/SSBindNCBIblastp2_2_3Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTabletu ExceptionsvtestBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindNCBIblastp2_2_3Test.java /0 89 CISY_ECOLI w{Q9RBA3 |{7org/biojava/bio/program/ssbind/ncbi_blastp_2.2.3.out.gz} ~  -.java/lang/AssertionErrorjava/lang/StringBuilder /9 Resource  could not be located /java/util/zip/GZIPInputStreamjava/io/BufferedInputStream / <.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 8org/biojava/bio/program/ssbind/SSBindNCBIblastp2_2_3Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/ExceptionsetTopHitValuesStrand InnerClassesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand#org/biojava/bio/seq/StrandedFeature!*,-./01>*+2 ,-34567891 ***  yo  L* +M',#YY+*YY,YN-* -!Y*"#2. 137+;.<:?d@wDFGH3*45.m:7:a;<=>? d@ABCD91\ *$%&L+'()2LOP3 45EFG915*+2(? @HIz xyPK /*?:N ?org/biojava/bio/program/ssbind/SSBindNCBIblastx2_0_11Test.class2 /M /N@xO PQ -R@LS -TU VW XY Z[ -\]^ _` ab c defg X[ h h -ij _ -k lmn $h lo -p qrs )t qu -vw Xxy$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis;Lorg/biojava/bio/program/ssbind/SSBindNCBIblastx2_0_11Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTablez{ Exceptions|testBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindNCBIblastx2_0_11Test.java 23 ;< CISY_ECOLI} ~ Q9R655 8org/biojava/bio/program/ssbind/ncbi_blastx_2.0.11.out.gz   01java/lang/AssertionErrorjava/lang/StringBuilder 2< Resource  could not be located 2java/util/zip/GZIPInputStreamjava/io/BufferedInputStreamncbi_blastx_2.0.11.out.gz 2 ?.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 9org/biojava/bio/program/ssbind/SSBindNCBIblastx2_0_11Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/Exception#org/biojava/bio/seq/StrandedFeaturePOSITIVEStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;setTopHitValuesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand!-/01234>*+5 -.6789:;<4& *** Y[  L* +M',#YY+*YY*  Y!N-*"#-$Y*%&5. 248-<0=<@fAEGHI6*780u=:<i>?@AB fCDEFG<4\ *'()L+*+,5MPQ6 78HIJ<45-.5)B @KL PPK /*?:8p >org/biojava/bio/program/ssbind/SSBindNCBIblastx2_2_3Test.class2 -K -L@0M NO +P@f Q +RS TU VW XY +Z[\ ]^ _` a bcd e e +fg ] +h ijk "e il +m nop 'q nr +st Vuv$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis:Lorg/biojava/bio/program/ssbind/SSBindNCBIblastx2_2_3Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTablewx ExceptionsytestBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindNCBIblastx2_2_3Test.java 01 9: CISY_ECOLIz { Q9RBA3 7org/biojava/bio/program/ssbind/ncbi_blastx_2.2.3.out.gz   ./java/lang/AssertionErrorjava/lang/StringBuilder 0: Resource  could not be located 0java/util/zip/GZIPInputStreamjava/io/BufferedInputStream 0 =.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 8org/biojava/bio/program/ssbind/SSBindNCBIblastx2_2_3Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/Exception#org/biojava/bio/seq/StrandedFeaturePOSITIVEStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;setTopHitValuesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand!+-./012>*+3 -.456789:2 *** "ko  L* +M',#YY+*YY,YN-* !-"Y*#$3. 248/<2=>@hA{EGHI4*562m;8>a<=>?@ hABCDE:2\ *%&'L+()*3MPQ4 56FGH:25+,3)@ @IJ~ |N}PK /*?:dY @org/biojava/bio/program/ssbind/SSBindNCBItblastn2_0_11Test.class2 .L .M@xN OP ,Q@HR OS ,TU VW XY Z[ ,\]^ _` ab c def g g ,hi _ ,j klm #g kn ,o pqr (s pt ,uv Xwx$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis SourceFile SSBindNCBItblastn2_0_11Test.java 12 :;ECGLTA01| } AX065483 9org/biojava/bio/program/ssbind/ncbi_tblastn_2.0.11.out.gz   /0java/lang/AssertionErrorjava/lang/StringBuilder 1; Resource  could not be located 1java/util/zip/GZIPInputStreamjava/io/BufferedInputStream 1 >.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult :org/biojava/bio/program/ssbind/SSBindNCBItblastn2_0_11Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/Exception#org/biojava/bio/seq/StrandedFeatureNEGATIVEStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;setTopHitValuesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VPOSITIVEsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand!,./0123>*+4 -.56789:;3$ **F F* ha)  L*+M',#YY+*YY,Y N-*!"-#Y*$%4. 2483<6=B@lAEGHI5*676m<9Ba=>?@A lBCDEF;3\ *&'(L+)*+4MPQ5 67GHI;35,-4)A @JK ~OPK /*?:- ?org/biojava/bio/program/ssbind/SSBindNCBItblastn2_2_3Test.class2 .L .M@0N OP ,Q@f`R OS ,TU VW XY Z[ ,\]^ _` ab c def g g ,hi _ ,j klm #g kn ,o pqr (s pt ,uv Xwx$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis;Lorg/biojava/bio/program/ssbind/SSBindNCBItblastn2_2_3Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTableyz Exceptions{testBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindNCBItblastn2_2_3Test.java 12 :;ECGLTA01| } AF148483 8org/biojava/bio/program/ssbind/ncbi_tblastn_2.2.3.out.gz   /0java/lang/AssertionErrorjava/lang/StringBuilder 1; Resource  could not be located 1java/util/zip/GZIPInputStreamjava/io/BufferedInputStream 1 >.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 9org/biojava/bio/program/ssbind/SSBindNCBItblastn2_2_3Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/Exception#org/biojava/bio/seq/StrandedFeatureNEGATIVEStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;setTopHitValuesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VPOSITIVEsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand!,./0123>*+4 -.56789:;3# **F F*  yN  L*+M',#YY+*YY,Y N-*!"-#Y*$%4. 2482<5=A@kA~EGHI5*675m<9Aa=>?@A kBCDEF;3\ *&'(L+)*+4MPQ5 67GHI;35,-4)A @JK ~OPK /*?:&H @org/biojava/bio/program/ssbind/SSBindNCBItblastx2_0_11Test.class2 .L .M@4N OP ,Q@PlR OS ,TU VW XY Z[ ,\]^ _` ab c def g g ,hi _ ,j klm #g kn ,o pqr (s pt ,uv Xwx$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis SourceFile SSBindNCBItblastx2_0_11Test.java 12 :;ECGLTA01| }  SSICDGLTP 9org/biojava/bio/program/ssbind/ncbi_tblastx_2.0.11.out.gz   /0java/lang/AssertionErrorjava/lang/StringBuilder 1; Resource  could not be located 1java/util/zip/GZIPInputStreamjava/io/BufferedInputStream 1 >.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult :org/biojava/bio/program/ssbind/SSBindNCBItblastx2_0_11Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/Exception#org/biojava/bio/seq/StrandedFeatureUNKNOWNStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;setTopHitValuesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VPOSITIVEsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand!,./0123>*+4 -.56789:;3( **C F* '   L*+M',#YY+*YY,Y N-*!"-#Y*$%4. 2487<:=F@pAEGHI5*67:m<9Fa=>?@A pBCDEF;3\ *&'(L+)*+4MPQ5 67GHI;35,-4)A @JK ~OPK /*?:s{ ?org/biojava/bio/program/ssbind/SSBindNCBItblastx2_2_3Test.class2 -K -L@4M NO +P@`Q +RS TU VW XY +Z[\ ]^ _` a bcd e e +fg ] +h ijk "e il +m nop 'q nr +st Vuv$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis;Lorg/biojava/bio/program/ssbind/SSBindNCBItblastx2_2_3Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTablewx ExceptionsytestBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindNCBItblastx2_2_3Test.java 01 9:ECGLTA01z { AF110311 8org/biojava/bio/program/ssbind/ncbi_tblastx_2.2.3.out.gz   ./java/lang/AssertionErrorjava/lang/StringBuilder 0: Resource  could not be located 0java/util/zip/GZIPInputStreamjava/io/BufferedInputStream 0 =.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 9org/biojava/bio/program/ssbind/SSBindNCBItblastx2_2_3Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/Exception#org/biojava/bio/seq/StrandedFeatureUNKNOWNStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;setTopHitValuesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand!+-./012>*+3 -.456789:2' **C F* !kN  L* +M',#YY+*YY,YN-* !-"Y*#$3. 2486<9=E@oAEGHI4*569m;8Ea<=>?@ oABCDE:2\ *%&'L+()*3MPQ4 56FGH:25+,3)@ @IJ~ |N}PK /*?:2 =org/biojava/bio/program/ssbind/SSBindWUblastn2_0a19Test.class2 -K -L@%M NO +P@Q +RS TU VW XY +Z[\ ]^ _` a bcd e e +fg ] +h ijk "e il +m nop 'q nr +st Vuv$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis9Lorg/biojava/bio/program/ssbind/SSBindWUblastn2_0a19Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTablewx ExceptionsytestBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindWUblastn2_0a19Test.java 01 9:U51677z { D63874 6org/biojava/bio/program/ssbind/wu_blastn_2.0a19.out.gz   ./java/lang/AssertionErrorjava/lang/StringBuilder 0: Resource  could not be located 0java/util/zip/GZIPInputStreamjava/io/BufferedInputStream 0 =.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 7org/biojava/bio/program/ssbind/SSBindWUblastn2_0a19Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/Exception#org/biojava/bio/seq/StrandedFeaturePOSITIVEStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;setTopHitValuesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand!+-./012>*+3 -.456789:2$ **  *  Mβ  L* +M',#YY+*YY,YN-* !-"Y*#$3. 2483<6=B@lAEGHI4*566m;8Ba<=>?@ lABCDE:2Z*%&'L+()*3MPQ456FGH:25+,3)@ @IJ~ |N}PK /*?:ӛ^7} } =org/biojava/bio/program/ssbind/SSBindWUblastp2_0a19Test.class2 ,J ,K@L *M@N *OP QR ST UV *WXY Z[ \] ^ _`a b b *cd Z *e fgh !b fi *j klm &n ko *pq Srs$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis9Lorg/biojava/bio/program/ssbind/SSBindWUblastp2_0a19Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTabletu ExceptionsvtestBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindWUblastp2_0a19Test.java /0 89sp|P09429|HMG1_HUMAN w{sp|P12682|HMG1_PIG |{6org/biojava/bio/program/ssbind/wu_blastp_2.0a19.out.gz} ~  -.java/lang/AssertionErrorjava/lang/StringBuilder /9 Resource  could not be located /java/util/zip/GZIPInputStreamjava/io/BufferedInputStream / <.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 7org/biojava/bio/program/ssbind/SSBindWUblastp2_0a19Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/ExceptionsetTopHitValuesStrand InnerClassesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand#org/biojava/bio/seq/StrandedFeature!*,-./01>*+2 ,-34567891 ***   L* +M',#YY+*YY,YN-* -!Y*"#2. 137*;-<9?c@vD~FGH3*45-m:79a;<~=>? c@ABCD91Z*$%&L+'()2LOP345EFG915*+2(? @HIz xyPK /*?:f =org/biojava/bio/program/ssbind/SSBindWUblastx2_0a19Test.class2 -K -L@spM NO +P@s Q +RS TU VW XY +Z[\ ]^ _` a bcd e e +fg ] +h ijk "e il +m nop 'q nr +st Vuv$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis9Lorg/biojava/bio/program/ssbind/SSBindWUblastx2_0a19Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTablewx ExceptionsytestBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindWUblastx2_0a19Test.java 01 9:sp|P09429|HMG1_HUMANz { sp|P12682|HMG1_PIG 6org/biojava/bio/program/ssbind/wu_blastx_2.0a19.out.gz   ./java/lang/AssertionErrorjava/lang/StringBuilder 0: Resource  could not be located 0java/util/zip/GZIPInputStreamjava/io/BufferedInputStream 0 =.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 7org/biojava/bio/program/ssbind/SSBindWUblastx2_0a19Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/Exception#org/biojava/bio/seq/StrandedFeaturePOSITIVEStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;setTopHitValuesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand!+-./012>*+3 -.456789:2 ** *    L* +M',#YY+*YY,YN-* !-"Y*#$3. 248.<1==@gAzEGHI4*561m;8=a<=>?@ gABCDE:2Z*%&'L+()*3MPQ456FGH:25+,3)@ @IJ~ |N}PK /*?:Uk >org/biojava/bio/program/ssbind/SSBindWUtblastn2_0a19Test.class2 -K -L@M NO +P@_Q +RS TU VW XY +Z[\ ]^ _` a bcd e e +fg ] +h ijk "e il +m nop 'q nr +st Vuv$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis:Lorg/biojava/bio/program/ssbind/SSBindWUtblastn2_0a19Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTablewx ExceptionsytestBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindWUtblastn2_0a19Test.java 01 9:X12597z { AF025664 7org/biojava/bio/program/ssbind/wu_tblastn_2.0a19.out.gz   ./java/lang/AssertionErrorjava/lang/StringBuilder 0: Resource  could not be located 0java/util/zip/GZIPInputStreamjava/io/BufferedInputStream 0 =.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 8org/biojava/bio/program/ssbind/SSBindWUtblastn2_0a19Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/Exception#org/biojava/bio/seq/StrandedFeaturePOSITIVEStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;setTopHitValuesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand!+-./012>*+3 -.456789:2# **8* /0b  L* +M',#YY+*YY,YN-* !-"Y*#$3. 2482<5=A@kA~EGHI4*565m;8Aa<=>?@ kABCDE:2\ *%&'L+()*3MPQ4 56FGH:25+,3)@ @IJ~ |N}PK /*?:qyH >org/biojava/bio/program/ssbind/SSBindWUtblastx2_0a19Test.class2 -K -L@M NO +P@yQ +RS TU VW XY +Z[\ ]^ _` a bcd e e +fg ] +h ijk "e il +m nop 'q nr +st Vuv$assertionsDisabledZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis:Lorg/biojava/bio/program/ssbind/SSBindWUtblastx2_0a19Test;nameLjava/lang/String;setUp()VresName resStreamLjava/io/InputStream;readerLorg/xml/sax/XMLReader; StackMapTablewx ExceptionsytestBlastResultHitCountresult2Lorg/biojava/bio/search/SeqSimilaritySearchResult; SourceFileSSBindWUtblastx2_0a19Test.java 01 9:U51677z { M64986 7org/biojava/bio/program/ssbind/wu_tblastx_2.0a19.out.gz   ./java/lang/AssertionErrorjava/lang/StringBuilder 0: Resource  could not be located 0java/util/zip/GZIPInputStreamjava/io/BufferedInputStream 0 =.org/biojava/bio/program/sax/BlastLikeSAXParser  org/xml/sax/InputSource  0org/biojava/bio/search/SeqSimilaritySearchResult 8org/biojava/bio/program/ssbind/SSBindWUtblastx2_0a19Test )org/biojava/bio/program/ssbind/SSBindCasejava/lang/Stringjava/io/InputStreamjava/lang/Exception#org/biojava/bio/seq/StrandedFeatureUNKNOWNStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;setTopHitValuesr(DLjava/lang/String;IILorg/biojava/bio/seq/StrandedFeature$Strand;IILorg/biojava/bio/seq/StrandedFeature$Strand;)VsetBotHitValuesjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetClassLoader()Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/Object;)V(Ljava/io/InputStream;)V searchStreamadapter5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;org/xml/sax/XMLReadersetContentHandler(Lorg/xml/sax/ContentHandler;)Vparse(Lorg/xml/sax/InputSource;)V searchResultsLjava/util/List;java/util/Listget(I)Ljava/lang/Object;getHits()Ljava/util/List;size()I assertEquals(II)VdesiredAssertionStatus()Z*org/biojava/bio/seq/StrandedFeature$Strand!+-./012>*+3 -.456789:2$ **  *  {  L* +M',#YY+*YY,YN-* !-"Y*#$3. 2483<6=B@lAEGHI4*566m;8Ba<=>?@ lABCDE:2Z*%&'L+()*3MPQ456FGH:25+,3)@ @IJ~ |N}PK .*?:Tw 9org/biojava/bio/program/ssbind/SeqSimilarityAdapter.class2p VW V XY Z [ \ ] ^ _ ` a b c d e f g h i jklm staxHandler9Lorg/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter;contentHandlerLorg/xml/sax/ContentHandler;()VCodeLineNumberTableLocalVariableTablethis5Lorg/biojava/bio/program/ssbind/SeqSimilarityAdapter;getSearchContentHandler/()Lorg/biojava/bio/search/SearchContentHandler;setSearchContentHandler0(Lorg/biojava/bio/search/SearchContentHandler;)V scHandler-Lorg/biojava/bio/search/SearchContentHandler; startDocument Exceptionsn endDocument characters([CII)Vch[CstartIendignorableWhitespacestartPrefixMapping'(Ljava/lang/String;Ljava/lang/String;)VprefixLjava/lang/String;uriendPrefixMapping(Ljava/lang/String;)VprocessingInstructiontargetdatasetDocumentLocator(Lorg/xml/sax/Locator;)VlocatorLorg/xml/sax/Locator; skippedEntityname startElementQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)VnsURI localNameqNameattrsLorg/xml/sax/Attributes; endElement9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V getProgram()Ljava/lang/String; setProgramprogram SourceFileSeqSimilarityAdapter.java 7org/biojava/bio/program/ssbind/SeqSimilarityStAXAdapter &org/biojava/utils/stax/SAX2StAXAdaptor o  %& '( + . /0 60 78 <= >8 AB E= GH NO PQ R=3org/biojava/bio/program/ssbind/SeqSimilarityAdapterjava/lang/Objectorg/xml/sax/ContentHandlerorg/xml/sax/SAXException.(Lorg/biojava/utils/stax/StAXContentHandler;)V! U**Y*Y*!1234" #$%& 2*!>" #$'( A *+ ! IJ" #$ )*+ 8 * ! N O"  #$,-. 8 * ! S T"  #$,-/0 Y *+ ! X Y"* #$ 12 34 54,-60 Y *+ ! ^ _"* #$ 12 34 54,-78 N *+,! d e"  #$ 9: ;:,-<= C *+! i j" #$ 9:,->8 N *+,! o p"  #$ ?: @:,-AB C *+! t u" #$ CDE= C *+! y z" #$ F:,-GH e*+,-! "4#$I:J:K:LM,-NO Y *+,-!  "* #$ I: J: K:,-PQ 2*!" #$R= A *+! 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SourceFileSimilarityPairBuilder.java qr opjava/util/HashMap gh ih jh *h +hjava/lang/StringBuffer q, mn) -.)org/biojava/bio/seq/db/IllegalIDExceptionjava/lang/StringBuilderAFailed to retrieve annotated query sequence from cache using ID ' /0 ' (unknown ID 12 q 34org/biojava/bio/seq/SequenceCFailed to retrieve annotated subject sequence from cache using ID ' fd 5r rorg/biojava/bio/BioException6 78Failed to build Similarity:9 : ;r <= >? klhitSequenceTypejava/lang/Stringprogram!Failed to determine sequence type@ ABtokenC DEF G queryStrandminusH I. J subjectStrand queryFrame KL subjectFramequerySequenceStartM NOquerySequenceEndsubjectSequenceStartsubjectSequenceEnd Pyunknown Q, querySequence /Rquery'org/biojava/bio/symbol/SimpleSymbolList ST qUsubjectSequencesubjectV WX8org/biojava/bio/seq/homol/SimilarityPairFeature$Template similarity Yd d$org/biojava/bio/symbol/RangeLocation qZ [\ ] ^ _` ab&org/biojava/bio/symbol/SimpleAlignment q? c df/org/biojava/bio/seq/homol/SimilarityPairFeature ghi jkl mn op%org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioErrorNAssertion failure creating SimilarityPairFeature. Template modification vetoed qq4org/biojava/bio/program/ssbind/SimilarityPairBuilder2org/biojava/bio/program/ssbind/ViewSequenceFactory+org/biojava/bio/search/SearchContentHandler*org/biojava/bio/seq/StrandedFeature$Strand java/util/MapqueryViewCachesubjectViewCache(I)V containsKey(Ljava/lang/Object;)Zappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;get&(Ljava/lang/Object;)Ljava/lang/Object;clearjava/lang/SystemerrLjava/io/PrintStream;java/io/PrintStreamprintlnprintStackTraceput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;putAll(Ljava/util/Map;)V/org/biojava/bio/program/ssbind/AlphabetResolverresolveAlphabet;(Ljava/lang/String;)Lorg/biojava/bio/symbol/FiniteAlphabet;%org/biojava/bio/symbol/FiniteAlphabetgetTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;#org/biojava/bio/seq/StrandedFeaturePOSITIVEjava/lang/ObjectequalsNEGATIVE startsWith(Ljava/lang/String;)Zjava/lang/IntegerparseInt(Ljava/lang/String;)ImakeQueryViewSequence setLength,(Ljava/lang/String;)Ljava/lang/StringBuffer; substring(I)Ljava/lang/String;@(Lorg/biojava/bio/seq/io/SymbolTokenization;Ljava/lang/String;)Vjava/lang/Double parseDouble(Ljava/lang/String;)Dtype(II)Vlocation!Lorg/biojava/bio/symbol/Location;strand0org/biojava/bio/program/ssbind/AnnotationFactorymakeAnnotation-(Ljava/util/Map;)Lorg/biojava/bio/Annotation; annotationLorg/biojava/bio/Annotation; alignment createFeaturesE(Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature; setSibling4(Lorg/biojava/bio/seq/homol/SimilarityPairFeature;)V org/biojava/utils/ChangeListener ALWAYS_VETO"Lorg/biojava/utils/ChangeListener;org/biojava/utils/ChangeTypeUNKNOWNLorg/biojava/utils/ChangeType;addChangeListenerC(Lorg/biojava/utils/ChangeListener;Lorg/biojava/utils/ChangeType;)V*(Ljava/lang/String;Ljava/lang/Throwable;)Vt$org/biojava/bio/seq/Feature$Templateorg/biojava/bio/seq/Feature!`abcdeIfdghihjhklmnopqrsO***Y*Y*Y*Y*Y * Y t& c` def*g5h@iNju Ovwxys;*+ #YY+*+to p-tu;vw;fdz-{|ys;* + #YY+* +tz {-u;vw;}dz-{~s>*+t uvwfds/*tu vws>*t uvwprs8 * t  u  vwrs+tu vwrs8 *t  u  vwrs+tu vwrsE**t u vwrs+tu vwrs+tu vwrsr*L+ tu vwzG sO *+,!Wt  u  vw  sO *+,!Wt  u  vw  sO *+,!Wt  u  vw  rsN**"**"*#^*$ *$%L-*& *&%L Y'(+)M*,*+#,L,M*- *-./0L*1 *1./0M*2 *2%.30L*4 *4%.30M*5%6>*7%66*8%66*9%66+0 6>6,0666**::Y:;: *& *&%: * <* *=%>W?@Y*#* AB!W* <* *C%>WD@Y*#* AB!W9 *E *E%F9 GYH:  IJ  K LYMN +O  P *QRGYH:  IJ  K LYMN ,O  P *QRSYT: U U VW: VW:XXYZ[YZ[: ]Y^ _<?\t&I !/AOakp|0CVipsvz    8#;$I%\(e*l+s,-./2456789;<=?BEF"H/J<R?MAOMSu>d^dkdp sd ; e  V:,A Nvw0C Vihz^A ,$''[4  {GW er PK .*?:Q7org/biojava/bio/program/ssbind/StAXHandlerBinding.class2    recognizer/Lorg/biojava/bio/program/xff/ElementRecognizer;factory3Lorg/biojava/bio/program/ssbind/StAXHandlerFactory;e(Lorg/biojava/bio/program/xff/ElementRecognizer;Lorg/biojava/bio/program/ssbind/StAXHandlerFactory;)VCodeLineNumberTableLocalVariableTablethis3Lorg/biojava/bio/program/ssbind/StAXHandlerBinding; SourceFileStAXHandlerBinding.java    1org/biojava/bio/program/ssbind/StAXHandlerBindingjava/lang/Object()V!   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Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.

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Process files as streams of records, each with tags with values.

Overview

Many files in biology are structured as multiple records, each of which can be broken down into lines composed from some tag and an associated value. For example, EMBL files have two letter tags and values extend from column 5 to the end of the line. There are a vast array of files all of which have broadly similar structures, and this package aims to provide a framework within which parsing strategies and data consumers can be reused as much as possible.

The data associated with each record is represented by a stream of events encapsulated by callbacks on the TagValueListener interface. It is up to the user to provide implementations of this interface that build static representations of the data if they so wish.

The Parser and Pushing Sub-Documents

Often file formats have embedded sub-documents. For example, in EMBL format files the feature table area is identical to that in GENBANK files if the first five columns are ignored. In ACeDB files, every time an ace-tag is found, it causes a new sub-document to be induced with its own structure and set of allowed tags and values. Python code uses indent depth to represent code blocks.

Parser allows TagValueListener objects to request that all of the values associated with the current tag should be handled by a new TagValueParser and TagValueListener pair. The Parser instance will use the original TagValueParser to process the line as before, and then take the value that would have been handed to the listener's value method, and present it to the newly registered TagValueParser to tokenize into tag and value portions. That tag and value will then be passed onto the new TagValueListener. The new TagValueListener can itself choose to push a new pair of parser and listener to start a new sub-sub-document. This can be repeated to arbitrary depth. As soon as a parser and listener pair are registered, the pushed listener receives a startRecord() message. Once the entire containing record ends (due to a record separator line such as "//", or because the end of file has been reached), or if the tag that caused the delegation ends, the pushed listener will receive the appropriate endTag() message and also endRecord().

TagDelegator is a useful helper class that always delegates to a given parser and listener pair on a given tag.

Rewriting the Event Stream

Often while parsing, you will need to change tag names or modify values. In the simple case, all the tags and values will be String instances. You will probably want different types, such as the numeric objects (Double, Int and their friends), or to instantiate your own objects from these Strings. Additionaly, some values are themselves better represented as lists of more fundamental items. There are several TagValueListener helper classes that extend TagValueWrapper that allow you to configure a chain of event transducors while writing the minimal amount of code.

TagMapper remaps a sub-set of the tags it sees. For example, it could be configured to replace all "FOO_ID" tags with "accession.number".

ValueChanger intercepts the value() calls for specific tags and uses either a ValueChanger.Changer or ValueChanger.Splitter instance to replace or sub-devide the value before passing it onto another listener.

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  L**Y~&*+M,*+*+YMW,$! &&$ !"#? *+ '   !$%6+&'PK .*?:ZNQ 7org/biojava/bio/program/unigene/SQLUnigeneFactory.class2 "N !O PQR ST !UVW NX Y Z [ \] P[ \^ _` Sa Sb Sc de fgh !i jkl mnopCREATE_DB_STATEMENTLjava/lang/String;()VCodeLineNumberTableLocalVariableTablethis3Lorg/biojava/bio/program/unigene/SQLUnigeneFactory;getCreateDBStatement()Ljava/lang/String; StackMapTable canAccept(Ljava/net/URL;)ZdbURLLjava/net/URL; loadUnigene;(Ljava/net/URL;)Lorg/biojava/bio/program/unigene/UnigeneDB;conPool&Lorg/biojava/utils/JDBCConnectionPool; Exceptions createUnigeneseLjava/sql/SQLException;dbString lastSlashIrootURLdbNameconnPoolstmtLjava/sql/Statement;nqr]sktt SourceFileSQLUnigeneFactory.java &' $%q u.jdbcr vw 01org/biojava/bio/BioExceptionjava/lang/StringBuilder(Can't resolve url to an sql unigene db: xy xz {. &|$org/biojava/utils/JDBCConnectionPool,org/biojava/bio/program/unigene/SQLUnigeneDB &}/ ~ create database s use -. java/sql/SQLExceptionCould not create database &1org/biojava/bio/program/unigene/SQLUnigeneFactoryjava/lang/Object.org/biojava/bio/program/unigene/UnigeneFactory java/net/URLjava/lang/Stringjava/sql/Statementjava/lang/Throwable getProtocolequals(Ljava/lang/Object;)Zappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString(Ljava/lang/String;)V)(Lorg/biojava/utils/JDBCConnectionPool;)V lastIndexOf(Ljava/lang/String;)I substring(II)Ljava/lang/String;(I)Ljava/lang/String; 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StackMapTableA4B ExceptionsC SourceFileUnigeneTools.java D  EFA GHjava/lang/StringI JKB LM NO PQ  RH SHT9org/biojava/bio/program/unigene/UnigeneTools$SplitAndProp6org/biojava/bio/program/tagvalue/SimpleTagValueWrapper1org/biojava/bio/program/tagvalue/TagValueListenerjava/util/regex/Matcher!org/biojava/utils/ParserException6(Lorg/biojava/bio/program/tagvalue/TagValueListener;)V getDelegate5()Lorg/biojava/bio/program/tagvalue/TagValueListener; startRecord()Vjava/util/regex/Patternmatcher3(Ljava/lang/CharSequence;)Ljava/util/regex/Matcher;find()Zgroup(I)Ljava/lang/String;startTag(Ljava/lang/Object;)VendTag endRecord,org/biojava/bio/program/unigene/UnigeneTools Q *+*,      U*N-,:*:-::- -+ - - 6    $,4<EKNTR,4 UU!"U#PD$9%&'()*1+,-.  > PK .*?:}-#-#2org/biojava/bio/program/unigene/UnigeneTools.class2                   #  % ( * * * * * * *    ! =" =# $ %& %'( =)*+ @, @- @. @/ ?01 G2 I 34 L56 789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVX pZ[] s^ _` sab _cdef |hijklmnopqrstuvwxyz|}~  _  HandleMapInterval InnerClasses SplitAndPropUNIGENE_ANNOTATION Lorg/biojava/bio/AnnotationType;LIBRARY_ANNOTATION factoriesLjava/util/List;shortName2SpeciesNameLjava/util/Map;()VCodeLineNumberTableLocalVariableTablethis.Lorg/biojava/bio/program/unigene/UnigeneTools;getSpeciesForShortName&(Ljava/lang/String;)Ljava/lang/String;nameLjava/lang/String;buildDataParserf(Lorg/biojava/bio/program/tagvalue/TagValueListener;)Lorg/biojava/bio/program/tagvalue/ParserListener; 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F4:L+;+<=M,*>,?Y@YABC*DEF&(+   "F  ? GYH4IYJKLYMNOPWQRPWNSPWTUPWVWPWXYPWZ[PW\]PW^_PW`aPWbcPWdePWfgPWhiPWjkPWlmPWnoPWpYqKpYrqLsYtM,u*vw,x*yw,z*yw,{*vw|Y,}NsYt:~*vw*vw|Y}:sYt:*vw*vw*vw*vw+vw|Y}:sYt:x*vw*vw*yw*yw*yw*yw*yw|Y}: sYt:  *vw *vw *vw *vw  *vw YYSYSYSvw *vw *vw -w "w w +vw ! w sYt:  *vw *vw *vw *vw Fb ceg+h8iEjRk_llmynopqrstuvw{|~#-7AJS^it}  )4?JU`z  JSt}TK ) 1 B#  s\ pWY |Wg W{     PK /*?:6,org/biojava/bio/program/unigene/package.html Objects for representing Unigene clusters.

Description

Unigene is a database of ESTs from different organisms and the libraries they were extracted from. This package provides an API for working with Unigene, including the ability to develop your own custom parsers, Objects and Interfaces for representing Unigene records and implementations that index the Unigene download flat files, or an SQL schema.

PK .*?:2z0org/biojava/bio/program/xff/BasicXFFHelper.class2 ()VCodeLineNumberTableLocalVariableTablethis,Lorg/biojava/bio/program/xff/BasicXFFHelper; getFeatureID1(Lorg/biojava/bio/seq/Feature;)Ljava/lang/String;fLorg/biojava/bio/seq/Feature; writeDetailsA(Lorg/biojava/utils/xml/XMLWriter;Lorg/biojava/bio/seq/Feature;)Vxw!Lorg/biojava/utils/xml/XMLWriter; Exceptions SourceFileBasicXFFHelper.java *org/biojava/bio/program/xff/BasicXFFHelperjava/lang/Object%org/biojava/bio/program/xff/XFFHelperjava/io/IOException!/*   6"  ?&  PK .*?:8ffHorg/biojava/bio/program/xff/ElementRecognizer$AllElementRecognizer.class2 ()VCodeLineNumberTableLocalVariableTablethisAllElementRecognizer InnerClassesDLorg/biojava/bio/program/xff/ElementRecognizer$AllElementRecognizer;filterStartElementQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)ZnsURILjava/lang/String; localNameqNameattrsLorg/xml/sax/Attributes;toString()Ljava/lang/String; SourceFileElementRecognizer.java ALLBorg/biojava/bio/program/xff/ElementRecognizer$AllElementRecognizerjava/lang/Object-org/biojava/bio/program/xff/ElementRecognizer!/* 5  T ; 4 - @    PK .*?:qq?org/biojava/bio/program/xff/ElementRecognizer$ByLocalName.class24 " # $%& "' () *+,- localNameLjava/lang/String;(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis ByLocalName InnerClasses;Lorg/biojava/bio/program/xff/ElementRecognizer$ByLocalName;filterStartElementQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)ZnsURIqNameattrsLorg/xml/sax/Attributes;toString()Ljava/lang/String; SourceFileElementRecognizer.java . / 01java/lang/StringBuilderByLocalName[name= 23] 9org/biojava/bio/program/xff/ElementRecognizer$ByLocalNamejava/lang/Object-org/biojava/bio/program/xff/ElementRecognizer()Vjava/lang/Stringequals(Ljava/lang/Object;)Zappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;!   F **+   [ ,*4     FY*   !   PK .*?:j<org/biojava/bio/program/xff/ElementRecognizer$ByNSName.class29 % & ' ()* %+ ,-. /012nsURILjava/lang/String; localName'(Ljava/lang/String;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisByNSName InnerClasses8Lorg/biojava/bio/program/xff/ElementRecognizer$ByNSName;filterStartElementQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)ZqNameattrsLorg/xml/sax/Attributes; StackMapTabletoString()Ljava/lang/String; SourceFileElementRecognizer.java 3  4 56java/lang/StringBuilder ByNSName[uri= 78 name=] !"6org/biojava/bio/program/xff/ElementRecognizer$ByNSNamejava/lang/Object-org/biojava/bio/program/xff/ElementRecognizer()Vjava/lang/Stringequals(Ljava/lang/Object;)Zappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;! Y**+*,ef gh y,*+*o4 @!"R(Y* *  t (#$   PK .*?:cI@org/biojava/bio/program/xff/ElementRecognizer$HasAttribute.class27 % & '() %* +, -./0 attributeNameLjava/lang/String;(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis HasAttribute InnerClasses()VCodeLineNumberTable SourceFileElementRecognizer.javaBorg/biojava/bio/program/xff/ElementRecognizer$AllElementRecognizer  -org/biojava/bio/program/xff/ElementRecognizerjava/lang/Object9org/biojava/bio/program/xff/ElementRecognizer$ByLocalName6org/biojava/bio/program/xff/ElementRecognizer$ByNSName:org/biojava/bio/program/xff/ElementRecognizer$HasAttribute# Y3"    PK /*?:m,,2org/biojava/bio/program/xff/FeatureHandler$1.class2  ()VCodeLineNumberTableLocalVariableTablethis InnerClasses.Lorg/biojava/bio/program/xff/FeatureHandler$1;getPartHandler_(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;)Lorg/biojava/utils/stax/StAXContentHandler;xffenv2Lorg/biojava/bio/program/xff/XFFFeatureSetHandler; SourceFileFeatureHandler.javaEnclosingMethod *org/biojava/bio/program/xff/FeatureHandler ,org/biojava/bio/program/xff/FeatureHandler$1java/lang/Object1org/biojava/bio/program/xff/XFFPartHandlerFactory5(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;)V0 /* H   = Y+ J    PK /*?:K1))2org/biojava/bio/program/xff/FeatureHandler$2.class23     !"#$this$0,Lorg/biojava/bio/program/xff/FeatureHandler;/(Lorg/biojava/bio/program/xff/FeatureHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses.Lorg/biojava/bio/program/xff/FeatureHandler$2;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileFeatureHandler.javaEnclosingMethod% &'  ( )+, -.0 1,org/biojava/bio/program/xff/FeatureHandler$2/org/biojava/utils/stax/StringElementHandlerBase*org/biojava/bio/program/xff/FeatureHandlergetTypeHandler-()Lorg/biojava/utils/stax/StAXContentHandler;()VgetFeatureTemplateTemplate(()Lorg/biojava/bio/seq/Feature$Template;java/lang/Stringtrim()Ljava/lang/String;2$org/biojava/bio/seq/Feature$Templatetypeorg/biojava/bio/seq/Feature    4 *+* -   G*+ /0!/* PK /*?:;$a--2org/biojava/bio/program/xff/FeatureHandler$3.class23     !"#$this$0,Lorg/biojava/bio/program/xff/FeatureHandler;/(Lorg/biojava/bio/program/xff/FeatureHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses.Lorg/biojava/bio/program/xff/FeatureHandler$3;setStringValue(Ljava/lang/String;)VsLjava/lang/String; SourceFileFeatureHandler.javaEnclosingMethod% &'  ( )+, -.0 1,org/biojava/bio/program/xff/FeatureHandler$3/org/biojava/utils/stax/StringElementHandlerBase*org/biojava/bio/program/xff/FeatureHandlergetSourceHandler-()Lorg/biojava/utils/stax/StAXContentHandler;()VgetFeatureTemplateTemplate(()Lorg/biojava/bio/seq/Feature$Template;java/lang/Stringtrim()Ljava/lang/String;2$org/biojava/bio/seq/Feature$Templatesourceorg/biojava/bio/seq/Feature    4 *+* 5   G*+ 78!/* PK /*?:0gx2org/biojava/bio/program/xff/FeatureHandler$4.class2; % &' () #*+,- ./0this$0,Lorg/biojava/bio/program/xff/FeatureHandler;/(Lorg/biojava/bio/program/xff/FeatureHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses.Lorg/biojava/bio/program/xff/FeatureHandler$4;setStringValue(Ljava/lang/String;)VexLjava/lang/Exception;sLjava/lang/String; StackMapTable+ Exceptions SourceFileFeatureHandler.javaEnclosingMethod1 23 4org.biojava.bio.program.xff.id5 67 89java/lang/Exceptionorg/xml/sax/SAXExceptionCouldn't set property :,org/biojava/bio/program/xff/FeatureHandler$4/org/biojava/utils/stax/StringElementHandlerBase*org/biojava/bio/program/xff/FeatureHandlergetOldIDHandler-()Lorg/biojava/utils/stax/StAXContentHandler;()Vjava/lang/Stringtrim()Ljava/lang/String;setFeatureProperty'(Ljava/lang/Object;Ljava/lang/Object;)V*(Ljava/lang/String;Ljava/lang/Exception;)V  4 *+*=  *+MY,  B ECDF  P  !"#$  PK /*?:+2org/biojava/bio/program/xff/FeatureHandler$5.class2-     !this$0,Lorg/biojava/bio/program/xff/FeatureHandler;/(Lorg/biojava/bio/program/xff/FeatureHandler;)VCodeLineNumberTableLocalVariableTablethis InnerClasses.Lorg/biojava/bio/program/xff/FeatureHandler$5;setLocationValue$(Lorg/biojava/bio/symbol/Location;)Vl!Lorg/biojava/bio/symbol/Location; SourceFileFeatureHandler.javaEnclosingMethod" #$  % &(* +,org/biojava/bio/program/xff/FeatureHandler$5/org/biojava/bio/program/xff/LocationHandlerBase*org/biojava/bio/program/xff/FeatureHandlergetLocationHandler-()Lorg/biojava/utils/stax/StAXContentHandler;()VgetFeatureTemplateTemplate(()Lorg/biojava/bio/seq/Feature$Template;,$org/biojava/bio/seq/Feature$Templatelocationorg/biojava/bio/seq/Feature   4 *+* K   D *+ M N   )' PK /*?:A40org/biojava/bio/program/xff/FeatureHandler.class2 E D D D D D D  D D        {  D ' D  D D D D '  D 9 ; = ? A DFEATURE_HANDLER_FACTORY3Lorg/biojava/bio/program/xff/XFFPartHandlerFactory;xffenv2Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;templateTemplate InnerClasses&Lorg/biojava/bio/seq/Feature$Template; startFiredZendFiredlevelI5(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;)VCodeLineNumberTableLocalVariableTablethis,Lorg/biojava/bio/program/xff/FeatureHandler;getXFFEnvironment4()Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;getFeatureTemplate(()Lorg/biojava/bio/seq/Feature$Template; StackMapTablecreateFeatureTemplatefireStartFeature()Vma!Lorg/biojava/bio/MergeAnnotation;cve'Lorg/biojava/utils/ChangeVetoException;templannLorg/biojava/bio/Annotation;origres ExceptionsfireEndFeaturesetFeatureProperty'(Ljava/lang/Object;Ljava/lang/Object;)VftkeyLjava/lang/Object;value startElement{(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;Lorg/biojava/utils/stax/DelegationManager;)VexLjava/lang/Exception;idLjava/lang/String;'Lorg/biojava/bio/seq/io/ParseException;nsURI localNameqNameattrsLorg/xml/sax/Attributes;dm*Lorg/biojava/utils/stax/DelegationManager; endElementd(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/utils/stax/StAXContentHandler;)Vhandler+Lorg/biojava/utils/stax/StAXContentHandler;getTypeHandler-()Lorg/biojava/utils/stax/StAXContentHandler;getSourceHandlergetOldIDHandlergetLocationHandler SourceFileFeatureHandler.java Sa JM NO PO QR HI _]$org/biojava/bio/seq/Feature$Template%org/biojava/bio/seq/io/ParseException:startFeature event has already been fired for this feature S \] Z[ horg/biojava/bio/MergeAnnotation %org/biojava/utils/ChangeVetoException"org/biojava/utils/AssertionFailure Sorg/biojava/bio/SmallAnnotation!org/biojava/bio/OverlayAnnotation S  5startFeature has not yet been fired for this feature.8endFeature event has already been fired for this feature a r r org.biojava.bio.program.xff.id qrjava/lang/Exceptionorg/xml/sax/SAXExceptionCouldn't set property Stype  source location details `a S  featureSet pa,org/biojava/bio/program/xff/FeatureHandler$2 S,org/biojava/bio/program/xff/FeatureHandler$3,org/biojava/bio/program/xff/FeatureHandler$4,org/biojava/bio/program/xff/FeatureHandler$5,org/biojava/bio/program/xff/FeatureHandler$1 FG*org/biojava/bio/program/xff/FeatureHandler-org/biojava/utils/stax/StAXContentHandlerBaseorg/biojava/bio/Annotationjava/lang/Stringorg/xml/sax/Attributes(org/biojava/utils/stax/DelegationManagerorg/biojava/bio/seq/Feature(Ljava/lang/String;)V0org/biojava/bio/program/xff/XFFFeatureSetHandlergetMergeAnnotation()Lorg/biojava/bio/Annotation; annotation addAnnotation(Lorg/biojava/bio/Annotation;)V(Ljava/lang/Throwable;)VgetFeatureListener(()Lorg/biojava/bio/seq/io/SeqIOListener;$org/biojava/bio/seq/io/SeqIOListener startFeature)(Lorg/biojava/bio/seq/Feature$Template;)V endFeatureaddFeatureProperty setPropertygetValue&(Ljava/lang/String;)Ljava/lang/String;*(Ljava/lang/String;Ljava/lang/Exception;)Vequals(Ljava/lang/Object;)Zdelegate.(Lorg/biojava/utils/stax/StAXContentHandler;)V(Ljava/lang/Exception;)VgetDetailsHandler1()Lorg/biojava/utils/stax/StAXContentHandlerBase;/(Lorg/biojava/bio/program/xff/FeatureHandler;)V!DEFGHIJMNOPOQRSTUj******+VXO PQRYZWXYHIZ[U/*VbW XY\]UO* ***VlmoW XY^_]U2Y VxW XY`aU* Y * L*M+N:,2-.Y:+,: :Y, ,: --:Y:Y:+*+*.JMVf#&.7@FJMOY]cgjo{WH7bcO deXYfMgh#|ih&yjh^!;klmmmn  o paU4* Y * Y **V".3W 4XY^o qrU;**+, %* N--Y-+,!V$/:W*sM;XY;tu;vu^ l o wxUP*Y`*/"#:*$%:'Y(),*+*,-,.+*/-,0+*1-|,"+*2-e,3+.**4:'Y5*6-1,7+(**4:'Y5*-"*-& V "*-/;>GU^lu Wf / yz{| y} y}XY~|||^5 -k V V o'U7*Yd*(**4**8:'Y5'* V*   ##$'(*&,'6*W>, y}7XY7~|7|7|7^  B o'U3 9Y*:V-W  XYU3 ;Y*<V5W  XYU3 =Y*>V=W  XYU3 ?Y*@VKW  XYaU# AYBCVHL2K 9;=?APK .*?:447*U U 5org/biojava/bio/program/xff/LocationHandlerBase.class2j @ A BC D' EFG HIJKL MN OP Q BRST U VWXlevelIlocation!Lorg/biojava/bio/symbol/Location;()VCodeLineNumberTableLocalVariableTablethis1Lorg/biojava/bio/program/xff/LocationHandlerBase; startElement{(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;Lorg/biojava/utils/stax/DelegationManager;)VstartsLjava/lang/String;stopsspanex!Ljava/lang/NumberFormatException;nsURI localNameqNameattrsLorg/xml/sax/Attributes;dm*Lorg/biojava/utils/stax/DelegationManager; StackMapTableYWZ[S Exceptions endElementd(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/utils/stax/StAXContentHandler;)Vhandler+Lorg/biojava/utils/stax/StAXContentHandler;setLocationValue$(Lorg/biojava/bio/symbol/Location;)V SourceFileLocationHandlerBase.java  \ ] Y ^_startZ `astoporg/xml/sax/SAXException-Missing start/stop attribute in location span b$org/biojava/bio/symbol/RangeLocationc de f ghjava/lang/NumberFormatExceptionError parsing location i <=/org/biojava/bio/program/xff/LocationHandlerBase-org/biojava/utils/stax/StAXContentHandlerBasejava/lang/Stringorg/xml/sax/Attributes(org/biojava/utils/stax/DelegationManagerorg/biojava/bio/symbol/Locationemptyequals(Ljava/lang/Object;)ZgetValue&(Ljava/lang/String;)Ljava/lang/String;(Ljava/lang/String;)Vjava/lang/IntegerparseInt(Ljava/lang/String;)I(II)VunionD(Lorg/biojava/bio/symbol/Location;)Lorg/biojava/bio/symbol/Location;*(Ljava/lang/String;Ljava/lang/Exception;)V!C***() *  !"#g {*Y`*i,`: : Y Y:**: Yil6 3 479(:3<==G@ZBiElCnDzHf (A$%36&%Z'n (){ !{*%{+%{,%{-.{/01*(22 $3222456 7 89*Yd* **P QRT4 !*%+%,%:;17 <=7 >?PK .*?:%%y885org/biojava/bio/program/xff/PropDetailHandler$1.class2  ()VCodeLineNumberTableLocalVariableTablethis InnerClasses1Lorg/biojava/bio/program/xff/PropDetailHandler$1;getPartHandler_(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;)Lorg/biojava/utils/stax/StAXContentHandler;xffenv2Lorg/biojava/bio/program/xff/XFFFeatureSetHandler; SourceFilePropDetailHandler.javaEnclosingMethod -org/biojava/bio/program/xff/PropDetailHandler /org/biojava/bio/program/xff/PropDetailHandler$1java/lang/Object1org/biojava/bio/program/xff/XFFPartHandlerFactory5(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;)V0 /* (   = Y+ *    PK .*?:S3org/biojava/bio/program/xff/PropDetailHandler.class2T 5 6 78 9:; < = >? @AB CD 5 GHIPROPDETAIL_HANDLER_FACTORY3Lorg/biojava/bio/program/xff/XFFPartHandlerFactory;keyLjava/lang/String;xffenv2Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;5(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;)VCodeLineNumberTableLocalVariableTablethis/Lorg/biojava/bio/program/xff/PropDetailHandler; startElement{(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;Lorg/biojava/utils/stax/DelegationManager;)VnsURI localNameqNameattrsLorg/xml/sax/Attributes;dm*Lorg/biojava/utils/stax/DelegationManager; StackMapTable ExceptionssetStringValue(Ljava/lang/String;)Vpex'Lorg/biojava/bio/seq/io/ParseException;sB()V SourceFilePropDetailHandler.java 2 J KL org/xml/sax/SAXExceptionNo key attribute for xff:prop , !M NOP QR%org/biojava/bio/seq/io/ParseException S/org/biojava/bio/program/xff/PropDetailHandler$1 InnerClasses -org/biojava/bio/program/xff/PropDetailHandler/org/biojava/utils/stax/StringElementHandlerBaseorg/xml/sax/AttributesgetValue&(Ljava/lang/String;)Ljava/lang/String;0org/biojava/bio/program/xff/XFFFeatureSetHandlergetFeatureListener(()Lorg/biojava/bio/seq/io/SeqIOListener;$org/biojava/bio/seq/io/SeqIOListeneraddFeatureProperty'(Ljava/lang/Object;Ljava/lang/Object;)V(Ljava/lang/Exception;)V!F **+23 4   !*** Y*+,- = >?A)B>**"*#*$*%&*'()*+,* *+  MY,  HKIJL  -./)T0 *12# Y(34F PK .*?:00org/biojava/bio/program/xff/PropertyWriter.class2\ . /0 12 34 56 578 19:; <= <> <? <@AB()VCodeLineNumberTableLocalVariableTablethis,Lorg/biojava/bio/program/xff/PropertyWriter; writeDetailsA(Lorg/biojava/utils/xml/XMLWriter;Lorg/biojava/bio/seq/Feature;)VkeyLjava/lang/Object;valueaiLjava/util/Iterator;xw!Lorg/biojava/utils/xml/XMLWriter;fLorg/biojava/bio/seq/Feature;aLorg/biojava/bio/Annotation; StackMapTableCDE ExceptionsF SourceFilePropertyWriter.java G HIC JKL MND OP QRjava/lang/String ST'http://www.biojava.org/2001/xff-biojavapropU VW XW YZ [W*org/biojava/bio/program/xff/PropertyWriter*org/biojava/bio/program/xff/BasicXFFHelperorg/biojava/bio/Annotationjava/util/Iteratorjava/lang/Objectjava/io/IOExceptionorg/biojava/bio/seq/Feature getAnnotation()Lorg/biojava/bio/Annotation;keys()Ljava/util/Set; java/util/Setiterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object; getProperty&(Ljava/lang/Object;)Ljava/lang/Object;org/biojava/utils/xml/XMLWriteropenTag'(Ljava/lang/String;Ljava/lang/String;)V attributeprint(Ljava/lang/String;)VcloseTag!/*! 1w,N-:[:-:+  +  ++  :$%&''/(2)<*D+G.Q/^0i1s2v3H'L<7bww !w"#p$%&'()).*+,-PK /*?:h]LL:org/biojava/bio/program/xff/StrandedFeatureHandler$1.class2  ()VCodeLineNumberTableLocalVariableTablethis InnerClasses6Lorg/biojava/bio/program/xff/StrandedFeatureHandler$1;getPartHandler_(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;)Lorg/biojava/utils/stax/StAXContentHandler;xffenv2Lorg/biojava/bio/program/xff/XFFFeatureSetHandler; SourceFileStrandedFeatureHandler.javaEnclosingMethod 2org/biojava/bio/program/xff/StrandedFeatureHandler 4org/biojava/bio/program/xff/StrandedFeatureHandler$1java/lang/Object1org/biojava/bio/program/xff/XFFPartHandlerFactory5(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;)V0 /* 0   = Y+ 2    PK /*?:|\x x 8org/biojava/bio/program/xff/StrandedFeatureHandler.class2k @ AC D EF GH IJ KL BM NO BP BQ RS D UVW inFeatureZSTRANDEDFEATURE_HANDLER_FACTORY3Lorg/biojava/bio/program/xff/XFFPartHandlerFactory;5(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;)VCodeLineNumberTableLocalVariableTablethis4Lorg/biojava/bio/program/xff/StrandedFeatureHandler;xffenv2Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;createFeatureTemplateYTemplate InnerClasses(()Lorg/biojava/bio/seq/Feature$Template;getStrandedFeatureTemplate0()Lorg/biojava/bio/seq/StrandedFeature$Template; startElement{(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;Lorg/biojava/utils/stax/DelegationManager;)VstrandsLjava/lang/String;ft.Lorg/biojava/bio/seq/StrandedFeature$Template;nsURI localNameqNameattrsLorg/xml/sax/Attributes;dm*Lorg/biojava/utils/stax/DelegationManager; StackMapTableZC Exceptions[()V SourceFileStrandedFeatureHandler.java  \,org/biojava/bio/seq/StrandedFeature$Template = ]'strand^ _` ()+Z ab cf Ff- gf hf *+4org/biojava/bio/program/xff/StrandedFeatureHandler$1 2org/biojava/bio/program/xff/StrandedFeatureHandler*org/biojava/bio/program/xff/FeatureHandleri$org/biojava/bio/seq/Feature$Templatejava/lang/Stringorg/xml/sax/SAXException#org/biojava/bio/seq/StrandedFeaturegetFeatureTemplateorg/xml/sax/AttributesgetValue&(Ljava/lang/String;)Ljava/lang/String;equals(Ljava/lang/Object;)ZPOSITIVEjStrand,Lorg/biojava/bio/seq/StrandedFeature$Strand;NEGATIVEUNKNOWNorg/biojava/bio/seq/Feature*org/biojava/bio/seq/StrandedFeature$Strand!G *+*7. 8  !"#'2Y;  ()2*?  *+"k*[:*:8  +    **+,-6 ILMNO'P2Q<RGTRWZZ__j`RM,-G./k k0-k1-k2-k34k567289 :;<=# Y0>?&"$X% B% dBePK .*?:E\  8org/biojava/bio/program/xff/XFFFeatureSetHandler$1.class2   SourceFileXFFFeatureSetHandler.javaEnclosingMethod 2org/biojava/bio/program/xff/XFFFeatureSetHandler$1 InnerClassesjava/lang/Object0org/biojava/bio/program/xff/XFFFeatureSetHandler  PK .*?:if >org/biojava/bio/program/xff/XFFFeatureSetHandler$Binding.class27 $ % & '( %) * +,- .01 recognizer/Lorg/biojava/bio/program/xff/ElementRecognizer;handlerFactory3Lorg/biojava/bio/program/xff/XFFPartHandlerFactory;this$02Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;Lorg/biojava/bio/program/xff/ElementRecognizer;Lorg/biojava/bio/program/xff/XFFPartHandlerFactory;)VCodeLineNumberTableLocalVariableTablethisBinding InnerClasses:Lorg/biojava/bio/program/xff/XFFFeatureSetHandler$Binding;erhftoString()Ljava/lang/String; SourceFileXFFFeatureSetHandler.java  2  java/lang/StringBuilder Binding[rec= 34 35 fact=] !68org/biojava/bio/program/xff/XFFFeatureSetHandler$Bindingjava/lang/Object()Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;0org/biojava/bio/program/xff/XFFFeatureSetHandler ^*+**,*-   !R(Y*  *    ("#  /PK .*?:88 Horg/biojava/bio/program/xff/XFFFeatureSetHandler$XFFDetailsHandler.class2i 8 9 :; <= >? @A @BC D EF G HI JKLMthis$02Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;5(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;)VCodeLineNumberTableLocalVariableTablethisXFFDetailsHandler InnerClassesDLorg/biojava/bio/program/xff/XFFFeatureSetHandler$XFFDetailsHandler; startElement{(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;Lorg/biojava/utils/stax/DelegationManager;)VbBinding:Lorg/biojava/bio/program/xff/XFFFeatureSetHandler$Binding;iInsURILjava/lang/String; localNameqNameattrsLorg/xml/sax/Attributes;dm*Lorg/biojava/utils/stax/DelegationManager; StackMapTable ExceptionsN endElement9(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)VOi(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;Lorg/biojava/bio/program/xff/XFFFeatureSetHandler$1;)Vx0x14Lorg/biojava/bio/program/xff/XFFFeatureSetHandler$1; SourceFileXFFFeatureSetHandler.java   PdetailsQ RST UVW XY Z[8org/biojava/bio/program/xff/XFFFeatureSetHandler$Binding \]^ _` abc def ghBorg/biojava/bio/program/xff/XFFFeatureSetHandler$XFFDetailsHandler-org/biojava/utils/stax/StAXContentHandlerBaseorg/xml/sax/SAXException2org/biojava/bio/program/xff/XFFFeatureSetHandler$1()Vjava/lang/Stringequals(Ljava/lang/Object;)Z0org/biojava/bio/program/xff/XFFFeatureSetHandler access$100D(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;)Ljava/util/List;java/util/Listsize()Iget(I)Ljava/lang/Object; recognizer/Lorg/biojava/bio/program/xff/ElementRecognizer;-org/biojava/bio/program/xff/ElementRecognizerfilterStartElementQ(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/xml/sax/Attributes;)ZhandlerFactory3Lorg/biojava/bio/program/xff/XFFPartHandlerFactory;1org/biojava/bio/program/xff/XFFPartHandlerFactorygetPartHandler_(Lorg/biojava/bio/program/xff/XFFFeatureSetHandler;)Lorg/biojava/utils/stax/StAXContentHandler;(org/biojava/utils/stax/DelegationManagerdelegate.(Lorg/biojava/utils/stax/StAXContentHandler;)V 4 *+*  a,*d6D* : +,-  * & 2DYZ`R2( F!"aa#$a%$a&$a'(a)*+  ?,-./_ ,  *  #$ %$ &$+ 2D*+ 34567> >0>PK .*?:cl6org/biojava/bio/program/xff/XFFFeatureSetHandler.class2 +n ,op o +q rs +t uv wx +yz| } ~ } + +    u   "o " " !} ) InnerClassesXFFDetailsHandlerBindingPROPERTY_XFF_IDLjava/lang/String; 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XFF is an experimental format, and both the format and the APIs in this package may change in the future.

The main class in this package is XFFFeatureSetHandler, which is intended as a content handler for XFF featureSet elements. By default, this class handles the XFF feature and strandedFeature types. Any other feature types are treated as one of these. It is, however, possible to plug in additional handlers to cope with sub-types of feature. The only detail type recognized is xff:prop -- all others are silently ignored. But again, it is easy to plug in extra StAX handlers for other detail types.

When writing a handler, for a new feature type, you will normally want to sub-class the existing FeatureHandler or StrandedFeatureHanlder classes.

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YL**M,},N:-6666*9,*,:6+YW6,N*+ W@V *-58 ; G P S^gw }Af >?c8c8*mOP-jdP5be88_f8;\g8UVBCh<\Ai_& ji_kk8ji_`lm?G!Y"M,#*$%&Y'N-()-**+,-+--,.*-/W@& #$&(&*1,6.;0F2A*GBCGOP?no(ps`at>?0(@[uvr &q PK .*?:l=  7org/biojava/bio/proteomics/IsoelectricPointCalc$1.class2   SourceFileIsoelectricPointCalc.javaEnclosingMethod 1org/biojava/bio/proteomics/IsoelectricPointCalc$1 InnerClassesjava/lang/Object/org/biojava/bio/proteomics/IsoelectricPointCalc  PK .*?:S Forg/biojava/bio/proteomics/IsoelectricPointCalc$ChargeCalculator.class2 ` a !b c d e f g h ijk b lm lno pq rs rtu v w rx ry zj{ |@$ }~ p pcountsLjava/util/Map;NtermLorg/biojava/bio/symbol/Symbol;Cterm hasFreeNTermZ hasFreeCTermthis$01Lorg/biojava/bio/proteomics/IsoelectricPointCalc;Y(Lorg/biojava/bio/proteomics/IsoelectricPointCalc;Lorg/biojava/bio/symbol/SymbolList;ZZ)VCodeLineNumberTableLocalVariableTablethisChargeCalculator InnerClassesBLorg/biojava/bio/proteomics/IsoelectricPointCalc$ChargeCalculator;peptide#Lorg/biojava/bio/symbol/SymbolList; residueCount4(Lorg/biojava/bio/symbol/SymbolList;)Ljava/util/Map;currCountAsIntI currCountLjava/lang/Integer;symresiduesLjava/util/Iterator; symbolCounts StackMapTableoucompute(D)DcrDpKcountisAcidvalueLjava/lang/Double;pHchargeaaI{(Lorg/biojava/bio/proteomics/IsoelectricPointCalc;Lorg/biojava/bio/symbol/SymbolList;ZZLorg/biojava/bio/proteomics/IsoelectricPointCalc$1;)Vx0x1x2x3x43Lorg/biojava/bio/proteomics/IsoelectricPointCalc$1; SourceFileIsoelectricPointCalc.java -. +, - #$ %& '& () *) 89 java/util/HashMap org/biojava/bio/symbol/Symbol  java/lang/Integer - java/lang/Double  @org/biojava/bio/proteomics/IsoelectricPointCalc$ChargeCalculatorjava/lang/Object$org/biojava/utils/math/ComputeObjectjava/util/Iterator java/util/Map1org/biojava/bio/proteomics/IsoelectricPointCalc$1()V!org/biojava/bio/symbol/SymbolListiterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object;/org/biojava/bio/proteomics/IsoelectricPointCalc access$000()Ljava/util/Map; containsKey(Ljava/lang/Object;)Zget&(Ljava/lang/Object;)Ljava/lang/Object;intValue()I(I)Vput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;keySet()Ljava/util/Set; java/util/Set doubleValue()Djava/lang/Mathpow(DD)D access$100 access$200! !"#$%&'&()*)+,-./7*+********, **0* m ghijk"n+o0p6q1*7257677()7*)89/S+ M Y N, |,:* *,  *E-:"6-YW-YW-0>xz|}#~0?LY^ez}1He:;Y5<=#k>&2567?@A$BCD E=FGH/J*: ::f9*9 6  !w9'g9 )  cogJ'g9 )  cocJs*5*:9'g9 ) cocJ*6*: w9'g9 ) cogJ)0z(7<CWekp| 1| IJ IJ C\KJWHLJ e:M) (w>&7hNOKJ IJ !NOKJ IJ "NO25PJQJR@B8COSCET@%SC89-W/f *+,0e1> 25 X, Y7 Z) [) \]^_4 p3UpPK .*?:"5org/biojava/bio/proteomics/IsoelectricPointCalc.class2 %r %s %t 1uv wxEy wz {| }~ } ?zG{   w  % % %    "u % %u %@Y @,?6C- /u InnerClassesChargeCalculatorPH_MINDPH_MAXEPSI pK_NtermCacheLjava/util/Map;pKCache pK_CtermCache calculator1Lorg/biojava/bio/proteomics/IsoelectricPointCalc;()VCodeLineNumberTableLocalVariableTablepKise/Lorg/biojava/bio/symbol/IllegalSymbolException;symLorg/biojava/bio/symbol/Symbol;this PK_NtermTable,Lorg/biojava/bio/symbol/SymbolPropertyTable;pKTable PK_CtermTableaaSymsLjava/util/Iterator; StackMapTablegetPI((Lorg/biojava/bio/symbol/SymbolList;ZZ)Dex2Lorg/biojava/bio/BioException;ex computeObj&Lorg/biojava/utils/math/ComputeObject;pIpeptide#Lorg/biojava/bio/symbol/SymbolList; hasFreeNTermZ hasFreeCTerm ExceptionsgetIsoelectricPoint&(Lorg/biojava/bio/symbol/SymbolList;)Dpi access$000()Ljava/util/Map; access$100 access$200 SourceFileIsoelectricPointCalc.java =; :; <; @ApK_Nterm pK_Cterm   org/biojava/bio/symbol/Symbol  java/lang/Double @ -org/biojava/bio/symbol/IllegalSymbolException @org/biojava/bio/proteomics/IsoelectricPointCalc$ChargeCalculator @ 67 87 97 org/biojava/bio/BioExceptionFError, the peptide probably contains only positive or negative charges @ /org/biojava/bio/symbol/IllegalAlphabetException >?/org/biojava/bio/proteomics/IsoelectricPointCalc WX java/util/HashMapjava/lang/Object1org/biojava/bio/proteomics/IsoelectricPointCalc$1*org/biojava/bio/symbol/SymbolPropertyTablejava/util/Iterator!org/biojava/bio/symbol/SymbolList$org/biojava/utils/math/ComputeObject org/biojava/bio/seq/ProteinToolsgetSymbolPropertyTable@(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolPropertyTable; getAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;%org/biojava/bio/symbol/FiniteAlphabetiterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object;getDoubleValue"(Lorg/biojava/bio/symbol/Symbol;)Djava/lang/Mathabs(D)D(D)V java/util/Mapput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;#()Lorg/biojava/bio/symbol/Alphabet; getTAlphabet(Lorg/biojava/bio/proteomics/IsoelectricPointCalc;Lorg/biojava/bio/symbol/SymbolList;ZZLorg/biojava/bio/proteomics/IsoelectricPointCalc$1;)V#org/biojava/utils/math/BinarySearchsolve,(DDDLorg/biojava/utils/math/ComputeObject;)D(Ljava/lang/String;)V initCause,(Ljava/lang/Throwable;)Ljava/lang/Throwable;round(D)J!%1 67 87 97 :; <; =; >?@AB*LMN :   :+9YW,9YW-9YW:g6CRAC DEG J*K6O@PLQ`TjUvVYZ[a^bcDR@tE7FG6HIJ? 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'b,- ./01#223A5G6M7^8d9j:{;<=C?@CABD(R9: ;-<-#u=-MK>-./.?)*45 .5@@ @@@@57JABCPK .*?:= T"T")org/biojava/bio/proteomics/MassCalc.class2q \ [ [  [ [ 4          4   [ [ ' I [ [        4 \   [   ! " [# [$% E &'( ') I * + , + + -@2cHk? H.@2\~? qu/0CmonoD ConstantValue@(HmonoNmono@,ROmono@/erJ7Cavg@(HavgNavg@,sl&lOavg@/[W>mSymbolPropertyHashLjava/util/HashMap;mVariableModPropertyHashtermMass(Ljava/lang/String;Z)VCodeLineNumberTableLocalVariableTablevalueLjava/lang/Double;npe Ljava/lang/NullPointerException;ise/Lorg/biojava/bio/symbol/IllegalSymbolException;symLorg/biojava/bio/symbol/Symbol;this%Lorg/biojava/bio/proteomics/MassCalc; isotopicTypeLjava/lang/String;MH_PLUSZsymbolPropertyTable,Lorg/biojava/bio/symbol/SymbolPropertyTable; symbolListLjava/util/Iterator; StackMapTable/123setSymbolModification(CD)VexLorg/biojava/bio/BioException; symbolTokenCmasstoke+Lorg/biojava/bio/seq/io/SymbolTokenization;4 ExceptionsaddVariableModification(C[D)Vresiduemasses[D$(Lorg/biojava/bio/symbol/Symbol;[D)ViImassListLjava/util/List;(removeVariableModifications(C)Z"(Lorg/biojava/bio/symbol/Symbol;)ZgetMolecularWeight&(Lorg/biojava/bio/symbol/SymbolList;)Das%Lorg/biojava/bio/symbol/AtomicSymbol;countmatches'Lorg/biojava/bio/symbol/FiniteAlphabet;sit proteinSeq#Lorg/biojava/bio/symbol/SymbolList;pepMassgapsPT5getMass9(Lorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;Z)DsymbolPropertyMapgetVariableMasses'(Lorg/biojava/bio/symbol/SymbolList;)[DpeptidevMassesgetVariableModMap()Ljava/util/HashMap;getSymbolPropertyMap getTermMass()D getVMassesmsg subMassesresMassmit allMassListLjava/util/Set; curResMasses6 calcTermMass(Ljava/lang/String;Z)DgetSymbolForChar"(C)Lorg/biojava/bio/symbol/Symbol; SourceFile MassCalc.java w7 v^java/util/HashMap st8 9: ut ;< =>3 ?@ ABorg/biojava/bio/symbol/Symbol CD EDjava/lang/Double2 FG wH IJjava/lang/NullPointerException-org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/BioErrorjava/lang/StringBuilder$Error setting properties for Symbol KL KM NO wPtoken QRorg/biojava/bio/BioExceptionExpected a tokenization KS4 TU java/util/LinkedList VW XYPROTEINZ [\] ^_avgMass5#org/biojava/bio/symbol/AtomicSymbol `a%org/biojava/bio/symbol/FiniteAlphabet bc dWSymbol eO has no mass associated wf is not atomic gWThe mass of the symbol  is unknown wh iY j java/util/HashSet klNo mass Set for Symbol java/util/List wm nc6 op1monoMass#org/biojava/bio/proteomics/MassCalcjava/lang/Objectjava/lang/String*org/biojava/bio/symbol/SymbolPropertyTablejava/util/Iterator)org/biojava/bio/seq/io/SymbolTokenization!org/biojava/bio/symbol/SymbolList java/util/Set()V org/biojava/bio/seq/ProteinToolsgetSymbolPropertyTable@(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolPropertyTable; getAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;iterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object;o'()Lorg/biojava/bio/symbol/AtomicSymbol;ugetDoubleValue"(Lorg/biojava/bio/symbol/Symbol;)D(D)Vput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;*(Ljava/lang/String;Ljava/lang/Throwable;)VgetTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;(C)Ljava/lang/StringBuilder; parseToken3(Ljava/lang/String;)Lorg/biojava/bio/symbol/Symbol;add(Ljava/lang/Object;)Zremove&(Ljava/lang/Object;)Ljava/lang/Object;&org/biojava/bio/symbol/AlphabetManageralphabetForName5(Ljava/lang/String;)Lorg/biojava/bio/symbol/Alphabet;org/biojava/bio/symbol/Alphabet getGapSymbol!()Lorg/biojava/bio/symbol/Symbol; getMatches#()Lorg/biojava/bio/symbol/Alphabet;size()IequalsgetName(Ljava/lang/String;)V containsKey4(Lorg/biojava/bio/symbol/Symbol;Ljava/lang/String;)Vget doubleValuesymbolAt"(I)Lorg/biojava/bio/symbol/Symbol;(Ljava/util/Collection;)VlengthsubList'(II)Lorg/biojava/bio/symbol/SymbolList;![\ ]^_`b^_Yc^_df^_gi^_jl^_Tm^_np^_qstutv^wxy**+*Y+N*Y : j  :ڻY-:*W:#:YY[x{[}zN (2<HX[lx{}{\ l |}}~HX2r)2(_ByL ::Y!Y"#$:*Y(W  z 9K{> LLL^ @9 O y] *%N*-,&z {*  y5'Y(N6,-Y,1)W**+-Wz$*4{4 555-  yN *%M*,+z {  yT**+,z { yS H-./N0:*1:   :2'cH34:55-6YY789:69  :  6 2:     c9 ' ocH609''cH'zn   &2:IU_hk "#$%&),./2{z $ = RO^ U2^  v^O ,!%(y2wJ+:*1: L  :2)YY78;:)cJ+9))cJ)z2 RTWX&Y.ZT]`^cajcpdug{R&:Swwwu^oj v^Cy!xI*<:+1: X  :=+YY>8?@A:(BcI(*CcI(z. wy{|&}0~Xdlov{H&Fd}_xxv^ptGy *+DM>,,\1*CcR,z{*  y/*z{ y/*z{ y/*z{ y 7EYFM+GN*<-='YH-8:Y::**-='Y**-AIJ: 'Y(:*<-A)WK: p B9+L,YMWA*++LND:6  # 1c9 ,Y MW ۧ,O:6,P:  BRzn5?BMdm} .4{5 ^ ( +[^"77/'B0 -4 ?$5'! y9I*0Q(RcI%(TcI*VQ(WcI (YcI(z*  '-17{ 997v^y6 MNY!-,Y"#$N-  z 4{4 66 +4 N PK /*?:Wơ\\-org/biojava/bio/proteomics/MassCalcTest.class2| }~ !   ! >>. &֕ !? qu !? H !@/erJ7 !@/[W> !@Q`fR !@Q '0 ! ! ! ! & 8 8 ! =q- 3 ! ! 8 8 8 8deltaD ConstantValue protAlpha'Lorg/biojava/bio/symbol/FiniteAlphabet;monoHavgHmonoOavgOmonoAlaavgAlasyms1#Lorg/biojava/bio/symbol/SymbolList;setUp()VCodeLineNumberTableLocalVariableTablethis)Lorg/biojava/bio/proteomics/MassCalcTest;protToke+Lorg/biojava/bio/seq/io/SymbolTokenization; Exceptions(Ljava/lang/String;)VnameLjava/lang/String;main([Ljava/lang/String;)VmctbeLorg/biojava/bio/BioException;args[Ljava/lang/String; StackMapTabletestStaticgetMolecularWeightprom1m2proXm3proX2m4ex/Lorg/biojava/bio/symbol/IllegalSymbolException;testStaticGetMassmass testGetMassmCalc%Lorg/biojava/bio/proteomics/MassCalc;testGetTermMasstestSetSymbolModificationnewAlatestAlphabetTolerancesyms SourceFileMassCalcTest.javaPROTEIN %org/biojava/bio/symbol/FiniteAlphabet BCtoken 'org/biojava/bio/symbol/SimpleSymbolListA V JK VW ?@ D@ E@ F@ G@ H@ I@'org/biojava/bio/proteomics/MassCalcTesttest LM rMorg/biojava/bio/BioException Marndceqghilkmfpstwyv avgMass xxxxxxxxxxxxxxxxxxxx xxxxxx-xxxxxxxxxxxxxx-org/biojava/bio/symbol/IllegalSymbolException WmonoMass #org/biojava/bio/proteomics/MassCalc V  achtyilqwjunit/framework/TestCase!org/biojava/bio/symbol/SymbolList&org/biojava/bio/symbol/AlphabetManageralphabetForName5(Ljava/lang/String;)Lorg/biojava/bio/symbol/Alphabet;getTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;@(Lorg/biojava/bio/seq/io/SymbolTokenization;Ljava/lang/String;)VprintStackTrace org/biojava/bio/seq/ProteinTools createProtein7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;getMolecularWeight&(Lorg/biojava/bio/symbol/SymbolList;)DgetMass9(Lorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;Z)D assertTrue(Z)Vjava/lang/Mathabs(D)D getMessage()Ljava/lang/String;fail assertEquals(DDD)V(Ljava/lang/String;Z)V getTermMass()DsetSymbolModification(CD)V!!> ?@A BCD@E@F@G@H@I@JK LMNg'**L*Y+ O= ?A&BP'QRSTU&VWN7*+ * ****** O& F, 013!4(6/76GP7QR7XY Z[N!Y"#L+$+%L+'&OL MNRPQTP  \R]^_`aUbcMN_ w()L+*I++,9(-.):*9(g/0-2):  *9  (g/0- L+45kn3O:XY Z[#]*^1_GaNbUckgneofvhP\ edK `e@Wf@*AgK1:h@NiK Uj@ oklwQRa,m@"m@"m@nopMNH* 6,H***cc*c' 7* 6,H***cc*c*c' 7* +,H* **cc*c' 7* +,H* **cc*c*c' 7O* ru x'{2~Q\vPQRq@U3rMN8Y69L***cc*c+* : 78Y69L***cc*c*c+* : 78Y+9L* **cc*c+* : 78Y+9L* **cc*c*c+* : 7O& ,7]hPQR stU3uMN8Y69L**c*c+; 78Y69L**c*c*c+; 78Y+9L**c*c+; 78Y+9L**c*c*c+; 7O& #.KVnyPQR stU3vMN?H8Y69N-A'<'**cc*c-* : 78Y69N-A'<'**cc*c*c-* : 78Y+9N-A'<'**cc*c-* : 78Y+9N-A'<'**cc*c*c-* : 7O: 2=DgryP QRw@ stU3xMN#=)L8Y69M,+:X L+453O"P*yKstkl#QRaZoz{PK .*?:Z0)org/biojava/bio/proteomics/Protease.class2 't &u vw xyz{ | }~ & & & &  `   v    &  #TRYPSINLjava/lang/String; ConstantValueLYS_CARG_CASP_N GLU_C_BICARB GLU_C_PHOS CHYMOTRYPCNBr9cleavageResidues#Lorg/biojava/bio/symbol/SymbolList;notCleaveResidues endoProteaseZname\(Lorg/biojava/bio/symbol/SymbolList;ZLorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis%Lorg/biojava/bio/proteomics/Protease; cleaveRes notCleaveRes StackMapTable ExceptionsJ(Lorg/biojava/bio/symbol/SymbolList;ZLorg/biojava/bio/symbol/SymbolList;)V Deprecated((Ljava/lang/String;ZLjava/lang/String;)V(Ljava/lang/String;Z)V cleavageResgetCleaveageResidues%()Lorg/biojava/bio/symbol/SymbolList;getName()Ljava/lang/String;getNotCleaveResiduesisEndoProtease()ZgetProteaseList()[Ljava/lang/String;sLjava/util/Set;names[Ljava/lang/String;getProteaseByName9(Ljava/lang/String;)Lorg/biojava/bio/proteomics/Protease; proteaseNamecreateSymbolList7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;seqsListprot'Lorg/biojava/bio/symbol/FiniteAlphabet; tokenization+Lorg/biojava/bio/seq/io/SymbolTokenization; readResolve()Ljava/lang/Object;exLorg/biojava/bio/BioException; SourceFile Protease.java A >?  -org/biojava/bio/symbol/IllegalSymbolException4Cleaveage residues must be from the PROTEIN alphabet A iJCleaveage residues must be from the PROTEIN alphabet or an EmptySymbolList ;< =< @* de  java/lang/String ab W <PROTEIN %org/biojava/bio/symbol/FiniteAlphabettoken 'org/biojava/bio/symbol/SimpleSymbolList A VW org/biojava/bio/BioExceptionorg/biojava/bio/BioErrorMAssertion Error: Cannot register Protease instance following de serialization A#org/biojava/bio/proteomics/Proteasejava/lang/Objectjava/io/SerializableTrypsinLys-CArg-CAsp-NGlu-C-bicarbonateGlu-C-phosphate Chymotrypsin!org/biojava/bio/symbol/SymbolListjava/io/ObjectStreamException()V getAlphabet#()Lorg/biojava/bio/symbol/Alphabet; org/biojava/bio/seq/ProteinTools)()Lorg/biojava/bio/symbol/FiniteAlphabet;(Ljava/lang/String;)Vorg/biojava/bio/symbol/AlphabetEMPTY_ALPHABET*org/biojava/bio/proteomics/ProteaseManagergetNames()Ljava/util/Set; java/util/Setsize()ItoArray(([Ljava/lang/Object;)[Ljava/lang/Object;trimequals(Ljava/lang/Object;)Z EMPTY_LIST&org/biojava/bio/symbol/AlphabetManageralphabetForName5(Ljava/lang/String;)Lorg/biojava/bio/symbol/Alphabet;getTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;@(Lorg/biojava/bio/seq/io/SymbolTokenization;Ljava/lang/String;)V registered(Ljava/lang/String;)ZregisterProtease((Lorg/biojava/bio/proteomics/Protease;)V*(Ljava/lang/String;Ljava/lang/Throwable;)V!&'( )*+,-*+./*+01*+23*+45*+67*+89*+:;<=<>?@* ABCW**+ Y-- Y *+ **- * D. `Y bcf7hAkFlKmPnVoE4WFGWH<W>?WI<W@*JKLLM!NAOCZ **D|Y E* FG H< >? I<N"PAQC}!****+ ***- DY  E*!FG!H*!>?!I*N"PARCt"****+ *** DY !E "FG"S*">?N"PTUC/* DE FGVWC/* DE FGXUC/* DE FGYZC/*DE FG [\CXK*L*+DE]^_`abC/*DE c*N"deC4++N-:Y+M,D'2 E44FG4f*2g<hi' jkJN"lmC$* **!*L#Y$+%""D E no$FGJEpNqrsPK .*?:m:##0org/biojava/bio/proteomics/ProteaseManager.class2} ^                 # &  * n  ;     B     K   K!| K" K# $%w& U U'( )* X+ ,-. \/0 name2ProteaseLjava/util/Map;docLorg/w3c/dom/Document;singletonInstance,Lorg/biojava/bio/proteomics/ProteaseManager;TRYPSINLjava/lang/String; ConstantValueLYS_CARG_CASP_N GLU_C_BICARB GLU_C_PHOS CHYMOTRYPCNBr()VCodeLineNumberTableLocalVariableTablethiscreateProtease(Lorg/biojava/bio/symbol/SymbolList;ZLorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;)Lorg/biojava/bio/proteomics/Protease; cleaveRes#Lorg/biojava/bio/symbol/SymbolList; endoProteaseZ notCleaveResnamep%Lorg/biojava/bio/proteomics/Protease; Exceptions1](Lorg/biojava/bio/symbol/SymbolList;ZLjava/lang/String;)Lorg/biojava/bio/proteomics/Protease;^(Ljava/lang/String;ZLjava/lang/String;Ljava/lang/String;)Lorg/biojava/bio/proteomics/Protease;L(Ljava/lang/String;ZLjava/lang/String;)Lorg/biojava/bio/proteomics/Protease;registerProtease((Lorg/biojava/bio/proteomics/Protease;)Vprot StackMapTablegetProteaseByName9(Ljava/lang/String;)Lorg/biojava/bio/proteomics/Protease; proteaseNameproteasegetNames()Ljava/util/Set;getAllProteases registered(Ljava/lang/String;)Z getInstance.()Lorg/biojava/bio/proteomics/ProteaseManager;createSymbolList7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;seqsList'Lorg/biojava/bio/symbol/FiniteAlphabet; tokenization+Lorg/biojava/bio/seq/io/SymbolTokenization; getTrypsin'()Lorg/biojava/bio/proteomics/Protease;exLorg/biojava/bio/BioException;getLys_CgetArg_CgetAsp_NgetGlu_C_bicarbonategetGlu_C_phosphategetChymotrypsingetCNBrcnode2Lorg/w3c/dom/Node;elLorg/w3c/dom/Element;contentjIcleavRes exceptResendoprotName proteaseNodesLorg/w3c/dom/NodeList;cnodechildi tablesStreamLjava/io/InputStream;isLorg/xml/sax/InputSource;parser#Ljavax/xml/parsers/DocumentBuilder;childrenmre$Ljava/util/MissingResourceException;eLjava/lang/Exception;2345 67(. SourceFileProteaseManager.java op#org/biojava/bio/proteomics/Protease o8 6 9x uv :; org/biojava/bio/BioExceptionjava/lang/StringBuilder5A Protease has already been registered with the name <= >; o? _`@ AB CD,No protease has been registered by that name EF GHjava/util/HashSet IJ oK LM cd*org/biojava/bio/proteomics/ProteaseManager7 N; OMPROTEINP QR%org/biojava/bio/symbol/FiniteAlphabettoken ST'org/biojava/bio/symbol/SimpleSymbolList oUTrypsin org/biojava/bio/BioError=Cannot retreive Trypsin, AlphabetManager.xml may be corrupted oVLys-C;Cannot retreive Lys-C, AlphabetManager.xml may be corruptedArg-C;Cannot retreive Arg-C, AlphabetManager.xml may be corruptedAsp-N;Cannot retreive Asp-N, AlphabetManager.xml may be corruptedGlu-C-bicarbonateGCannot retreive Glu_C_bicarbonate, AlphabetManager.xml may be corruptedGlu-C-phosphateECannot retreive Glu_C_phosphate, AlphabetManager.xml may be corrupted ChymotrypsinBCannot retreive Chymotrypsin, AlphabetManager.xml may be corrupted:Cannot retreive CNBr, AlphabetManager.xml may be corruptedjava/util/HashMap abW XY.org/biojava/bio/proteomics/ProteaseManager.xmlZ [\$Couldn't locate ProteaseManager.xml.org/xml/sax/InputSource o]^ _` ab3 cde fg hi4 jk lmorg/w3c/dom/Element n; op qr5 s;java/lang/Boolean tu"java/util/MissingResourceExceptionv wx y;z {?java/lang/Exception |pjava/lang/Object-org/biojava/bio/symbol/IllegalSymbolExceptionjava/io/InputStream!javax/xml/parsers/DocumentBuilderorg/w3c/dom/NodeListorg/w3c/dom/Node!org/biojava/bio/symbol/SymbolListjava/lang/String\(Lorg/biojava/bio/symbol/SymbolList;ZLorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;)V EMPTY_LISTgetName()Ljava/lang/String;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString(Ljava/lang/String;)V java/util/Mapput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;get&(Ljava/lang/Object;)Ljava/lang/Object;keySetjava/util/CollectionsunmodifiableSet (Ljava/util/Set;)Ljava/util/Set;values()Ljava/util/Collection;(Ljava/util/Collection;)V containsKey(Ljava/lang/Object;)Ztrimequals&org/biojava/bio/symbol/AlphabetManageralphabetForName5(Ljava/lang/String;)Lorg/biojava/bio/symbol/Alphabet;getTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;@(Lorg/biojava/bio/seq/io/SymbolTokenization;Ljava/lang/String;)V*(Ljava/lang/String;Ljava/lang/Throwable;)Vorg/biojava/utils/ClassToolsgetClassLoader*(Ljava/lang/Class;)Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;(Ljava/io/InputStream;)V(javax/xml/parsers/DocumentBuilderFactory newInstance,()Ljavax/xml/parsers/DocumentBuilderFactory;newDocumentBuilder%()Ljavax/xml/parsers/DocumentBuilder;parse1(Lorg/xml/sax/InputSource;)Lorg/w3c/dom/Document;org/w3c/dom/DocumentgetDocumentElement()Lorg/w3c/dom/Element; getChildNodes()Lorg/w3c/dom/NodeList; getLength()Iitem(I)Lorg/w3c/dom/Node; getNodeName getAttribute&(Ljava/lang/String;)Ljava/lang/String; getFirstChild()Lorg/w3c/dom/Node; getNodeValue booleanValue()Zjava/lang/SystemerrLjava/io/PrintStream; getMessagejava/io/PrintStreamprintlnprintStackTrace1^ _`ab cdefg(hfg-ifg/jfg1kfg3lfg5mfg7nfg9opq/*r7s td)uvqoY*,-:r s4wxyz{x|f }~ )uqdY*,N--rs*wxyz|f}~ )uqV*,-rs*wfyz{f|f )uqK *,rs  wf yz |f )qv7* ! Y Y  ***Wr (6s 7~( qk*L+ Y+r sf ~ q$ r q+Yr q4 *rs  f)q= Yr q2** !"#M,$%N&Y-*'L+r& 0 s*2f0x&  qX()K*Y+*, rs  F qX-)K*Y.*, r "#s  F qX/)K*Y0*, r,./s  F qX1)K*Y2*, r8:;s  F qX3)K*Y4*, rDFGs  F qX5)K*Y6*, rPRSs  F qX7)K*Y8*, r\^_s  F qX9)K*Y:*, rhjks  Fpq;Y<=>?@K* YABY*CLDEM,+F==GHN6-I-J:KK:LM ::6 NO: : H: 6   I  J:KK:L:PQ:R :2S :T UYVW6  : :Y  : N KY*Z[K*]jmXj{\r18 :>CD(G1H8I@KNL\MfNnOqRxSVWXYZ\]^_`bcdefg hi"j0n5o<pAqHsY]_udLj|mxnyx|{z|{}s}|fof xxz f ~ fxQP1982Nn |((8!4 BMPK .*?:l|kϒ /org/biojava/bio/proteomics/StructureTools.class2m !I J K L M N O P Q R ST UVWX YZ [\]&'()*+,-^_` abcstruct'Lorg/biojava/bio/symbol/FiniteAlphabet;_%Lorg/biojava/bio/symbol/AtomicSymbol;chgiebts()VCodeLineNumberTableLocalVariableTablethis+Lorg/biojava/bio/proteomics/StructureTools; getStructure)()Lorg/biojava/bio/symbol/FiniteAlphabet;get_'()Lorg/biojava/bio/symbol/AtomicSymbol;getCgetHgetGgetIgetEgetBgetTgetSsTok+Lorg/biojava/bio/seq/io/SymbolTokenization;Ljava/lang/Throwable; StackMapTable^ SourceFileStructureTools.java ./ "# $% &% '% (% )% *% +% ,% -% STRUCTUREd ef%org/biojava/bio/symbol/FiniteAlphabettoken gh i jk#org/biojava/bio/symbol/AtomicSymboljava/lang/Throwableorg/biojava/bio/BioError'Could not initialise structure alphabet .l)org/biojava/bio/proteomics/StructureToolsjava/lang/Object&org/biojava/bio/symbol/AlphabetManageralphabetForName5(Ljava/lang/String;)Lorg/biojava/bio/symbol/Alphabet;getTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;)org/biojava/bio/seq/io/SymbolTokenization parseToken3(Ljava/lang/String;)Lorg/biojava/bio/symbol/Symbol;*(Ljava/lang/String;Ljava/lang/Throwable;)V1 ! "#$%&%'%(%)%*%+%,%-% ./0/*1"2 34560.1D2 34780.1H2 34980.1L2 34:80.1P2 34;80.1T2 34<80.1X2 34=80.1\2 34>80. 1`2 34?80. 1d2 34@80. 1h2 34A/0' K******* * * KY*1>1 35$627@8N9\:j;x<=@>?A2~BC ,DE F GHPK /*?: 0org/biojava/bio/proteomics/aaindex/AAindex.class2_ B C D E F G H I JK L MNO P QR SR TUVWPROTEIN_ALPHABET!Lorg/biojava/bio/symbol/Alphabet;accessionNumberLjava/lang/String; descriptionlitdbEntryNumbers[Ljava/lang/String;articleAuthors articleTitlejournalReferencecommentsimilarEntriesLjava/util/Map;(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis,Lorg/biojava/bio/proteomics/aaindex/AAindex; StackMapTableVX Exceptions()Ljava/lang/String;getArticleAuthorssetArticleAuthors getComment setCommentgetArticleTitlesetArticleTitlegetDescriptionsetDescriptiongetJournalReferencesetJournalReferencegetLITDBEntryNumbers()[Ljava/lang/String;setLITDBEntryNumbers([Ljava/lang/String;)V()Ljava/util/Map;()V SourceFile AAindex.java  #Y       java/util/HashMap #? !"java/lang/NullPointerExceptionaccessionNumber is null. #$ Z[\ ]^*org/biojava/bio/proteomics/aaindex/AAindex0org/biojava/bio/symbol/SimpleSymbolPropertyTablejava/lang/String6(Lorg/biojava/bio/symbol/Alphabet;Ljava/lang/String;)Vclone()Ljava/lang/Object; org/biojava/bio/seq/ProteinTools getAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;!  !"#$%J*+******* * Y + Y*+&6 zK PUZ_!d&i+n6{:|D~I'J()J*D+,- .%/*&' ()/.%/*&' ()0$%>*+& '()1.%/* &' ()2$%>*+ & '() 3.%/*&' ()4$%>*+& '()5.%/*&' ()6$%>*+& '()7.%/*&' ()8$%>*+& '()9:%P**&' ()* L;<%e+ **+& '()* !=%/* &' ()>?%&D@APK .*?:\) \<org/biojava/bio/proteomics/aaindex/AAindexStreamReader.class2  T U T T    T     T  T  T      % % % % % % % T % % %  `}  R TOKENIZERLjava/lang/String; ConstantValueaa [Lorg/biojava/bio/symbol/Symbol;readerLjava/io/BufferedReader;linekeyCharC stringValue(Ljava/io/Reader;)VCodeLineNumberTableLocalVariableTablethis8Lorg/biojava/bio/proteomics/aaindex/AAindexStreamReader;Ljava/io/Reader; Exceptions(Ljava/io/BufferedReader;)V StackMapTableeof()ZeLjava/io/IOException; readSection()V stringBufferLjava/lang/StringBuffer;hasNext nextTable.()Lorg/biojava/bio/symbol/SymbolPropertyTable;iI!Ljava/lang/NumberFormatException; keyValuePairs[Ljava/lang/String;similarEntriesLjava/util/Map;headersAndIndicesaaIndex,Lorg/biojava/bio/proteomics/aaindex/AAindex; tokenizer+Lorg/biojava/bio/seq/io/SymbolTokenization;Lorg/biojava/bio/BioException;%Ljava/lang/IndexOutOfBoundsException; SourceFileAAindexStreamReader.javajava/io/BufferedReader bc bk bu \] ^Xjava/lang/NullPointerExceptionreader is null. b  java/io/IOException _`java/lang/StringBuffer  org/biojava/bio/BioException b op aX java/util/NoSuchElementException tujava/lang/StringBuilderExpected 'H' but found: ' '.*org/biojava/bio/proteomics/aaindex/AAindex \s+     Z[ java/lang/NumberFormatExceptionNaN  Invalid key char found:   token  org/biojava/bio/symbol/SymbolA RNDQEGHLKMFPSTWYV u#java/lang/IndexOutOfBoundsException6org/biojava/bio/proteomics/aaindex/AAindexStreamReaderjava/lang/Object>org/biojava/bio/proteomics/aaindex/SymbolPropertyTableIterator java/util/Map(Ljava/lang/String;)VreadLine()Ljava/lang/String;java/lang/Stringlength()IcharAt(I)C substring(I)Ljava/lang/String;append,(Ljava/lang/String;)Ljava/lang/StringBuffer;endsWith(Ljava/lang/String;)Z(Ljava/lang/Throwable;)VtoString-(Ljava/lang/String;)Ljava/lang/StringBuilder;(C)Ljava/lang/StringBuilder;trimsetDescriptionsplit'(Ljava/lang/String;)[Ljava/lang/String;setLITDBEntryNumbers([Ljava/lang/String;)VsetArticleAuthorssetArticleTitlesetJournalReference()Ljava/util/Map;java/lang/DoublevalueOf&(Ljava/lang/String;)Ljava/lang/Double;put8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;setDoubleProperty4(Lorg/biojava/bio/symbol/Symbol;Ljava/lang/String;)V setCommentPROTEIN_ALPHABET!Lorg/biojava/bio/symbol/Alphabet;org/biojava/bio/symbol/AlphabetgetTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;)org/biojava/bio/seq/io/SymbolTokenization parseToken3(Ljava/lang/String;)Lorg/biojava/bio/symbol/Symbol;printStackTrace!TUVWXY9 Z[\]^X_`aXbcdE *Y+e  f gh \ij bkd****+ Y *+*+ e" !)f*gh*\]lmnj opd8*** ** L*%( e" %()+f)qr8ghl  ^s @tudt** YL* #+*W* +W**  MY,**  *+?JM e6 ,8?JMNWksf N qrtgh`vwlx*Ms jypdB *ef  ghl @z{d* Y**H&YY *!" #$%Y*&'L*G** */AnCDSIJR^Ty+*(+*)*++*,+*-+*.*)*M+/N6,d-,2,`201Wu*)*:6,+22 `23:+2253ӧ4+*6))YY7 *!" #$+9KN4e&?NUY   !$/9K$N!P"\b&e(m)p+s-2fR#|}P q~20|}/gghNMlD/a  " m[  "jud289:K;Y*<=SY*>=SY*?=SY*@=SY*A=SY*B=SY*C=SY*D=SY*E=SY *F=SY *G=SY *H=SY *I=SY *J=SY*K=SY*L=SY*M=SY*N=SY*O=SY*P=S2K*QK*S Re* hnp{|  } ~f q ql GPK /*?:mF9 9 @org/biojava/bio/proteomics/aaindex/AAindexStreamReaderTest.class2 *TU VW XY Z[\ ]^_` a b c def gh ij ik l m n go p q r s t u v w x y z{ |} ~c ~ z Z ()VCodeLineNumberTableLocalVariableTablethis3@BAP@VC]DgEnFuG|HIJKLMNOPQRS/\ 6 789:,;<3=>9?@+AB01 CDEFG5HIJK8@LM*NHIOPQRSPK /*?:4org/biojava/bio/proteomics/aaindex/AAindexTest.class2 4\ ]^ _` 4abc d e f g hi j kl m no p qr s tu v wxy z { |} ~ " | |          2aaindex,Lorg/biojava/bio/proteomics/aaindex/AAindex;()VCodeLineNumberTableLocalVariableTablethis0Lorg/biojava/bio/proteomics/aaindex/AAindexTest;main([Ljava/lang/String;)Vargs[Ljava/lang/String;setUp ExceptionstestAccessionNumbertestGetArticleAuthorstestSetArticleAuthorstestGetCommenttestSetCommenttestGetArticleTitletestSetArticleTitletestGetDescriptiontestSetDescriptiontestGetJournalReferencetestSetJournalReferencetestGetLITDBEntryNumberstestSetLITDBEntryNumberstestSimilarEntries testGetNametestGetAlphabettestDoubleValuee/Lorg/biojava/bio/symbol/IllegalSymbolException; StackMapTable SourceFileAAindexTest.java 78 56.org/biojava/bio/proteomics/aaindex/AAindexTest B8*org/biojava/bio/proteomics/aaindex/AAindextest 7 authors comment title  description journal java/lang/Stringlit ?  java/lang/Double 7  1.0  "IllegalSymbolException not thrown. -org/biojava/bio/symbol/IllegalSymbolException 8junit/framework/TestCasejava/lang/Exceptionjunit/textui/TestRunnerrun(Ljava/lang/Class;)V(Ljava/lang/String;)VaccessionNumber()Ljava/lang/String; assertEquals'(Ljava/lang/String;Ljava/lang/String;)VgetArticleAuthors assertNull(Ljava/lang/Object;)VsetArticleAuthors getComment setCommentgetArticleTitlesetArticleTitlegetDescriptionsetDescriptiongetJournalReferencesetJournalReferencegetLITDBEntryNumbers()[Ljava/lang/String;setLITDBEntryNumberssimilarEntries()Ljava/util/Map; java/util/Mapsize()I(II)V(D)Vput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;get&(Ljava/lang/Object;)Ljava/lang/Object;'(Ljava/lang/Object;Ljava/lang/Object;)VgetName org/biojava/bio/seq/ProteinTools getAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;#()Lorg/biojava/bio/symbol/Alphabet;gln'()Lorg/biojava/bio/symbol/AtomicSymbol;setDoubleProperty4(Lorg/biojava/bio/symbol/Symbol;Ljava/lang/String;)VgetDoubleValue"(Lorg/biojava/bio/symbol/Symbol;)D(DDD)Vorg/biojava/bio/seq/DNAToolsafailprintStackTrace!4567898 **: &3; 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(ig jk lm 78table is null. nop qr`org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB$SimpleSymbolPropertyTableIterator stu vw (x y= name is null. z{)org/biojava/bio/seq/db/IllegalIDExceptionjava/lang/StringBuilderNo table found with name |}. ~o *org/biojava/bio/symbol/SymbolPropertyTable B>org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBjava/lang/Object8org/biojava/bio/proteomics/aaindex/SymbolPropertyTableDB>org/biojava/bio/proteomics/aaindex/SymbolPropertyTableIteratororg/biojava/bio/BioException(Ljava/lang/String;)VhasNext()Z nextTable.()Lorg/biojava/bio/symbol/SymbolPropertyTable;getName()Ljava/lang/String; java/util/Mapput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;values()Ljava/util/Collection;java/util/Collectioniterator()Ljava/util/Iterator;(Ljava/util/Iterator;)Vsize containsKey(Ljava/lang/Object;)Zappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toStringget&(Ljava/lang/Object;)Ljava/lang/Object;keySet!!"#&'()*K***Y+og pq, -.(/*)*+ Y+ *+  +}~(,)-.)012345678*i + Y *+ +W+, -. 9:250;*@Y*+, -.<=*4 *+,  -.9>*I+ Y*+#YY+*++;,I-.I?@2,5AB*4 * +,  -.CD% !$PK /*?:we/Horg/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBTest.class2 2`a bcd `e fg hi fj kl mn opq r stu v j wxy z k{ |} ~   g    ~  * -()VCodeLineNumberTableLocalVariableTablethisDLorg/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBTest;main([Ljava/lang/String;)Vargs[Ljava/lang/String;testEmptyConstructordb:Lorg/biojava/bio/proteomics/aaindex/SymbolPropertyTableDB;testNonEmptyConstructordbInit@Lorg/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB;t1,Lorg/biojava/bio/symbol/SymbolPropertyTable;t2iterator@Lorg/biojava/bio/proteomics/aaindex/SymbolPropertyTableIterator;tablesLjava/util/ArrayList; StackMapTableady Exceptions testAddTablee Ljava/lang/NullPointerException;namesLjava/util/Set; testTable+Lorg/biojava/bio/seq/db/IllegalIDException; SourceFile$SimpleSymbolPropertyTableDBTest.java 34Borg/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBTest >org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBDatabase is not empty. +Database does not return an empty iterator.  0org/biojava/bio/symbol/SimpleSymbolPropertyTable protein 3 dna 3$Database has wrong number of tables.java/util/ArrayList 3 )Iterator returned wrong number of tables. 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PK /*?:`>OVV'org/biojava/bio/proteomics/package.html Utilities to aid in performing various physical analysis of proteins. 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!"D**+*+ *+ =**O*O#& PQ RS$U/V6W=UCY$ &%D&'D()*&+,-."/*#a$ &'/0">*# jk$&'12"S**+O# vw$ &'3456789"D**+.#$&'3467:2"S**+O# $ &'34567;9"r**+.=*#$ &'34 <*67=>"h+ * 4 Y Y + * * M* N6,0,*.O*.6- *OϻY+*,-*#* CKS]hq$>q<V4%&'?@KRSJ*ECAA*+BAAA+BAAA6 CDPK /*?:Zg0m m 2org/biojava/bio/search/SeqContentPatternTest.class2 )EF GHIJKLMNOPQ GR S T GU V WX YZ ([\]^ (_`abc Yd (efghijklmno()VCodeLineNumberTableLocalVariableTablethis.Lorg/biojava/bio/search/SeqContentPatternTest; testTooShortzero#Lorg/biojava/bio/symbol/SymbolList;onefivesixMatch sixNoMatch sevenMatch1 sevenMatch2 sevenMatchAll sevenNoMatchscp*Lorg/biojava/bio/search/SeqContentPattern;scm#Lorg/biojava/bio/search/BioMatcher; Exceptionspq SourceFileSeqContentPatternTest.java *+r staaaaaaaaaaaattttttaaaaaattaaaaaaaaaaaaattttttt(org/biojava/bio/search/SeqContentPattern uv *w xy Iz {| }~#No hits of length 6 in seq length 0 #No hits of length 6 in seq length 1#No hits of length 6 in seq length 5Hit found in matching 6 Just the one hitNo hit in non-matching 6 Hit in 7-1Hit in 7-1 at 1 No more hits in 7-1 Hit in 7-2Hit in 7-2 at 2No more hits in 7-2 Hit in 7-allHit in 7-all at 1Hit in 7-all at 2No hit in seven no hits,org/biojava/bio/search/SeqContentPatternTestjunit/framework/TestCase-org/biojava/bio/symbol/IllegalSymbolException/org/biojava/bio/symbol/IllegalAlphabetExceptionorg/biojava/bio/seq/DNATools createDNA7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;getDNA)()Lorg/biojava/bio/symbol/FiniteAlphabet;*(Lorg/biojava/bio/symbol/FiniteAlphabet;)V setLength(I)V'()Lorg/biojava/bio/symbol/AtomicSymbol; setMinCounts)(Lorg/biojava/bio/symbol/AtomicSymbol;I)VmatcherH(Lorg/biojava/bio/symbol/SymbolList;)Lorg/biojava/bio/search/BioMatcher;!org/biojava/bio/search/BioMatcherfind()Z assertFalse(Ljava/lang/String;Z)V assertTruestart()I assertEquals(Ljava/lang/String;II)V!()*+,/*- . /01+, xLMN::: : : : Y :    +:   ,:   -:   :    :   :      : ! 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Interfaces and classes for representing sequence similarity search results.

PK /*?:B"""org/biojava/bio/search/package.inf!!BioJavaBuildTool1 Core Packages PK .*?:Y  /org/biojava/bio/seq/AbstractFeatureHolder.class2u I JK LM NO I P QR QST JU VWXY Z N P[ \] Z^_`a()VCodeLineNumberTableLocalVariableTablethis+Lorg/biojava/bio/seq/AbstractFeatureHolder;filterH(Lorg/biojava/bio/seq/FeatureFilter;)Lorg/biojava/bio/seq/FeatureHolder;#Lorg/biojava/bio/seq/FeatureFilter;recurseZ StackMapTableI(Lorg/biojava/bio/seq/FeatureFilter;Z)Lorg/biojava/bio/seq/FeatureHolder;cve'Lorg/biojava/utils/ChangeVetoException;rfLjava/util/Iterator;r#Lorg/biojava/bio/seq/FeatureHolder;featLorg/biojava/bio/seq/Feature;fffres)Lorg/biojava/bio/seq/SimpleFeatureHolder;Ob_cTWa createFeaturedTemplate InnerClassesE(Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;temp&Lorg/biojava/bio/seq/Feature$Template; Exceptionse removeFeature (Lorg/biojava/bio/seq/Feature;)V SourceFileAbstractFeatureHolder.java c f$g hi "('org/biojava/bio/seq/SimpleFeatureHolder jkb lm noorg/biojava/bio/seq/Feature pq rF%org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioError@Assertion failed: Couldn't add a feature to my new FeatureHolder sBAssertion failure: Should be able to manipulate this FeatureHolder t=This FeatureHolder does not support creation of new Features.8This FeatureHolder does not support removal of Features.)org/biojava/bio/seq/AbstractFeatureHolder$org/biojava/utils/AbstractChangeable!org/biojava/bio/seq/FeatureHolderjava/util/Iterator!org/biojava/bio/seq/FeatureFilter$org/biojava/bio/seq/Feature$Templateorg/biojava/bio/BioException top_levelorg/biojava/bio/seq/FilterUtilsareProperSubsetI(Lorg/biojava/bio/seq/FeatureFilter;Lorg/biojava/bio/seq/FeatureFilter;)Zfeatures()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object;accept (Lorg/biojava/bio/seq/Feature;)Z addFeature(Ljava/lang/String;)V*(Ljava/lang/String;Ljava/lang/Throwable;)V!/*(  !"#d+=*+ /0  !"$%&'@"( YN*:s  :+ - :Y@+::"-  :Y-/58 ftw F456$7/95>8::;D@HASBfDtIwEyFLMf : )*y )*\)+,S2-.$a/0z1, !2$%&34'956)78569: ;6Z: <@> YR ! 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B**Y$"% z +N,:*-() +4    PK /*?:W# .org/biojava/bio/seq/CircularSequenceTest.class2 .Y Z[ -\ Z] -^ Z_ -` Za -bcd Ze -fg h -i jk lmn o pq -r s -tuv w x lyz{| }~  - Z  - pk pdnaLorg/biojava/bio/seq/Sequence;circ"Lorg/biojava/bio/seq/CircularView;aLorg/biojava/bio/symbol/Symbol;cgt(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis*Lorg/biojava/bio/seq/CircularSequenceTest;nameLjava/lang/String;setUp()V Exceptions testLocationscloc)Lorg/biojava/bio/symbol/CircularLocation;lLjava/util/ArrayList; StackMapTablezv testSubStr testSymbolAt testSubLists#Lorg/biojava/bio/symbol/SymbolList;symsEqI(Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/SymbolList;)ZiIb SourceFileCircularSequenceTest.java 89 3 34 5 54 6 64 7 74 atcgctcaga /0 org/biojava/bio/seq/CircularView 8 12  atcgc  gaajava/util/ArrayList 8B 'org/biojava/bio/symbol/CircularLocationctgaacatc aatagaatcgaatc  RS(org/biojava/bio/seq/CircularSequenceTestjunit/framework/TestCasejava/lang/Exceptionorg/biojava/bio/seq/DNATools'()Lorg/biojava/bio/symbol/AtomicSymbol;createDNASequenceD(Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;!(Lorg/biojava/bio/seq/Sequence;)Vorg/biojava/bio/seq/Sequencelength()I$org/biojava/bio/symbol/LocationToolsmakeCircularLocation.(III)Lorg/biojava/bio/symbol/CircularLocation;symbolsH(Lorg/biojava/bio/symbol/SymbolList;)Lorg/biojava/bio/symbol/SymbolList;!org/biojava/bio/symbol/SymbolList seqString()Ljava/lang/String; assertEquals'(Ljava/lang/String;Ljava/lang/String;)V get5PrimeEnd assertTrue(Z)Vadd(Ljava/lang/Object;)Zunion9(Ljava/util/Collection;)Lorg/biojava/bio/symbol/Location;subStr(II)Ljava/lang/String;symbolAt"(I)Lorg/biojava/bio/symbol/Symbol;'(Ljava/lang/Object;Ljava/lang/Object;)V createDNA7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;subList'(II)Lorg/biojava/bio/symbol/SymbolList;java/lang/Objectequals!-./0123454647489:j"*+**** ;2+ ,-.!3<"=>"?@AB:M*  *Y* ;8 9:< =>CDEB:r* L+*  * L +*  * L+ +* YM,* W, * W,* W,L++* ;>=>!@1ACCSDdEvH~JLMOPQR< =>FG~fHIJ`K@kL@MB:K *!"*!#*!$* !$*  !;WXY+Z:[J\< K=>NB:y?**%&** %&**%&* *%&;`ab.c>d< ?=>OB:t4#'L+*()**(* (*;hjk3l<4=>.PQCDRS:8++,+>+++,,,;opq0p6s<*#TU8=>83Q8VQJ WXPK /*?:W W &org/biojava/bio/seq/CircularView.class2 "Y "Z ![ !\ "] "^ "[_ ` a b ?c defgh i !j !kl m "no pq [ r stuv wxyF(Lorg/biojava/bio/seq/Sequence;Lorg/biojava/bio/seq/FeatureRealizer;)VCodeLineNumberTableLocalVariableTablethis"Lorg/biojava/bio/seq/CircularView;seqLorg/biojava/bio/seq/Sequence;fr%Lorg/biojava/bio/seq/FeatureRealizer;!(Lorg/biojava/bio/seq/Sequence;)V realValue(I)IvalI StackMapTablesymbolAt"(I)Lorg/biojava/bio/symbol/Symbol;indexsubStr(II)Ljava/lang/String;toEndLjava/lang/String; fromStartstartend createFeature{Template InnerClassesE(Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;template&Lorg/biojava/bio/seq/Feature$Template;loc!Lorg/biojava/bio/symbol/Location;fLorg/biojava/bio/seq/Feature;| Exceptions}subList'(II)Lorg/biojava/bio/symbol/SymbolList;eLjava/lang/Exception;)Lorg/biojava/bio/symbol/SimpleSymbolList;editLorg/biojava/bio/symbol/Edit;xoqt SourceFileCircularView.java #$ #. ~ /0 45 78java/lang/StringBuilder # F| 'org/biojava/bio/symbol/CircularLocationorg/biojava/bio/BioException1Only CircularLocations may exceed sequence length # 'org/biojava/bio/seq/SimpleFeatureHolder LM'org/biojava/bio/symbol/SimpleSymbolList #org/biojava/bio/symbol/Edit # Qjava/lang/Exceptionorg/biojava/bio/BioError1Couldn't construct subList, this shouldn't happen # org/biojava/bio/seq/CircularView%org/biojava/bio/seq/impl/ViewSequence$org/biojava/bio/seq/Feature$Templateorg/biojava/bio/symbol/Location%org/biojava/utils/ChangeVetoExceptionlength()I()Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;locationgetMax(Ljava/lang/String;)VrealizeFeatureh(Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;getAddedFeatures%()Lorg/biojava/bio/seq/FeatureHolder; addFeature (Lorg/biojava/bio/seq/Feature;)V&(Lorg/biojava/bio/symbol/SymbolList;)V((IILorg/biojava/bio/symbol/SymbolList;)V (Lorg/biojava/bio/symbol/Edit;)V*(Ljava/lang/String;Ljava/lang/Throwable;)Vorg/biojava/bio/seq/Feature!!"#$%I*+,& 78' ()*+,-#.%>*+& ;<'()*+/0%Z*p< *`<&?@A'()12345%> **&P' () 6278%>*<*= ***N*:Y -  &cd fgj"k*l'4"9:*;:>()><2>=23>B%7+ M, *, Y**+N*--&#*5'*7()7CD2EF* GH3#IJKLM%!e*<*= *Y*NY**:Y`-::Y JQT&2  &8JQTVb'HV NO&?;P8-9PJQRe()e<2e=23;STTUV WXA ?z@ PK .*?:c[3org/biojava/bio/seq/ComponentFeature$Template.class2 componentSequenceNameLjava/lang/String;componentSequenceLorg/biojava/bio/seq/Sequence;componentLocation!Lorg/biojava/bio/symbol/Location;()VCodeLineNumberTableLocalVariableTablethisTemplate InnerClasses/Lorg/biojava/bio/seq/ComponentFeature$Template; SourceFileComponentFeature.java -org/biojava/bio/seq/ComponentFeature$Template,org/biojava/bio/seq/StrandedFeature$Template$org/biojava/bio/seq/ComponentFeature#org/biojava/bio/seq/StrandedFeature!   /* f   PK .*?:m*org/biojava/bio/seq/ComponentFeature.class2Template InnerClassesgetComponentSequence ()Lorg/biojava/bio/seq/Sequence;getComponentLocation#()Lorg/biojava/bio/symbol/Location;getComponentSequenceName()Ljava/lang/String;isComponentResolvable()Z SourceFileComponentFeature.java$org/biojava/bio/seq/ComponentFeaturejava/lang/Object#org/biojava/bio/seq/StrandedFeature-org/biojava/bio/seq/ComponentFeature$Template     PK .*?:J$org/biojava/bio/seq/DNATools$1.class2   SourceFile DNATools.javaEnclosingMethod org/biojava/bio/seq/DNATools$1 InnerClassesjava/lang/Objectorg/biojava/bio/seq/DNATools  PK .*?:-nAA@org/biojava/bio/seq/DNATools$DNAComplementTranslationTable.class2/ " " #$ #%&'(()VCodeLineNumberTableLocalVariableTablethisDNAComplementTranslationTable InnerClasses? 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Can't find index for    #java/lang/IndexOutOfBoundsExceptionNo symbol for index   org/biojava/bio/symbol/Symbol#Really confused. 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SourceFileFeatureHolderUtilsTest.java 34attagagg HI ,- .- /-'org/biojava/bio/seq/SimpleFeatureHolder 01 21   ,org/biojava/bio/seq/StrandedFeature$Template JK$org/biojava/bio/symbol/RangeLocation 3 foo K *org/biojava/bio/seq/FeatureHolderUtilsTestjunit/framework/TestCasejava/lang/Exception%org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioExceptionorg/biojava/bio/seq/DNAToolscreateDNASequenceD(Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence; addFeature (Lorg/biojava/bio/seq/Feature;)V&org/biojava/bio/seq/FeatureHolderUtilsunionk(Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/seq/FeatureHolder;)Lorg/biojava/bio/seq/FeatureHolder;!org/biojava/bio/seq/FeatureHoldercontainsFeature (Lorg/biojava/bio/seq/Feature;)Z assertTrue(Z)V countFeatures()I assertEquals(II)V intersect assertFalsenotfeatureHolderAsSet4(Lorg/biojava/bio/seq/FeatureHolder;)Ljava/util/Set; java/util/Setcontains(Ljava/lang/Object;)Zaddremove#org/biojava/bio/seq/StrandedFeaturelocation!Lorg/biojava/bio/symbol/Location;POSITIVEStrand,Lorg/biojava/bio/seq/StrandedFeature$Strand;strandsourceorg/biojava/bio/AnnotationEMPTY_ANNOTATIONLorg/biojava/bio/Annotation; annotation createFeatureE(Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;*org/biojava/bio/seq/StrandedFeature$Strand$org/biojava/bio/seq/Feature$Templateorg/biojava/bio/seq/Feature!*+,-.-/-0121345/*6&7 89:45lL**+**+ **+  * Y **** * Y ** ** 6. 0234)647?8J:U;`<k=7l89d;<=>?45>**L+*+* +* +6@ AB&C3D=E7>89 2@A=BC45>**L+* +*+* +6H IJ&K3L=M7>89 2@A=BD45>**L+*+* +* +6P QR&S3T=U7>89 2@A=BE45`*L+*+* +* +* W+* +* W+* 6& XYZ"[/]:^G_R`_a7`89XFGHI56YN-,- Y!"-#$-%&-'(+-)6ef gh!i'j.k7*6896@A6JK.LO=PBQRNnM nM PK .*?:f)org/biojava/bio/seq/FeatureRealizer.class2  realizeFeatureTemplate InnerClasses(Lorg/biojava/bio/seq/Sequence;Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature; Exceptions SourceFileFeatureRealizer.java#org/biojava/bio/seq/FeatureRealizerjava/lang/Object$org/biojava/bio/seq/Feature$Templateorg/biojava/bio/BioExceptionorg/biojava/bio/seq/Feature     PK .*?:,NV1org/biojava/bio/seq/FeatureTypes$Repository.class2getName()Ljava/lang/String;getTypes()Ljava/util/Set;getTypeType InnerClasses;(Ljava/lang/String;)Lorg/biojava/bio/seq/FeatureTypes$Type; Exceptions SourceFileFeatureTypes.java+org/biojava/bio/seq/FeatureTypes$Repository Repositoryjava/lang/Objectorg/biojava/bio/Annotatable%org/biojava/bio/seq/FeatureTypes$Type java/util/NoSuchElementException org/biojava/bio/seq/FeatureTypes       PK .*?:O >org/biojava/bio/seq/FeatureTypes$RepositoryImpl$TypeImpl.class2d > ? @ A BC ? D EG I JK JLM ?N O !PQ RSTVannLorg/biojava/bio/Annotation;nameLjava/lang/String;schema#Lorg/biojava/bio/seq/FeatureFilter;parentsLjava/util/Set;this$0XRepositoryImpl InnerClasses1Lorg/biojava/bio/seq/FeatureTypes$RepositoryImpl;x(Lorg/biojava/bio/seq/FeatureTypes$RepositoryImpl;Ljava/lang/String;Lorg/biojava/bio/seq/FeatureFilter;Ljava/util/Set;)VCodeLineNumberTableLocalVariableTablethisTypeImpl:Lorg/biojava/bio/seq/FeatureTypes$RepositoryImpl$TypeImpl;getChangeSupportA(Lorg/biojava/utils/ChangeType;)Lorg/biojava/utils/ChangeSupport;ctLorg/biojava/utils/ChangeType;cs!Lorg/biojava/utils/ChangeSupport; getAnnotation()Lorg/biojava/bio/Annotation;getName()Ljava/lang/String; getSchema%()Lorg/biojava/bio/seq/FeatureFilter; getParents()Ljava/util/Set;getURI SourceFileFeatureTypes.java $ %Y    org/biojava/bio/SimpleAnnotation  -.Z/org/biojava/bio/Annotatable$AnnotationForwarderAnnotationForwarder %[\ ]0 ^_java/lang/StringBuilderuri:biojava.org:types/ `a 56/ b68org/biojava/bio/seq/FeatureTypes$RepositoryImpl$TypeImpl$org/biojava/utils/AbstractChangeablec%org/biojava/bio/seq/FeatureTypes$TypeType/org/biojava/bio/seq/FeatureTypes$RepositoryImpl()Vorg/biojava/bio/Annotatable6(Ljava/lang/Object;Lorg/biojava/utils/ChangeSupport;)Vorg/biojava/bio/AnnotationPROPERTYaddChangeListenerC(Lorg/biojava/utils/ChangeListener;Lorg/biojava/utils/ChangeType;)Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString org/biojava/bio/seq/FeatureTypes  $%&'%*+**,*-**Y([ \]^_$`)*%*,%%%-.'c*+ M* Y*, ,(cde) *,/01234'/*(i) *,56'/*(m) *,78'/*(q) *,9:'/*(u) *,;6'P&Y**(y) &*,<=#"!U" !+ FH UW PK .*?:i 5org/biojava/bio/seq/FeatureTypes$RepositoryImpl.class2 L MN L OP L Q RT V WX WY Z[ Z\^_` La bc d e fg h ZijklRepositoryImpl InnerClassesTypeImplnameLjava/lang/String;typesLjava/util/Map;annLorg/biojava/bio/Annotation;(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis1Lorg/biojava/bio/seq/FeatureTypes$RepositoryImpl;getChangeSupportA(Lorg/biojava/utils/ChangeType;)Lorg/biojava/utils/ChangeSupport;ctLorg/biojava/utils/ChangeType;cs!Lorg/biojava/utils/ChangeSupport; getAnnotation()Lorg/biojava/bio/Annotation;getName()Ljava/lang/String;getTypes()Ljava/util/Set;getTypeType;(Ljava/lang/String;)Lorg/biojava/bio/seq/FeatureTypes$Type;type'Lorg/biojava/bio/seq/FeatureTypes$Type; StackMapTable^ Exceptions createTypem(Ljava/lang/String;Lorg/biojava/bio/seq/FeatureFilter;Ljava/util/Set;)Lorg/biojava/bio/seq/FeatureTypes$Type;schema#Lorg/biojava/bio/seq/FeatureFilter;parentsLjava/util/Set; SourceFileFeatureTypes.java )n #$java/util/HashMap %& org/biojava/bio/SimpleAnnotation '( 01o/org/biojava/bio/Annotatable$AnnotationForwarderAnnotationForwarder )pq r3 stu v; wxy%org/biojava/bio/seq/FeatureTypes$Type java/util/NoSuchElementExceptionjava/lang/StringBuilderCould not find type z{ in repository 89 |9 )*8org/biojava/bio/seq/FeatureTypes$RepositoryImpl$TypeImpl )} ~/org/biojava/bio/seq/FeatureTypes$RepositoryImpl$org/biojava/utils/AbstractChangeable+org/biojava/bio/seq/FeatureTypes$Repository Repository()Vorg/biojava/bio/Annotatable6(Ljava/lang/Object;Lorg/biojava/utils/ChangeSupport;)Vorg/biojava/bio/AnnotationPROPERTYaddChangeListenerC(Lorg/biojava/utils/ChangeListener;Lorg/biojava/utils/ChangeType;)V java/util/MapkeySetget&(Ljava/lang/Object;)Ljava/lang/Object; org/biojava/bio/seq/FeatureTypesappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toStringx(Lorg/biojava/bio/seq/FeatureTypes$RepositoryImpl;Ljava/lang/String;Lorg/biojava/bio/seq/FeatureFilter;Ljava/util/Set;)Vput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;!#$%&'()*+d **+*Y*Y, - ./ #$01+c*+ M* Y*, ,,!"#- ./234567+/*,'- ./89+/*,+- ./:;+4 *,/-  ./<>+;*+M,*YY+*,,4569;- ;./;#$-?@A9BCDE+wY*+,-:*+W,J KL-4./#$FGHI ?@JK!*] "]= SU ]m PK .*?:T(+org/biojava/bio/seq/FeatureTypes$Type.class2 getSchema%()Lorg/biojava/bio/seq/FeatureFilter;getName()Ljava/lang/String; getParents()Ljava/util/Set;getURI SourceFileFeatureTypes.java%org/biojava/bio/seq/FeatureTypes$TypeType InnerClassesjava/lang/Objectorg/biojava/bio/Annotatable org/biojava/bio/seq/FeatureTypes       PK .*?:o= &org/biojava/bio/seq/FeatureTypes.class2 %] $^_`a ]b c d e fg h fi fjk lm n op q r $s t )u )v wx wy z{ z|} $t $~ "]RepositoryImpl InnerClassesType Repository repositoriesLjava/util/Map; URI_PREFIXLjava/lang/String; ConstantValue()VCodeLineNumberTableLocalVariableTablethis"Lorg/biojava/bio/seq/FeatureTypes; getRepositoryA(Ljava/lang/String;)Lorg/biojava/bio/seq/FeatureTypes$Repository;namerep-Lorg/biojava/bio/seq/FeatureTypes$Repository; StackMapTable_ ExceptionsgetRepositoryNames()Ljava/util/Set; addRepository0(Lorg/biojava/bio/seq/FeatureTypes$Repository;)VreposremoveRepositorygetType;(Ljava/lang/String;)Lorg/biojava/bio/seq/FeatureTypes$Type;urinamesslashIrepNametypeName isSubTypeOfQ(Lorg/biojava/bio/seq/FeatureTypes$Type;Lorg/biojava/bio/seq/FeatureTypes$Type;)ZpuriiLjava/util/Iterator;subType'Lorg/biojava/bio/seq/FeatureTypes$Type; superTypeparentsLjava/util/Set; SourceFileFeatureTypes.java 12 ,-+org/biojava/bio/seq/FeatureTypes$Repository java/util/NoSuchElementExceptionjava/lang/StringBuilderCould not find repository: 1 A uri:biojava.org:types =All types start with: uri:biojava.org:types while processing / 89 FG A   java/lang/String NOorg/biojava/utils/SmallMap org/biojava/bio/seq/FeatureTypesjava/lang/Object/org/biojava/bio/seq/FeatureTypes$RepositoryImpl%org/biojava/bio/seq/FeatureTypes$Type java/util/Setjava/util/Iteratorappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/String;)V java/util/MapkeySetgetNameput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;remove&(Ljava/lang/Object;)Ljava/lang/Object; startsWith(Ljava/lang/String;)Zlength()I substring(I)Ljava/lang/String;indexOf(Ljava/lang/String;)I(II)Ljava/lang/String; getParentsgetURIcontains(Ljava/lang/Object;)Ziterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object;!$%,-./01233*4 B5 67 893v(L+YY* +4WY Z&]5(:/!;<=&>? @A3!  4f BC3?* * W4 op5 D< EC3>* W4 xy5 D< FG3W*YY* *`L*=+N+`:-:4" $07>GM5>WH/0'I/7 JK>L/GM/M ;<=$ NO3?*M,+,N--: +!4(3=543 P/QR?ST?UT8VW=XYZ23' "Y#4 I J[\(&$' )$* $+ PK .*?:d;];org/biojava/bio/seq/FilterUtils$DelegatingTransformer.class2- ! " # $ %'()t1FilterTransformer InnerClasses3Lorg/biojava/bio/seq/FilterUtils$FilterTransformer;t2this$0!Lorg/biojava/bio/seq/FilterUtils;(Lorg/biojava/bio/seq/FilterUtils;Lorg/biojava/bio/seq/FilterUtils$FilterTransformer;Lorg/biojava/bio/seq/FilterUtils$FilterTransformer;)VCodeLineNumberTableLocalVariableTablethisDelegatingTransformer7Lorg/biojava/bio/seq/FilterUtils$DelegatingTransformer; transformH(Lorg/biojava/bio/seq/FeatureFilter;)Lorg/biojava/bio/seq/FeatureFilter;ff#Lorg/biojava/bio/seq/FeatureFilter;res StackMapTable* SourceFileFilterUtils.java  + ,5org/biojava/bio/seq/FilterUtils$DelegatingTransformerjava/lang/Object1org/biojava/bio/seq/FilterUtils$FilterTransformer!org/biojava/bio/seq/FeatureFilter()Vorg/biojava/bio/seq/FilterUtils! ^*+**,*-. /01   t*+M,*+M,4 568   &  &PK .*?: PDD7org/biojava/bio/seq/FilterUtils$FilterTransformer.class2   transformH(Lorg/biojava/bio/seq/FeatureFilter;)Lorg/biojava/bio/seq/FeatureFilter; SourceFileFilterUtils.java 1org/biojava/bio/seq/FilterUtils$FilterTransformerFilterTransformer InnerClassesjava/lang/Objectorg/biojava/bio/seq/FilterUtils   PK .*?:HH%org/biojava/bio/seq/FilterUtils.class2" FGH IJ K L MN O P QR O QS T UV WXY bZ[ ]^ ]`b de d g hi jkl $F mn 'o 'K pq +Is -Iu /w x xy 3x{ 5x} 7I      > @ BF Dw    I K   O Q S U W Y [I b b b              j h  >   u         U  S     DelegatingTransformer InnerClassesFilterTransformer()VCodeLineNumberTableLocalVariableTablethis!Lorg/biojava/bio/seq/FilterUtils;areProperSubsetI(Lorg/biojava/bio/seq/FeatureFilter;Lorg/biojava/bio/seq/FeatureFilter;)Zand_supAnd'Lorg/biojava/bio/seq/FeatureFilter$And;and_subor_subOr&Lorg/biojava/bio/seq/FeatureFilter$Or;or_supnot_sup#Lorg/biojava/bio/seq/FeatureFilter;subsup StackMapTableNR areDisjointand_aand_bor_aor_bnot_anot_babextractOverlappingLocationF(Lorg/biojava/bio/seq/FeatureFilter;)Lorg/biojava/bio/symbol/Location;ffal1!Lorg/biojava/bio/symbol/Location;l2ffoffareEqualf1fLjava/util/List;f2ff1f2byType7(Ljava/lang/String;)Lorg/biojava/bio/seq/FeatureFilter;typeLjava/lang/String;bySourcesourcebyClass6(Ljava/lang/Class;)Lorg/biojava/bio/seq/FeatureFilter;clazzLjava/lang/Class; 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translate@(Lorg/biojava/bio/symbol/Symbol;)Lorg/biojava/bio/symbol/Symbol;sLorg/biojava/bio/symbol/Symbol; Exceptions) untranslategetSourceAlphabet#()Lorg/biojava/bio/symbol/Alphabet;getTargetAlphabet**(Lorg/biojava/bio/seq/NucleotideTools$1;)Vx0'Lorg/biojava/bio/seq/NucleotideTools$1; SourceFileNucleotideTools.java  + , -.Horg/biojava/bio/seq/NucleotideTools$NucleotideComplementTranslationTablejava/lang/Object1org/biojava/bio/symbol/ReversibleTranslationTable-org/biojava/bio/symbol/IllegalSymbolException%org/biojava/bio/seq/NucleotideTools$1#org/biojava/bio/seq/NucleotideTools complement getNucleotide)()Lorg/biojava/bio/symbol/FiniteAlphabet;   /*    9+    9+    .    .    9*    !# #PK .*?:|-_pp)org/biojava/bio/seq/NucleotideTools.class2G X X X X X X X X X X X X X X X X Y X X @    X[  @ % % 2 % $ % , X   % X X X    D @  2 @ N @ X  @ T      InnerClasses$NucleotideComplementTranslationTablecomplementTable3Lorg/biojava/bio/symbol/ReversibleTranslationTable; nucleotide'Lorg/biojava/bio/symbol/FiniteAlphabet;nucleotideTokens+Lorg/biojava/bio/seq/io/SymbolTokenization;a%Lorg/biojava/bio/symbol/AtomicSymbol;gcturLorg/biojava/bio/symbol/Symbol;ymkswbdhvnsymbolToComplementLjava/util/Map;'()Lorg/biojava/bio/symbol/AtomicSymbol;CodeLineNumberTable!()Lorg/biojava/bio/symbol/Symbol;()VLocalVariableTablethis%Lorg/biojava/bio/seq/NucleotideTools; getNucleotide)()Lorg/biojava/bio/symbol/FiniteAlphabet;createNucleotide7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;pseLorg/biojava/bio/BioException;Ljava/lang/String; StackMapTable ExceptionscreateNucleotideSequenceD(Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;nameindex"(Lorg/biojava/bio/symbol/Symbol;)IsymforIndex"(I)Lorg/biojava/bio/symbol/Symbol;I complement@(Lorg/biojava/bio/symbol/Symbol;)Lorg/biojava/bio/symbol/Symbol; forSymbol"(C)Lorg/biojava/bio/symbol/Symbol;tokenCH(Lorg/biojava/bio/symbol/SymbolList;)Lorg/biojava/bio/symbol/SymbolList;list#Lorg/biojava/bio/symbol/SymbolList;reverseComplement5()Lorg/biojava/bio/symbol/ReversibleTranslationTable;nucleotideToken"(Lorg/biojava/bio/symbol/Symbol;)CjLjava/util/Iterator;lLjava/util/Set;asmatchesisymsgapLjava/lang/Throwable;  SourceFileNucleotideTools.java de fe ge he ie jk lk mk nk ok pk qk rk sk tk uk |} `a 'org/biojava/bio/symbol/SimpleSymbolList |org/biojava/bio/BioExceptionorg/biojava/bio/BioError.Something has gone badly wrong with Nucleotide |.org/biojava/bio/seq/impl/SimpleSequenceFactory  org/biojava/bio/SimpleAnnotation  -org/biojava/bio/symbol/IllegalSymbolExceptionjava/lang/StringBuilder&Really confused. Can't find index for    |#java/lang/IndexOutOfBoundsExceptionNo symbol for index  vw! "#org/biojava/bio/symbol/Symbol#Really confused. Can't find symbol  Unable to find symbol for token $ ^% &' ( ^_ bc) *+, -. NUCLEOTIDE/ 01%org/biojava/bio/symbol/FiniteAlphabetagcturymkswbdhvn 2#org/biojava/bio/symbol/AtomicSymboljava/util/HashMap 3{ 45 67 89 :; <= >? @Ajava/util/HashSet BC DEHorg/biojava/bio/seq/NucleotideTools$NucleotideComplementTranslationTable |Fjava/lang/Throwable$Unable to initialize NucleotideTools#org/biojava/bio/seq/NucleotideToolsjava/lang/Object%org/biojava/bio/seq/NucleotideTools$1/org/biojava/bio/symbol/IllegalAlphabetException!org/biojava/bio/symbol/SymbolListjava/util/Iterator java/util/SetgetTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;@(Lorg/biojava/bio/seq/io/SymbolTokenization;Ljava/lang/String;)V*(Ljava/lang/String;Ljava/lang/Throwable;)VcreateSequence(Lorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/bio/Annotation;)Lorg/biojava/bio/seq/Sequence;validate"(Lorg/biojava/bio/symbol/Symbol;)Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;getName()Ljava/lang/String;toString(Ljava/lang/String;)V(I)Ljava/lang/StringBuilder; java/util/Mapget&(Ljava/lang/Object;)Ljava/lang/Object;(C)Ljava/lang/StringBuilder;&org/biojava/bio/symbol/SymbolListViews translateq(Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/TranslationTable;)Lorg/biojava/bio/symbol/SymbolList;reverse)org/biojava/bio/seq/io/SymbolTokenizationtokenizeSymbol3(Lorg/biojava/bio/symbol/Symbol;)Ljava/lang/String;java/lang/StringcharAt(I)C&org/biojava/bio/symbol/AlphabetManageralphabetForName5(Ljava/lang/String;)Lorg/biojava/bio/symbol/Alphabet;symbolAt getGapSymbolput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object; getAllSymbols8(Lorg/biojava/bio/symbol/FiniteAlphabet;)Ljava/util/Set;iterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object; getMatches#()Lorg/biojava/bio/symbol/Alphabet;size()Iadd(Ljava/lang/Object;)Z getAmbiguity0(Ljava/util/Set;)Lorg/biojava/bio/symbol/Symbol;*(Lorg/biojava/bio/seq/NucleotideTools$1;)V1XY^_`abcdefegeheiejklkmknkokpkqkrksktkuk vw dxyz fxyz gxyz hxyz ixyz j{yz l{yz m{yz n{y z o{y z p{y z q{y z r{y z s{yz t{yz u{yz|}y3*z ~  yz y!LY+*LY+z6 8:<~  c !`U$ y%Y*+ Y!"MY,z`hj~  %`%Y$ yV******#$Y%Y&'(*)(*+z2  "$+-6~ Vk $ yG,Y%Y&-(.*/z.  #(,~ G, ys*****0*12L++*#Y%Y&3(*)(*4z> !( , 37DHJS~skD/ok  $ yMagctu$Y%Y&5(6*+z. <> @BDFH$J(L.N2R~ M $ y2*78zj~  y5 *978z~   ^y:z y8;*<=z~ k$}y>?@;Y;AK*BC*BC*BC*BC*BC*B*B*B* B * B * B * B * B *B*B*BDYE0FL0++GWHIM,Jn,K2N-L@:MKNYO:P:JK2QRW0-SGWTYU:KYW*Vz$ %2?LYfq|'2;Nfz}~RD";?^k'Sa t%ck h> :!  \ZXTX] PK .*?:7+org/biojava/bio/seq/OptimizableFilter.class2    isProperSubset&(Lorg/biojava/bio/seq/FeatureFilter;)Z isDisjoint SourceFileOptimizableFilter.java%org/biojava/bio/seq/OptimizableFilterjava/lang/Object!org/biojava/bio/seq/FeatureFilterPK .*?:kޛ.*.*&org/biojava/bio/seq/ProteinTools.class2  [ [ [  [ R    [ ! " #$%  [&'  () [*+, [-. [/0 [12 [34 [56 [78 [9: [;< [= [>? [@A [BC [DE [FG [HI [JK [LM [NO [PQ [RS [TU [VWX N Y Z[\] R^ _` _a bc defg hij klm no ap qr qs tuv wx fy z{ Y|} [~ k  x   x  x b k proteinAlpha'Lorg/biojava/bio/symbol/FiniteAlphabet; proteinTAlpha tokenToSymbolLjava/util/Map;propertyTableMap()VCodeLineNumberTableLocalVariableTablethis"Lorg/biojava/bio/seq/ProteinTools; getAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet; getTAlphabetgetSymbolPropertyTable@(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolPropertyTable;nameLjava/lang/String; createProtein7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;eLorg/biojava/bio/BioException; theProteinp+Lorg/biojava/bio/seq/io/SymbolTokenization; StackMapTable ExceptionscreateGappedProteinSequenceJ(Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/bio/seq/GappedSequence; theProtein1proteinLorg/biojava/bio/seq/Sequence;protein1$Lorg/biojava/bio/seq/GappedSequence;posIcreateProteinSequenceD(Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;seala'()Lorg/biojava/bio/symbol/AtomicSymbol;aargrasnnaspdcyscglnqgluglyghishileileullyskmetmphefpropylosecusersthrttrpwtyryvalvter%Lorg/biojava/bio/symbol/AtomicSymbol;Ljava/util/Iterator;stLjava/lang/Exception; tablesStreamLjava/io/InputStream;isLorg/xml/sax/InputSource;parser#Ljavax/xml/parsers/DocumentBuilder;mre$Ljava/util/MissingResourceException;valueelLorg/w3c/dom/Element;jtokenLorg/biojava/bio/symbol/Symbol; properyNodesLorg/w3c/dom/NodeList;cnodeLorg/w3c/dom/Node;childmonoMassPropertyTable2Lorg/biojava/bio/symbol/SimpleSymbolPropertyTable;avgMassPropertyTablepK_NtermPropertyTablepKPropertyTablepK_CtermPropertyTableHydropathicityTabletokenschildrendocLorg/w3c/dom/Document;ev} SourceFileProteinTools.java  *org/biojava/bio/symbol/SymbolPropertyTable org/biojava/bio/BioExceptionorg/biojava/bio/BioError+Something has gone badly wrong with Protein 'org/biojava/bio/symbol/SimpleSymbolList -  -org/biojava/bio/seq/impl/SimpleGappedSequence   .org/biojava/bio/seq/impl/SimpleSequenceFactory  org/biojava/bio/SimpleAnnotation 1Something has gone badly wrong with ProteinTAlpha A#org/biojava/bio/symbol/AtomicSymbol R N D C Q E G H L K M F P O U S T W Y V *java/util/HashMapPROTEIN %org/biojava/bio/symbol/FiniteAlphabet PROTEIN-TERM     java/lang/Exception" Could not initialize ProteinTools org/biojava/bio/seq/ProteinTools ,org/biojava/bio/symbol/ResidueProperties.xml &Couldn't locate ResidueProperties.xml. org/xml/sax/InputSource    "java/util/MissingResourceException    0org/biojava/bio/symbol/SimpleSymbolPropertyTable monoMass avgMasspK_NtermpKpK_Ctermhydropathicity    org/w3c/dom/Element residue    java/lang/Objectjava/lang/String)org/biojava/bio/seq/io/SymbolTokenization-org/biojava/bio/symbol/IllegalSymbolExceptionorg/biojava/bio/seq/Sequence"org/biojava/bio/seq/GappedSequencejava/util/Iteratororg/w3c/dom/Documentjava/io/InputStreamorg/w3c/dom/NodeListorg/w3c/dom/Nodeorg/biojava/bio/symbol/Symbol java/util/Mapget&(Ljava/lang/Object;)Ljava/lang/Object;getTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;*(Ljava/lang/String;Ljava/lang/Throwable;)V@(Lorg/biojava/bio/seq/io/SymbolTokenization;Ljava/lang/String;)V replaceAll8(Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;!(Lorg/biojava/bio/seq/Sequence;)VindexOf(II)I addGapInView(I)VcreateSequence(Lorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/bio/Annotation;)Lorg/biojava/bio/seq/Sequence;&org/biojava/bio/symbol/AlphabetManageralphabetForName5(Ljava/lang/String;)Lorg/biojava/bio/symbol/Alphabet;iterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object;tokenizeSymbol3(Lorg/biojava/bio/symbol/Symbol;)Ljava/lang/String;put8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;org/biojava/utils/ClassToolsgetClassLoader*(Ljava/lang/Class;)Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;(Ljava/lang/String;)V(Ljava/io/InputStream;)V(javax/xml/parsers/DocumentBuilderFactory newInstance,()Ljavax/xml/parsers/DocumentBuilderFactory;newDocumentBuilder%()Ljavax/xml/parsers/DocumentBuilder;!javax/xml/parsers/DocumentBuilderparse1(Lorg/xml/sax/InputSource;)Lorg/w3c/dom/Document;java/lang/SystemerrLjava/io/PrintStream; getMessage()Ljava/lang/String;java/io/PrintStreamprintlnprintStackTrace6(Lorg/biojava/bio/symbol/Alphabet;Ljava/lang/String;)VgetDocumentElement()Lorg/w3c/dom/Element; getChildNodes()Lorg/w3c/dom/NodeList; getLength()Iitem(I)Lorg/w3c/dom/Node; getNodeNameequals(Ljava/lang/Object;)Z getAttribute&(Ljava/lang/String;)Ljava/lang/String; parseToken3(Ljava/lang/String;)Lorg/biojava/bio/symbol/Symbol;setDoubleProperty4(Lorg/biojava/bio/symbol/Symbol;Ljava/lang/String;)V![53*  7 *  &L LM Y , Y+*     &$  E*M,+NY-:*-6`*-`6" "(3B>EE <6,"#" %Y*+YM Y,    %%Y & !! ") &#!1 $9 &%!A &I &'!Q (Y &)!a *i &+!q ,y &-! . &/! 0 &1! 2 &3! 4 &5! 6 &7! 8 &9! : &;! < &=! > &?! @ &A!! B) &C!1 D9 &E!A FI &G!Q HY &I!a Ji &K!p Lx &M!}޻NYONYOPQRSQR KTL+U!+V!M*,W,XWܧK YZ* K[\]^L+ Y_`aY+bMcdN-,eKLg+hiL+jkYlmnLkYlonMkYlpnNkYlqn:kYlrn:kYlsn:l :*tu:6  vQ w:  x5 x:  yz{ |:  }:  u:6vw:  x x:~|:m{|:+ o{|:, p{|:- cq{|: Br{|: !s{|:  m+XWo,XWp-XWqXWrXWsXWL YZ+ ehYvfvYY:NF HLM*N5OGPQQbReVhTiUt\vfijmnotpqtrsw| &5@HKRalw !,5BMVcnw}V"Q>'50i $   , M n l w @= R+ )Z  & vg>&B Ml !7 !1  M   PK /*?:*org/biojava/bio/seq/ProteinToolsTest.class2 @[\ ]^_ `a ?bcd ?e ?f gh ?i gj ?kl gm no gp gq gr gs gt gu gv gw gx gy gz g{ g| g} g~ g g g g g g g g g g g g g g g g g g g g g g g g g g g g g gtokens+Lorg/biojava/bio/seq/io/SymbolTokenization; proteinAlpha'Lorg/biojava/bio/symbol/FiniteAlphabet; proteinTAlpha(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis&Lorg/biojava/bio/seq/ProteinToolsTest;nameLjava/lang/String;setUp()V Exceptions testGetAlpha StackMapTabletestCreateProteinaa#Lorg/biojava/bio/symbol/SymbolList; SourceFileProteinToolsTest.java FG PROTEIN-TERM token ABPROTEIN%org/biojava/bio/symbol/FiniteAlphabet CD ED arndcqeghilkmfpstwyvuo*x  $org/biojava/bio/seq/ProteinToolsTestjunit/framework/TestCasejava/lang/Exception!org/biojava/bio/symbol/SymbolList&org/biojava/bio/symbol/AlphabetManageralphabetForName5(Ljava/lang/String;)Lorg/biojava/bio/symbol/Alphabet;org/biojava/bio/symbol/AlphabetgetTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization; org/biojava/bio/seq/ProteinTools getAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet; assertEquals'(Ljava/lang/Object;Ljava/lang/Object;)V getTAlphabet assertTrue(Z)V createProtein7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;symbolAt"(I)Lorg/biojava/bio/symbol/Symbol;a'()Lorg/biojava/bio/symbol/AtomicSymbol;alarargnasndaspccysqglneglugglyhhisiilelleuklysmmetfphepprossertthrwtrpytyrvvalusecopylter!?@ABCDEDFGH>*+I 23JKLMNOPH_)** * I79:(<J )KLQRSPH9* * * * IA CF&G8HJ 9KLT"@@UPH[L+++++++++++++++ +!+ "+ #+ $+ %+ &+ '+ (+ )+ *+ ++,+-+.+/+0+1+2+3+4+5+6+7+8+9+:+;+<+=+>I/LOP0RESZUoVXY[\^_ab0dFe\grhjkmnpq s"t8vNwdyzz|}*@VlJKLVWTZX@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@QRYZPK /*?:,P$org/biojava/bio/seq/RNATools$1.class2   SourceFile RNATools.javaEnclosingMethod org/biojava/bio/seq/RNATools$1 InnerClassesjava/lang/Objectorg/biojava/bio/seq/RNATools  PK /*?: 55@org/biojava/bio/seq/RNATools$RNAComplementTranslationTable.class2- ! ! "# "$%&()VCodeLineNumberTableLocalVariableTablethisRNAComplementTranslationTable InnerClasses ? $< G@ ABCD < <EF GH GI JK JL GM GN GO GPQ GR ST UV UWXY =Z[\ ?< A] ^_ J`a Gbc def ghij Lk lm ln op qr Us tu tvw Ux <y Uz &{ =| U}~   = = ^ ^  = A ^ v#  & *  |# T G S    |      G InnerClassesRNAComplementTranslationTablecomplementTable3Lorg/biojava/bio/symbol/ReversibleTranslationTable;transcriptionTable9Lorg/biojava/bio/symbol/SimpleReversibleTranslationTable;rna'Lorg/biojava/bio/symbol/FiniteAlphabet; geneticCodesLjava/util/Map;a%Lorg/biojava/bio/symbol/AtomicSymbol;gcunLorg/biojava/bio/symbol/Symbol;symbolToComplement'()Lorg/biojava/bio/symbol/AtomicSymbol;CodeLineNumberTable!()Lorg/biojava/bio/symbol/Symbol;()VLocalVariableTablethisLorg/biojava/bio/seq/RNATools;getRNA)()Lorg/biojava/bio/symbol/FiniteAlphabet;getCodonAlphabet createRNA7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;eLorg/biojava/bio/BioException;Ljava/lang/String;p+Lorg/biojava/bio/seq/io/SymbolTokenization; StackMapTableX+ ExceptionscreateRNASequenceD(Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;senameindex"(Lorg/biojava/bio/symbol/Symbol;)IsymforIndex"(I)Lorg/biojava/bio/symbol/Symbol;I complement@(Lorg/biojava/bio/symbol/Symbol;)Lorg/biojava/bio/symbol/Symbol;sC forSymbol"(C)Lorg/biojava/bio/symbol/Symbol;tokenCttokeH(Lorg/biojava/bio/symbol/SymbolList;)Lorg/biojava/bio/symbol/SymbolList;list#Lorg/biojava/bio/symbol/SymbolList;reverseComplement transcribe Deprecated5()Lorg/biojava/bio/symbol/ReversibleTranslationTable;getGeneticCodeF(Ljava/lang/String;)Lorg/biojava/bio/symbol/ManyToOneTranslationTable;5(I)Lorg/biojava/bio/symbol/ManyToOneTranslationTable; tableNametable/Lorg/biojava/bio/symbol/SimpleGeneticCodeTable; table_numtablesLjava/util/Set;itLjava/util/Iterator;getGeneticCodeNames()Ljava/util/Set; translatesymsloadGeneticCodesnum descriptionteLorg/w3c/dom/Element;fromto fromSymbolsfromStoStnLorg/w3c/dom/Node;jsourcetargetsourceAtargetAtargetP translatesLorg/w3c/dom/NodeList;cnodechildi tablesStreamLjava/io/InputStream;isLorg/xml/sax/InputSource;parser#Ljavax/xml/parsers/DocumentBuilder;docLorg/w3c/dom/Document;childrenLjava/lang/Exception;jw(YlasmatchesgapLjava/lang/Throwable; SourceFile RNATools.java (RNA x RNA x RNA) %org/biojava/bio/symbol/FiniteAlphabet org/biojava/bio/BioExceptionorg/biojava/bio/BioError'Something has gone badly wrong with RNA 'org/biojava/bio/symbol/SimpleSymbolList .org/biojava/bio/seq/impl/SimpleSequenceFactory  org/biojava/bio/SimpleAnnotation  -org/biojava/bio/symbol/IllegalSymbolExceptionjava/lang/StringBuilder&Really confused. Can't find index for    #java/lang/IndexOutOfBoundsExceptionNo symbol for index   org/biojava/bio/symbol/Symbol#Really confused. Can't find symbol .Cannot find the 'token' Tokenization for RNA!?     0org/biojava/bio/symbol/ManyToOneTranslationTable    java/lang/String-org/biojava/bio/symbol/SimpleGeneticCodeTable "java/lang/IllegalArgumentException-There is no genetic code table at that number    UNIVERSAL org/biojava/bio/seq/RNATools )org/biojava/bio/seq/TranslationTables.xml &Couldn't locate TranslationTables.xml.org/xml/sax/InputSource        org/w3c/dom/Element       transl_tablevalue     `' is not a valid codon  #org/biojava/bio/symbol/AtomicSymbol  java/lang/Exception$Couldn't parse TranslationTables.xmlRNAagcun java/util/HashMap       java/util/HashSet  :org/biojava/bio/seq/RNATools$RNAComplementTranslationTable 7org/biojava/bio/symbol/SimpleReversibleTranslationTable  java/lang/ThrowableUnable to initialize RNAToolsjava/lang/Objectorg/biojava/bio/seq/RNATools$1)org/biojava/bio/seq/io/SymbolTokenization/org/biojava/bio/symbol/IllegalAlphabetException java/util/Setjava/util/Iteratorjava/io/InputStream!javax/xml/parsers/DocumentBuilderorg/w3c/dom/Documentorg/w3c/dom/NodeListorg/w3c/dom/Node!org/biojava/bio/symbol/SymbolList&org/biojava/bio/symbol/AlphabetManager!generateCrossProductAlphaFromName5(Ljava/lang/String;)Lorg/biojava/bio/symbol/Alphabet;getTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;*(Ljava/lang/String;Ljava/lang/Throwable;)V@(Lorg/biojava/bio/seq/io/SymbolTokenization;Ljava/lang/String;)VcreateSequence(Lorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/bio/Annotation;)Lorg/biojava/bio/seq/Sequence;validate"(Lorg/biojava/bio/symbol/Symbol;)Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;getName()Ljava/lang/String;toString(Ljava/lang/String;)V(I)Ljava/lang/StringBuilder; java/util/Mapget&(Ljava/lang/Object;)Ljava/lang/Object;valueOf(C)Ljava/lang/String; parseToken3(Ljava/lang/String;)Lorg/biojava/bio/symbol/Symbol;&org/biojava/bio/symbol/SymbolListViewsq(Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/TranslationTable;)Lorg/biojava/bio/symbol/SymbolList;reverseiterator()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object;getTableNumber()IkeySet getAlphabet#()Lorg/biojava/bio/symbol/Alphabet;windowedSymbolListI(Lorg/biojava/bio/symbol/SymbolList;I)Lorg/biojava/bio/symbol/SymbolList;org/biojava/utils/ClassToolsgetClassLoader*(Ljava/lang/Class;)Ljava/lang/ClassLoader;java/lang/ClassLoadergetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;(Ljava/io/InputStream;)V(javax/xml/parsers/DocumentBuilderFactory newInstance,()Ljavax/xml/parsers/DocumentBuilderFactory;newDocumentBuilder%()Ljavax/xml/parsers/DocumentBuilder;parse1(Lorg/xml/sax/InputSource;)Lorg/w3c/dom/Document;getDocumentElement()Lorg/w3c/dom/Element; getChildNodes()Lorg/w3c/dom/NodeList; getLengthitem(I)Lorg/w3c/dom/Node; getNodeNameequals(Ljava/lang/Object;)Z getAttribute&(Ljava/lang/String;)Ljava/lang/String;alphabetForNameQ(Lorg/biojava/bio/symbol/FiniteAlphabet;Lorg/biojava/bio/symbol/FiniteAlphabet;)V getTagNamejava/lang/Integer'(Ljava/lang/String;)Ljava/lang/Integer;intValuesetTableNumber(I)VsetDescriptionlengthtoList()Ljava/util/List; getSymbol1(Ljava/util/List;)Lorg/biojava/bio/symbol/Symbol;setTranslationM(Lorg/biojava/bio/symbol/AtomicSymbol;Lorg/biojava/bio/symbol/AtomicSymbol;)Vput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;symbolAt getGapSymbol getAllSymbols8(Lorg/biojava/bio/symbol/FiniteAlphabet;)Ljava/util/Set; getMatchessizeadd getAmbiguity0(Ljava/util/Set;)Lorg/biojava/bio/symbol/Symbol;#(Lorg/biojava/bio/seq/RNATools$1;)Vorg/biojava/bio/seq/DNAToolsgetDNA1G       3*    !   &L  LMY,Y+*    &$  %Y*+YMY,  %%Y M**** *YY *! "#*  "$- M  >$YY% &"'&  # >$ h****(*)*L++ *YY+ *! ",6  !(, 9 = ? Hh9/   '-L  MNY.-,+/"%#$&* '"  2*012  5 *201>   2*31K  4U 5^ 7 6*)7  E8L+9M,:*,;ӻ?Y@A&  ,58;4, EA :  , ! 6B W*C *DK*EF1   GHIJK* YK,LY*MLNOM,+PN-QR:6SzT:U^U:V:WXDYZ: [Z: \Z:  ] :  ] :  Y :=Y  ^:R:6ST:UU:_`X0aZbc6dZ:efvgZ:hZ::i$YYj  k ", lmn:/n:o(6 pWKYr*q/ #*0=LW_bir| &-47BMT_  &BhM]TV 6 +    WfiTrK@ #*0=   %    !r    aH)         B cs] Y tK*un*un*un*un*uvYw(xL(++pWy9M,:n,;*N-z :{K|Y}:~::;*W(-pWY4Y55555vYw6KY*SV~X Z[,\9]F^S_]agdpe{hijklmnprsuv"w.x:yF{P|SV}W~bR"?^St4pW >:!Z GG PK /*?::U4 *org/biojava/bio/seq/RNAToolsTest$1$1.class2P D EFGHthis$1I InnerClasses$Lorg/biojava/bio/seq/RNAToolsTest$1;'(Lorg/biojava/bio/seq/RNAToolsTest$1;)VCodeLineNumberTableLocalVariableTablethis&Lorg/biojava/bio/seq/RNAToolsTest$1$1;size()IgetName()Ljava/lang/String; getAnnotation()Lorg/biojava/bio/Annotation;addChangeListener%(Lorg/biojava/utils/ChangeListener;)Vcl"Lorg/biojava/utils/ChangeListener;iterator()Ljava/util/Iterator; getAlphabets()Ljava/util/List;C(Lorg/biojava/utils/ChangeListener;Lorg/biojava/utils/ChangeType;)VctLorg/biojava/utils/ChangeType; addSymbol"(Lorg/biojava/bio/symbol/Symbol;)VsLorg/biojava/bio/symbol/Symbol; ExceptionsJK getSymbol1(Ljava/util/List;)Lorg/biojava/bio/symbol/Symbol;rlLjava/util/List;removeChangeListener removeSymbol getAmbiguity0(Ljava/util/Set;)Lorg/biojava/bio/symbol/Symbol;symsLjava/util/Set; getGapSymbol!()Lorg/biojava/bio/symbol/Symbol; isUnchanging!(Lorg/biojava/utils/ChangeType;)Zcontains"(Lorg/biojava/bio/symbol/Symbol;)ZvalidategetTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;nameLjava/lang/String;L SourceFileRNAToolsTest.javaEnclosingMethod MN  O$org/biojava/bio/seq/RNAToolsTest$1$1java/lang/Object%org/biojava/bio/symbol/FiniteAlphabet"org/biojava/bio/seq/RNAToolsTest$1-org/biojava/bio/symbol/IllegalSymbolException%org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioException getMatches#()Lorg/biojava/bio/symbol/Alphabet;()V    4 *+*@   ,B  ,F  ,J  5N ,Q  ,U   ?Y !"#$ 5]%&'()*+ 6a,-'(. 5e/$ 5i%&'()01 6m23'(.  ?q !"45 ,u 67 6y!"89 6}%&:$ 5%&'(;< 6=>'?@ABC PK /*?:~9(org/biojava/bio/seq/RNAToolsTest$1.class24 ( )* +,-.this$0"Lorg/biojava/bio/seq/RNAToolsTest;%(Lorg/biojava/bio/seq/RNAToolsTest;)VCodeLineNumberTableLocalVariableTablethis InnerClasses$Lorg/biojava/bio/seq/RNAToolsTest$1;getName()Ljava/lang/String; getMatches#()Lorg/biojava/bio/symbol/Alphabet; getAnnotation()Lorg/biojava/bio/Annotation;addChangeListener%(Lorg/biojava/utils/ChangeListener;)Vcl"Lorg/biojava/utils/ChangeListener;C(Lorg/biojava/utils/ChangeListener;Lorg/biojava/utils/ChangeType;)VctLorg/biojava/utils/ChangeType;removeChangeListener isUnchanging!(Lorg/biojava/utils/ChangeType;)Z SourceFileRNAToolsTest.javaEnclosingMethod/ 01  2$org/biojava/bio/seq/RNAToolsTest$1$1 3"org/biojava/bio/seq/RNAToolsTest$1java/lang/Objectorg/biojava/bio/symbol/Symbol org/biojava/bio/seq/RNAToolsTestcreateBadSymbol!()Lorg/biojava/bio/symbol/Symbol;()V'(Lorg/biojava/bio/seq/RNAToolsTest$1;)V   4 *+* :   , <  3 Y* @   ,   5  ?    5   ?  !" 6 #$%&'PK /*?:v[([(&org/biojava/bio/seq/RNAToolsTest.class2~ X W W    W   W W  W W W      W  W               K K   (  ! U#$%(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis"Lorg/biojava/bio/seq/RNAToolsTest;nameLjava/lang/String; testSymbols()V ExceptionstestCreateRNASequenceGetName sequenceNamesequenceLorg/biojava/bio/seq/Sequence;&testCreateRNASequenceAnnotationIsEmptytestCreateRNASequenceURNIsBlank$testCreateRNASequenceSequenceCorrectsequenceStringtestGetCodonAlphabetthreeCopiesOfRNAAlphabetLjava/util/List; testCreateRNA&testComplementAtestComplementCtestComplementGtestComplementU'testComplementSymbolFromAnotherAlphabete/Lorg/biojava/bio/symbol/IllegalSymbolException; StackMapTabletestComplementBadSymbolLorg/biojava/bio/BioError;testComplementListtestReverseComplementtestTranscribe testTranslatetestForSymbolAtestForSymbolCtestForSymbolGtestForSymbolUtestForSymbolWithBadChar testForIndex0 testForIndex1 testForIndex2 testForIndex3testForIndexWithBadIndex%Ljava/lang/IndexOutOfBoundsException; testIndexA testIndexG testIndexC testIndexU"testIndexSymbolFromAnotherAlphabettestIndexBadSymboltestGeneticCodecodonLorg/biojava/bio/symbol/Symbol; xlatedResiduecodonILjava/util/Iterator;residuecodonsLjava/util/Set;aaI geneticCode2Lorg/biojava/bio/symbol/ManyToOneTranslationTable;aaAlfa'Lorg/biojava/bio/symbol/FiniteAlphabet; tableNames geneticCode1 geneticCode2 descriptionnumberIise'()*$ assertEqualsA(Lorg/biojava/bio/symbol/Symbol;Lorg/biojava/bio/symbol/Symbol;)VexpectedactualI(Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/SymbolList;)VexpectedTokenization+Lorg/biojava/bio/seq/io/SymbolTokenization;actualTokenizationLorg/biojava/bio/BioException;#Lorg/biojava/bio/symbol/SymbolList;getRNATokenization-()Lorg/biojava/bio/seq/io/SymbolTokenization;createBadSymbol!()Lorg/biojava/bio/symbol/Symbol; SourceFileRNAToolsTest.java YZa + ,- ./ 0c ,g ,u ,the nameuacg- 123 45 678 9:; <= >? @5'org/biojava/bio/seq/impl/SimpleSequence A5 BCD EF GCH IJ K LM NO PQ R S,,Should have thrown an IllegalSymbolException TZ-org/biojava/bio/symbol/IllegalSymbolException Should have thrown a BioErrororg/biojava/bio/BioErroraugcuacg PU cgua VUgcaugcat WM XU@FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGY ZMuuuuucuuauugucuuccucaucguauuacuaauaguguugcugauggcuucuccuacugccucccccaccgcaucaccaacagcgucgccgacggauuaucauaaugacuaccacaacgaauaacaaaaagaguagcagaaggguugucguaguggcugccgcagcggaugacgaagaggguggcggaggg [U \] ^_/Should have thrown an IndexOutOfBoundsException#java/lang/IndexOutOfBoundsException `a b UNIVERSAL cd ef gC( hi) j= klorg/biojava/bio/symbol/Symbol' mn* [Q op qr cs-org/biojava/bio/symbol/SimpleGeneticCodeTable t5 Standard Code urv wxtokeny z{org/biojava/bio/BioException Y|"org/biojava/bio/seq/RNAToolsTest$1 InnerClasses Y} org/biojava/bio/seq/RNAToolsTestjunit/framework/TestCase/org/biojava/bio/symbol/IllegalAlphabetException0org/biojava/bio/symbol/ManyToOneTranslationTable%org/biojava/bio/symbol/FiniteAlphabetjava/util/Iterator java/util/Setorg/biojava/bio/seq/RNATools'()Lorg/biojava/bio/symbol/AtomicSymbol;)org/biojava/bio/seq/io/SymbolTokenizationtokenizeSymbol3(Lorg/biojava/bio/symbol/Symbol;)Ljava/lang/String;'(Ljava/lang/String;Ljava/lang/String;)VcreateRNASequenceD(Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;org/biojava/bio/seq/SequencegetName()Ljava/lang/String; getAnnotation()Lorg/biojava/bio/Annotation;org/biojava/bio/AnnotationasMap()Ljava/util/Map; java/util/MapisEmpty()Z assertTrue(Z)VgetURN seqStringgetRNA)()Lorg/biojava/bio/symbol/FiniteAlphabet;java/util/CollectionsnCopies%(ILjava/lang/Object;)Ljava/util/List;getCodonAlphabet&org/biojava/bio/symbol/AlphabetManagergetCrossProductAlphabet3(Ljava/util/List;)Lorg/biojava/bio/symbol/Alphabet;'(Ljava/lang/Object;Ljava/lang/Object;)V createRNA7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;tokenizeSymbolList7(Lorg/biojava/bio/symbol/SymbolList;)Ljava/lang/String; complement@(Lorg/biojava/bio/symbol/Symbol;)Lorg/biojava/bio/symbol/Symbol;org/biojava/bio/seq/DNAToolstfailH(Lorg/biojava/bio/symbol/SymbolList;)Lorg/biojava/bio/symbol/SymbolList;reverseComplement createDNA transcribe org/biojava/bio/seq/ProteinTools createProtein translate forSymbol"(C)Lorg/biojava/bio/symbol/Symbol;forIndex"(I)Lorg/biojava/bio/symbol/Symbol;index"(Lorg/biojava/bio/symbol/Symbol;)I(II)VgetGeneticCodeF(Ljava/lang/String;)Lorg/biojava/bio/symbol/ManyToOneTranslationTable; assertNotNull(Ljava/lang/Object;)V getTAlphabetiterator()Ljava/util/Iterator;hasNextnext()Ljava/lang/Object; untranslate0(Lorg/biojava/bio/symbol/Symbol;)Ljava/util/Set;getGeneticCodeNames()Ljava/util/Set;size()I5(I)Lorg/biojava/bio/symbol/ManyToOneTranslationTable;getDescriptiongetTableNumber!org/biojava/bio/symbol/SymbolList getAlphabet#()Lorg/biojava/bio/symbol/Alphabet;org/biojava/bio/symbol/AlphabetgetTokenization?(Ljava/lang/String;)Lorg/biojava/bio/seq/io/SymbolTokenization;(Ljava/lang/Throwable;)V%(Lorg/biojava/bio/seq/RNAToolsTest;)V!WX'YZ[>*+\ @A]^_`abc[E** *  * \CD"E3FDG] E^_d%ec[_ L+M+,\JK LM] ^_fa ghd%ic[X L+\PQR]^_ghd%jc[P L+\UVW]^_ ghd%kc[PL++ \Z[\]^_lad%mc[OL+\_`a]^_ nopc[B*\ de] ^_dq%rc[<*  !\ h i] ^_d%sc[<*  !\ l m] ^_d%tc[<* !\ p q] ^_d%uc[<* !\ t u] ^_d%vc[j" W#$L %\yz |{}]wx^_yOz{c[k*& W'$L (\ ]w|^_yP}d%~c[@*)*+,\ ] ^_dq%c[@*-*.,\ ] ^_dq%c[@*/012,\ ] ^_dq%c[@*3456,\ ] ^_dq%c[; *a7!\  ]  ^_d%c[; *c7!\  ]  ^_d%c[; * g7!\  ]  ^_d%c[; * u7!\  ]  ^_d%c[i$7W#$L %\ ]wx^_yNzc[: *8!\  ]  ^_d%c[: * 8!\  ]  ^_d%c[: *8!\  ]  ^_d%c[: * 8!\  ]  ^_d%c[h8W9$L :\ ]w^_yMc[9 ;<\  ]  ^_d%c[9  ;<\  ]  ^_d%c[9 ;<\  ]  ^_d%c[9  ;<\  ]  ^_d%c[j";W#$L %\ ]wx^_yOzc[k*&;W#$L %\ ]wx^_yPzc[ =>L+?@M,?,AN-BT-CD:+E:?F:B$CD:+G:*!اHN-I<=>:J:KL:MKN6<L%\j "-7<O[ e m p sw !][eE+-C79Zw@.(ax^_y.+*Fz[Z*+*,\ $%] ^_d%[=+OPQN,OPQ:-+, N(Y-S/2R\)*+/.2,3-</]>!3 w=^_==yr dq%[ePTL(Y+S R\3 4 5] w^_yK[3 UY*V\:]  ^_" UPK .*?:U%\0org/biojava/bio/seq/RealizingFeatureHolder.class2 realizeFeatureTemplate InnerClassesh(Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature; Exceptions SourceFileRealizingFeatureHolder.java*org/biojava/bio/seq/RealizingFeatureHolderjava/lang/Object!org/biojava/bio/seq/FeatureHolder$org/biojava/bio/seq/Feature$Templateorg/biojava/bio/BioExceptionorg/biojava/bio/seq/Feature      PK .*?:^X Ȩ.org/biojava/bio/seq/RemoteFeature$Region.class2&     "#location!Lorg/biojava/bio/symbol/Location;seqIDLjava/lang/String;isRemoteZ7(Lorg/biojava/bio/symbol/Location;Ljava/lang/String;Z)VCodeLineNumberTableLocalVariableTablethisRegion InnerClasses*Lorg/biojava/bio/seq/RemoteFeature$Region; getLocation#()Lorg/biojava/bio/symbol/Location;getSeqID()Ljava/lang/String;()Z SourceFileRemoteFeature.java $  %(org/biojava/bio/seq/RemoteFeature$Regionjava/lang/Object()V!org/biojava/bio/seq/RemoteFeature1   l**+*,* *  /* /*  /*  !PK .*?:ʚ0org/biojava/bio/seq/RemoteFeature$Resolver.class2 resolveB(Lorg/biojava/bio/seq/RemoteFeature;)Lorg/biojava/bio/seq/Feature; Exceptions SourceFileRemoteFeature.java*org/biojava/bio/seq/RemoteFeature$ResolverResolver InnerClassesjava/lang/Object)org/biojava/bio/seq/db/IllegalIDExceptionorg/biojava/bio/BioException!org/biojava/bio/seq/RemoteFeature   PK .*?:tҦ  0org/biojava/bio/seq/RemoteFeature$Template.class2Q , -. /0 , 1 2 #/ #3 3 #4 4 #5 57 8 8 69;regionsLjava/util/List;resolver<Resolver InnerClasses,Lorg/biojava/bio/seq/RemoteFeature$Resolver;()VCodeLineNumberTableLocalVariableTablethisTemplate,Lorg/biojava/bio/seq/RemoteFeature$Template;>)(Lorg/biojava/bio/seq/Feature$Template;)V theTemplate&Lorg/biojava/bio/seq/Feature$Template; StackMapTable;> SourceFileRemoteFeature.java ? @A BAjava/util/ArrayList   CD ED FGH,org/biojava/bio/seq/StrandedFeature$Template IL MLN*org/biojava/bio/seq/RemoteFeature$Template*org/biojava/bio/seq/RemoteFeature$ResolverO$org/biojava/bio/seq/Feature$Templateorg/biojava/bio/symbol/Locationempty!Lorg/biojava/bio/symbol/Location;locationtypeLjava/lang/String;source annotationLorg/biojava/bio/Annotation;#org/biojava/bio/seq/StrandedFeaturestrandPStrand,Lorg/biojava/bio/seq/StrandedFeature$Strand;UNKNOWN!org/biojava/bio/seq/RemoteFeatureorg/biojava/bio/seq/Feature*org/biojava/bio/seq/StrandedFeature$Strand!V***Y*NO PQR  "$Y**+* **+ *+ *+ +*+ ***6 \] ^_a"b*c2d9eGgNiSjXkY "Y%&'(),*+*: :! #=! 6! J6KPK .*?:;mm'org/biojava/bio/seq/RemoteFeature.class2Region InnerClassesResolverTemplate getRegions()Ljava/util/List;getRemoteFeature()Lorg/biojava/bio/seq/Feature; Exceptions getResolver.()Lorg/biojava/bio/seq/RemoteFeature$Resolver; SourceFileRemoteFeature.java!org/biojava/bio/seq/RemoteFeaturejava/lang/Object#org/biojava/bio/seq/StrandedFeature(org/biojava/bio/seq/RemoteFeature$Region*org/biojava/bio/seq/RemoteFeature$Resolver*org/biojava/bio/seq/RemoteFeature$Templateorg/biojava/bio/BioException    PK /*?:'++.org/biojava/bio/seq/SeqSerializationTest.class2 1\]^ _`a bc d 0eg hi j k lm n o $pq hrs t t u v wxyz { | } } ~ 0 0 0 $ $ $ 0seqLorg/biojava/bio/seq/Sequence;seq2(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis*Lorg/biojava/bio/seq/SeqSerializationTest;nameLjava/lang/String;setUp()VsftTemplate InnerClasses&Lorg/biojava/bio/seq/Feature$Template;osLjava/io/ByteArrayOutputStream;oosLjava/io/ObjectOutputStream;oisLjava/io/ObjectInputStream; ExceptionscompareSymbolListI(Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/SymbolList;)Zsl1#Lorg/biojava/bio/symbol/SymbolList;sl2si1Ljava/util/Iterator;si2 StackMapTable testSymbols testAlphabet testFeaturestestTokenization SourceFileSeqSerializationTest.java 56'org/biojava/bio/seq/impl/SimpleSequenceaacgtaggttccatgc  fragment1 5 23$org/biojava/bio/seq/Feature$Template 5?test = = $org/biojava/bio/symbol/RangeLocation 5 java/io/ByteArrayOutputStreamjava/io/ObjectOutputStreamjava/io/BufferedOutputStream 5 ? ?java/io/ObjectInputStreamjava/io/BufferedInputStreamjava/io/ByteArrayInputStream 5 5 org/biojava/bio/seq/Sequence 43  LM (org/biojava/bio/seq/SeqSerializationTestjunit/framework/TestCasejava/lang/Exceptionjava/util/Iteratororg/biojava/bio/seq/DNATools createDNA7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;org/biojava/bio/AnnotationEMPTY_ANNOTATIONLorg/biojava/bio/Annotation;f(Lorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/bio/Annotation;)Vorg/biojava/bio/seq/Featuretypesource annotation(II)Vlocation!Lorg/biojava/bio/symbol/Location; createFeatureE(Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;(Ljava/io/OutputStream;)V writeObject(Ljava/lang/Object;)Vflushclose toByteArray()[B([B)V(Ljava/io/InputStream;)V readObject()Ljava/lang/Object;!org/biojava/bio/symbol/SymbolListlength()Iiterator()Ljava/util/Iterator;hasNext()Znext assertTrue(Z)V getAlphabet#()Lorg/biojava/bio/symbol/Alphabet; countFeatures seqString()Ljava/lang/String; assertEquals'(Ljava/lang/String;Ljava/lang/String;)V!012343567>*+8 569:;<=>?7F*Y Y L+ + ++Y*+W+Y  *+WYMYY,N-*--YYY, !":*#$%8F9>?%@+A2B?CJEYFdHlI|JKLMOP94:;@ClHDE|8FG HIJKLM7=+&,&+'N,':-(-))8"STWX Y)Z9[;_94=:;=NO=PO%QR SRT UUV?7>***%*+8 ef9 :;JKW?7W*,*%,+8 ij9 :;T@JKX?7W*-*%-+8 mn9 :;T@JKY?7D*.*%./8 qr9 :;Z[B  fA PK .*?:Q.$$"org/biojava/bio/seq/Sequence.class2   getURN()Ljava/lang/String;getName SourceFile Sequence.javaorg/biojava/bio/seq/Sequencejava/lang/Object!org/biojava/bio/symbol/SymbolList!org/biojava/bio/seq/FeatureHolderorg/biojava/bio/Annotatable  PK .*?:7f@xx+org/biojava/bio/seq/SequenceAnnotator.class2  annotate>(Lorg/biojava/bio/seq/Sequence;)Lorg/biojava/bio/seq/Sequence; Exceptions  SourceFileSequenceAnnotator.java%org/biojava/bio/seq/SequenceAnnotatorjava/lang/Objectorg/biojava/bio/BioException/org/biojava/bio/symbol/IllegalAlphabetException%org/biojava/utils/ChangeVetoException  PK .*?:SU55)org/biojava/bio/seq/SequenceFactory.class2  createSequence(Lorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/bio/Annotation;)Lorg/biojava/bio/seq/Sequence; SourceFileSequenceFactory.java Deprecated#org/biojava/bio/seq/SequenceFactoryjava/lang/ObjectPK .*?:兺88*org/biojava/bio/seq/SequenceIterator.class2  hasNext()Z nextSequence ()Lorg/biojava/bio/seq/Sequence; Exceptions SourceFileSequenceIterator.java$org/biojava/bio/seq/SequenceIteratorjava/lang/Object java/util/NoSuchElementExceptionorg/biojava/bio/BioException   PK .*?:F]'org/biojava/bio/seq/SequenceTools.class2 .    - -        -   ! # - -  * ()VCodeLineNumberTableLocalVariableTablethis#Lorg/biojava/bio/seq/SequenceTools;createSequence(Lorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/bio/Annotation;)Lorg/biojava/bio/seq/Sequence;syms#Lorg/biojava/bio/symbol/SymbolList;uriLjava/lang/String;nameannLorg/biojava/bio/Annotation; subSequence@(Lorg/biojava/bio/seq/Sequence;II)Lorg/biojava/bio/seq/Sequence;seqLorg/biojava/bio/seq/Sequence;startIend ExceptionsR(Lorg/biojava/bio/seq/Sequence;IILjava/lang/String;)Lorg/biojava/bio/seq/Sequence;Strand InnerClasses~(Lorg/biojava/bio/seq/Sequence;IILjava/lang/String;Lorg/biojava/bio/seq/StrandedFeature$Strand;)Lorg/biojava/bio/seq/Sequence;strand,Lorg/biojava/bio/seq/StrandedFeature$Strand;s StackMapTablereverseComplement>(Lorg/biojava/bio/seq/Sequence;)Lorg/biojava/bio/seq/Sequence;viewG(Lorg/biojava/bio/seq/Sequence;)Lorg/biojava/bio/seq/impl/ViewSequence;Y(Lorg/biojava/bio/seq/Sequence;Ljava/lang/String;)Lorg/biojava/bio/seq/impl/ViewSequence;l(Lorg/biojava/bio/seq/Sequence;Lorg/biojava/bio/seq/FeatureRealizer;)Lorg/biojava/bio/seq/impl/ViewSequence;fr%Lorg/biojava/bio/seq/FeatureRealizer; gappedViewD(Lorg/biojava/bio/seq/Sequence;)Lorg/biojava/bio/seq/GappedSequence; maskSequenced(Lorg/biojava/bio/seq/Sequence;Lorg/biojava/bio/symbol/RangeLocation;)Lorg/biojava/bio/seq/Sequence;loc&Lorg/biojava/bio/symbol/RangeLocation;gSeq$Lorg/biojava/bio/seq/GappedSequence; createDummyD(Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;(Lorg/biojava/bio/symbol/Alphabet;ILorg/biojava/bio/symbol/Symbol;Ljava/lang/String;Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;alpha!Lorg/biojava/bio/symbol/Alphabet;lengthsymLorg/biojava/bio/symbol/Symbol;addAllFeaturesD(Lorg/biojava/bio/seq/Sequence;Lorg/biojava/bio/seq/FeatureHolder;)Vfh#Lorg/biojava/bio/seq/FeatureHolder; addFeaturesI(Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/seq/FeatureHolder;)Vf2addLorg/biojava/bio/seq/Feature;addediLjava/util/Iterator;toAddTo thingsToAdd SourceFileSequenceTools.java /0'org/biojava/bio/seq/impl/SimpleSequence /$org/biojava/bio/seq/impl/SubSequence / / ?H N ST(org/biojava/bio/seq/impl/RevCompSequence /%org/biojava/bio/seq/impl/ViewSequence / /-org/biojava/bio/seq/impl/SimpleGappedSequence java/lang/StringBuilder : [\ i&org/biojava/bio/seq/impl/DummySequence /&org/biojava/bio/symbol/DummySymbolList /org/biojava/bio/SmallAnnotation 67 st  org/biojava/bio/seq/Feature !org/biojava/bio/seq/SequenceToolsjava/lang/Object#java/lang/IndexOutOfBoundsException*org/biojava/bio/seq/StrandedFeature$Strandorg/biojava/bio/seq/Sequence/org/biojava/bio/symbol/IllegalAlphabetException"java/lang/IllegalArgumentException-org/biojava/bio/symbol/IllegalSymbolException%org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioExceptionjava/util/Iteratorf(Lorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/bio/Annotation;)V#(Lorg/biojava/bio/seq/Sequence;II)V5(Lorg/biojava/bio/seq/Sequence;IILjava/lang/String;)V#org/biojava/bio/seq/StrandedFeatureNEGATIVE!(Lorg/biojava/bio/seq/Sequence;)V3(Lorg/biojava/bio/seq/Sequence;Ljava/lang/String;)VF(Lorg/biojava/bio/seq/Sequence;Lorg/biojava/bio/seq/FeatureRealizer;)V$org/biojava/bio/symbol/RangeLocationgetMin()IgetMaxgetName()Ljava/lang/String;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString"org/biojava/bio/seq/GappedSequenceaddGapsInSource(II)V'(Ljava/lang/String;Ljava/lang/String;)VD(Lorg/biojava/bio/symbol/Alphabet;ILorg/biojava/bio/symbol/Symbol;)V!org/biojava/bio/seq/FeatureHolderfeatures()Ljava/util/Iterator;hasNext()Znext()Ljava/lang/Object; makeTemplateTemplate(()Lorg/biojava/bio/seq/Feature$Template; createFeatureE(Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;$org/biojava/bio/seq/Feature$Template1-./013*2 233 45 671T Y*+,-283* 89 :; <; => ?@1I Y*2O3  AB CD EDFG ?H1T Y*-2g3* AB CD ED <;FG ?L1*-:  :2 3>ABCDED<;MN OBPQFGR ST13 Y* 23  ABFR UV13 Y* 23  AB UW1> Y*+23 AB <; UX1> Y*+23 AB YZ [\13 Y*23  AB ]^1U*++Y*+M,+,*,,d,2/:S3 UABU_`/&abFGc de1> Y*+ 23 :; <; df1j!Y*,"-#Y$%234ghiDjk:;<;Fl mn1>*+&2  !3ABopFqr st12+'M,($,)*N*-+,:-&ٱ2()*(+.,1-34uv(wv*xy2zp2{pP |)Fqr}~KIJ* PK .*?: x~(org/biojava/bio/seq/SimpleAssembly.class2, G  F F  F F F F           (    ( * F  / (  9   7 9 G F  @ F nameLjava/lang/String;uri annotationLorg/biojava/bio/Annotation;features)Lorg/biojava/bio/seq/SimpleFeatureHolder;assembly.Lorg/biojava/bio/seq/impl/AssembledSymbolList;featureRealizer%Lorg/biojava/bio/seq/FeatureRealizer;annotationForwarder#Lorg/biojava/utils/ChangeForwarder;((ILjava/lang/String;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis$Lorg/biojava/bio/seq/SimpleAssembly;lengthI'(Ljava/lang/String;Ljava/lang/String;)V getAlphabet#()Lorg/biojava/bio/symbol/Alphabet;()IsymbolAt"(I)Lorg/biojava/bio/symbol/Symbol;possubList'(II)Lorg/biojava/bio/symbol/SymbolList;startend seqString()Ljava/lang/String;subStr(II)Ljava/lang/String;iterator()Ljava/util/Iterator;toList()Ljava/util/List;edit (Lorg/biojava/bio/symbol/Edit;)VeLorg/biojava/bio/symbol/Edit; ExceptionsgetNamegetURN getAnnotation()Lorg/biojava/bio/Annotation; countFeaturesfilterI(Lorg/biojava/bio/seq/FeatureFilter;Z)Lorg/biojava/bio/seq/FeatureHolder;ff#Lorg/biojava/bio/seq/FeatureFilter;recurseZH(Lorg/biojava/bio/seq/FeatureFilter;)Lorg/biojava/bio/seq/FeatureHolder;containsFeature (Lorg/biojava/bio/seq/Feature;)ZfLorg/biojava/bio/seq/Feature; createFeatureTemplate InnerClassesE(Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;l!Lorg/biojava/bio/symbol/Location;iLjava/util/Iterator;cf&Lorg/biojava/bio/seq/ComponentFeature;loctemp&Lorg/biojava/bio/seq/Feature$Template; StackMapTable removeFeature (Lorg/biojava/bio/seq/Feature;)VrealizeFeatureh(Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;cft/Lorg/biojava/bio/seq/ComponentFeature$Template;gopher#Lorg/biojava/bio/seq/FeatureHolder;fhgetChangeSupportA(Lorg/biojava/utils/ChangeType;)Lorg/biojava/utils/ChangeSupport;ctLorg/biojava/utils/ChangeType;cs!Lorg/biojava/utils/ChangeSupport; getSchema%()Lorg/biojava/bio/seq/FeatureFilter; SourceFileSimpleAssembly.java W org/biojava/bio/SimpleAnnotation MN T ST,org/biojava/bio/seq/impl/AssembledSymbolList QR'org/biojava/bio/seq/SimpleFeatureHolder OP JK LK  ab ^c de gh kl mn op qr st Op ~c     corg/biojava/bio/BioExceptionCoordinates out of range W -org/biojava/bio/seq/ComponentFeature$Template     org/biojava/bio/symbol/Location org/biojava/bio/BioError)Can't create overlapping ComponentFeature $org/biojava/bio/seq/ComponentFeature  c   IComponentFeatures can only be attached directly to SimpleAssembly objects*org/biojava/bio/seq/SimpleComponentFeature Worg/biojava/bio/seq/FeatureECannot [currently] realize features on components of SimpleAssemblies  ! UV" #$)org/biojava/utils/ChangeForwarder$RetyperRetyper% & W' |} ()* +"org/biojava/bio/seq/SimpleAssembly$org/biojava/utils/AbstractChangeableorg/biojava/bio/seq/Sequence*org/biojava/bio/seq/RealizingFeatureHolder/org/biojava/bio/symbol/IllegalAlphabetException%org/biojava/utils/ChangeVetoException$org/biojava/bio/seq/Feature$Templatejava/util/Iterator!org/biojava/bio/seq/FeatureHolderorg/biojava/utils/ChangeSupport()V$org/biojava/bio/seq/impl/FeatureImplDEFAULT setLength(I)VlocationgetMin(Ljava/lang/String;)VgetComponentLocationSet()Ljava/util/Set; java/util/SethasNext()Znext()Ljava/lang/Object;overlaps$(Lorg/biojava/bio/symbol/Location;)Z addFeature getLocation#()Lorg/biojava/bio/symbol/Location;getMax putComponent)(Lorg/biojava/bio/seq/ComponentFeature;)VremoveComponent$(Lorg/biojava/bio/symbol/Location;)VU(Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/seq/ComponentFeature$Template;)V getParent%()Lorg/biojava/bio/seq/FeatureHolder;#org/biojava/bio/seq/FeatureRealizer(Lorg/biojava/bio/seq/Sequence;Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;org/biojava/bio/Annotatable ANNOTATION!org/biojava/utils/ChangeForwarderorg/biojava/bio/AnnotationPROPERTYT(Ljava/lang/Object;Lorg/biojava/utils/ChangeSupport;Lorg/biojava/utils/ChangeType;)VaddChangeListenerC(Lorg/biojava/utils/ChangeListener;Lorg/biojava/utils/ChangeType;)V!org/biojava/bio/seq/FeatureFilter top_level!FGHIJKLKMNOPQRSTUVWXY?**Y**Y * Y *, *-* Z& \DHM!N,]1^6_>`[*?\]?^_?JK?LKW`Y7**Y**Y * Y *+ *,Z"lDHM!N,m1n6o[ 7\]7JK7LKabY2* Zv[ \]^cY2* Zz[ \]deY= * Z~[ \] f_ghYH * Z[  \] i_ j_klY2* Z[ \]mnYH * Z[  \] i_ j_opY2* Z[ \]qrY2* Z[ \]stYA * +Z [ \] uvwxyzlY/* Z[ \]{lY/*Z[ \]|}Y/*Z[ \]OpY2* Z[ \]~cY2* Z[ \]YH * +Z[  \]  Y= * +Z[ \] Y= * +Z[ \] Yl+ Y!"+#=* $%M,&','(N-+) *Y+,**+-M* ,.,/7,/N-0:1* * 1* -2,ZF 4>KUX_gns{[H>+-s/{'\]_E)Aw yYf+/* +34* +5Z[\]wyYY,#!+* Y6",#N7Y*-8+N-9!-/ Y:"-9;N**+,<Z.  %'.5?L[4 '2Y\]YY  w Y:*+=M*>.+ +?#*@Y*,AB>*C*>?D,Z ( 8[ :\]:4 Y.EZ[ \]9 #/ @ PK /*?:ey,org/biojava/bio/seq/SimpleAssemblyTest.class2 ?klm no@ pq r >stB >uw xy z{ | } v~     > x z | } v      > >  0k >  7  fragment1Lorg/biojava/bio/seq/Sequence; fragment2assembly(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis(Lorg/biojava/bio/seq/SimpleAssemblyTest;nameLjava/lang/String;setUp()VsftTemplate InnerClasses.Lorg/biojava/bio/seq/StrandedFeature$Template;templ/Lorg/biojava/bio/seq/ComponentFeature$Template; ExceptionstestAssembledSymbolstestProjectedFeaturesf#Lorg/biojava/bio/seq/FeatureHolder;pfLorg/biojava/bio/seq/Feature;pfl!Lorg/biojava/bio/symbol/Location;compareSymbolListI(Lorg/biojava/bio/symbol/SymbolList;Lorg/biojava/bio/symbol/SymbolList;)Zsl1#Lorg/biojava/bio/symbol/SymbolList;sl2si1Ljava/util/Iterator;si2 StackMapTable SourceFileSimpleAssemblyTest.java DE'org/biojava/bio/seq/impl/SimpleSequenceaacgta  D @Attgatgc BA,org/biojava/bio/seq/StrandedFeature$Template DN project_test Ltest L $org/biojava/bio/symbol/RangeLocation D ^ "org/biojava/bio/seq/SimpleAssembly D CA-org/biojava/bio/seq/ComponentFeature$Template component A ^  acgtngcatcaa _` acgtacgtnnaa(org/biojava/bio/seq/FeatureFilter$ByTypeByType   org/biojava/bio/seq/Feature   &org/biojava/bio/seq/SimpleAssemblyTestjunit/framework/TestCasejava/lang/Exceptionjava/util/Iteratororg/biojava/bio/seq/DNATools createDNA7(Ljava/lang/String;)Lorg/biojava/bio/symbol/SymbolList;org/biojava/bio/AnnotationEMPTY_ANNOTATIONLorg/biojava/bio/Annotation;f(Lorg/biojava/bio/symbol/SymbolList;Ljava/lang/String;Ljava/lang/String;Lorg/biojava/bio/Annotation;)V#org/biojava/bio/seq/StrandedFeaturetypesource annotationNEGATIVEStrand,Lorg/biojava/bio/seq/StrandedFeature$Strand;strand(II)Vlocationorg/biojava/bio/seq/Sequence createFeatureE(Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;((ILjava/lang/String;Ljava/lang/String;)V$org/biojava/bio/seq/ComponentFeaturePOSITIVEcomponentSequencecomponentLocationlength()I assertTrue(Z)VsubList'(II)Lorg/biojava/bio/symbol/SymbolList;!org/biojava/bio/seq/FeatureFilterfilterI(Lorg/biojava/bio/seq/FeatureFilter;Z)Lorg/biojava/bio/seq/FeatureHolder;!org/biojava/bio/seq/FeatureHolder countFeatures assertEqualsfeatures()Ljava/util/Iterator;next()Ljava/lang/Object; getLocation#()Lorg/biojava/bio/symbol/Location;org/biojava/bio/symbol/LocationgetMingetMax!org/biojava/bio/symbol/SymbolListiteratorhasNext()Z*org/biojava/bio/seq/StrandedFeature$Strand$org/biojava/bio/seq/Feature$Template!>?@ABACADEF>*+G 01HIJKLMNF*Y*Y    Y L+++++Y* +W*Y YM,, ,!,"#,Y$,*%,Y&*,W,#,Y $,* %,Y* '&*,WGf48.=6><?B@IAPB]ChEyFGHIKLMNOQRSTUVH IJ6ORSTUVWNFo**()***+,)***+-)***+.)***  +/)*GZ\'^>`UbndH oIJUVXNFK*0Y12L+34+567M,8N-9 4-: 4Ghij-k4l?mJnH*KIJ7YZ-[\4]^UV_`F=+;,;+<N,<:-=-66G"qruv w)x9y;}H4=IJ=ab=cb%de feg hhijQ* vP P 0v7P PK .*?:Y$$0org/biojava/bio/seq/SimpleComponentFeature.class2[ ` (  ( _ ( 4 _ _ ( _ ( _ ( _ ( _ ( _ ( _ _ _ 4 4 _ " ! _  ( _ _ _ _ _ _ _ 4  @ _ 7 6 _   >   _ _ 4 @ _   M! L"# % Q" K& '( ) * +,-. Z/ ]123parent#Lorg/biojava/bio/seq/FeatureHolder;projectedFeatureslocation!Lorg/biojava/bio/symbol/Location;typeLjava/lang/String;sourcetypeTermLorg/biojava/ontology/Term; sourceTerm annotationLorg/biojava/bio/Annotation;strand4Strand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;componentSequenceLorg/biojava/bio/seq/Sequence;componentLocation translationITemplateU(Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/seq/ComponentFeature$Template;)VCodeLineNumberTableLocalVariableTablethis,Lorg/biojava/bio/seq/SimpleComponentFeature;temp/Lorg/biojava/bio/seq/ComponentFeature$Template; StackMapTable2526 Exceptions makeTemplate7(()Lorg/biojava/bio/seq/Feature$Template;cftlocationContent$(Lorg/biojava/bio/symbol/Location;)IsliLjava/util/Iterator;lcontent8isComponentResolvable()ZgetComponentSequenceName()Ljava/lang/String; getStrand.()Lorg/biojava/bio/seq/StrandedFeature$Strand; setStrand/(Lorg/biojava/bio/seq/StrandedFeature$Strand;)V getLocation#()Lorg/biojava/bio/symbol/Location; setLocation$(Lorg/biojava/bio/symbol/Location;)Vloc getParent%()Lorg/biojava/bio/seq/FeatureHolder; getSequence ()Lorg/biojava/bio/seq/Sequence;fhgetType getTypeTerm()Lorg/biojava/ontology/Term; setSource(Ljava/lang/String;)V setSourceTerm(Lorg/biojava/ontology/Term;)V getSource getSourceTermsetType setTypeTerm getAnnotation()Lorg/biojava/bio/Annotation; getSymbols%()Lorg/biojava/bio/symbol/SymbolList;syms#Lorg/biojava/bio/symbol/SymbolList;getComponentSequencegetComponentLocationgetProjectedFeatures countFeatures()Ifeatures()Ljava/util/Iterator;containsFeature (Lorg/biojava/bio/seq/Feature;)ZfLorg/biojava/bio/seq/Feature;filterH(Lorg/biojava/bio/seq/FeatureFilter;)Lorg/biojava/bio/seq/FeatureHolder;ff#Lorg/biojava/bio/seq/FeatureFilter; childFilter9I(Lorg/biojava/bio/seq/FeatureFilter;Z)Lorg/biojava/bio/seq/FeatureHolder;recurseZ createFeatureE(Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;&Lorg/biojava/bio/seq/Feature$Template; removeFeature (Lorg/biojava/bio/seq/Feature;)V getSchema%()Lorg/biojava/bio/seq/FeatureFilter; SourceFileSimpleComponentFeature.java x: storg/biojava/bio/BioExceptionXThis implementation of ComponentFeature requires that sequences must already be resolved x de ueJComponent and container locations must contain an equal number of symbols. ;JCan only include contiguous segments in an assembly [may change in future] ab fg hg ij< =j kj lm nr> ?r @ A vw5org/biojava/bio/seq/projection/ProjectedFeatureHolder3org/biojava/bio/seq/projection/TranslateFlipContext xB xC cb Dr9Strand must be specified when creating a ComponentFeature-org/biojava/bio/seq/ComponentFeature$Template E8 F GHorg/biojava/bio/symbol/Location I%org/biojava/utils/ChangeVetoExceptionorg/biojava/utils/ChangeEvent JK xL&Can't change strand as it is immutable xM NK(Can't change location as it is immutableorg/biojava/bio/seq/Feature org/biojava/bio/seq/Sequence6 OK&Can't change source as it is immutable PK$Can't change type as it is immutable QR 5 9%org/biojava/bio/seq/FeatureFilter$AndAnd*org/biojava/bio/seq/FeatureFilter$ByParentByParent)org/biojava/bio/seq/FeatureFilter$ByClassByClass$org/biojava/bio/seq/ComponentFeature xS xT%org/biojava/bio/seq/FeatureFilter$NotNot U xVW XY Zb 2Can't create features in a ComponentFeature (yet?)'java/lang/UnsupportedOperationException.Can't remove features from a ComponentFeature.+org/biojava/bio/seq/FeatureFilter$ByFeature ByFeature x*org/biojava/bio/seq/SimpleComponentFeatureorg/biojava/utils/Unchangeable*org/biojava/bio/seq/StrandedFeature$Strand!org/biojava/bio/seq/FeatureHolderorg/biojava/ontology/Term$org/biojava/bio/seq/Feature$Templatejava/util/Iterator!org/biojava/bio/seq/FeatureFilter()V isContiguousorg/biojava/ontology/OntoToolsANY#org/biojava/bio/seq/StrandedFeatureNEGATIVEgetMaxgetMinK(Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/seq/FeatureHolder;IZ)V5(Lorg/biojava/bio/seq/projection/ProjectionContext;)VPOSITIVE blockIteratorhasNextnext()Ljava/lang/Object;getNameSTRANDLorg/biojava/utils/ChangeType;W(Ljava/lang/Object;Lorg/biojava/utils/ChangeType;Ljava/lang/Object;Ljava/lang/Object;)V4(Lorg/biojava/utils/ChangeEvent;Ljava/lang/String;)VLOCATIONSOURCETYPEsymbolsH(Lorg/biojava/bio/symbol/SymbolList;)Lorg/biojava/bio/symbol/SymbolList;(Ljava/lang/Class;)V&(Lorg/biojava/bio/seq/FeatureFilter;)V top_levelI(Lorg/biojava/bio/seq/FeatureFilter;Lorg/biojava/bio/seq/FeatureFilter;)Vorg/biojava/bio/seq/FilterUtils areDisjointI(Lorg/biojava/bio/seq/FeatureFilter;Lorg/biojava/bio/seq/FeatureFilter;)ZEMPTY_FEATURE_HOLDER _`N abcbdefghgijkjlmnrstuevw xz{8 F*, Y*,*, Y , ,  Y *+ *, *,*,*, ,*, ,*,*,*,*,,9*,,` *!Y"Y*** #$%M,&9*,,d *!Y"Y*** #$% Y'|fEF GJ(L2OJPTSYUaViWqXYZ[]^`abefg;kEm} F~FabFN  jPb? 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A BC D EF EG HI J EK LM NO P QR QS ET EUVWXfeaturesLjava/util/List;schema#Lorg/biojava/bio/seq/FeatureFilter;()VCodeLineNumberTableLocalVariableTablethis)Lorg/biojava/bio/seq/SimpleFeatureHolder;&(Lorg/biojava/bio/seq/FeatureFilter;)V getFeatures()Ljava/util/List; countFeatures()I()Ljava/util/Iterator; addFeature (Lorg/biojava/bio/seq/Feature;)VceLorg/biojava/utils/ChangeEvent; changeSupport!Lorg/biojava/utils/ChangeSupport;fLorg/biojava/bio/seq/Feature; StackMapTableVYZ[\ Exceptions] removeFeaturecontainsFeature (Lorg/biojava/bio/seq/Feature;)Z getSchema%()Lorg/biojava/bio/seq/FeatureFilter; SourceFileSimpleFeatureHolder.java java/util/ArrayList ^ _ ` a& b'c de fg hij kl mnorg/biojava/utils/ChangeEvent oZ pq rq si ti'org/biojava/bio/seq/SimpleFeatureHolder)org/biojava/bio/seq/AbstractFeatureHolderjava/io/Serializableorg/biojava/bio/seq/Featureorg/biojava/utils/ChangeSupportjava/lang/Objectjava/lang/Throwable%org/biojava/utils/ChangeVetoException!org/biojava/bio/seq/FeatureFilteralljava/util/Listsizeiteratororg/biojava/utils/ListToolsnonRemoveIterator*(Ljava/util/Iterator;)Ljava/util/Iterator; hasListeners()Zadd(Ljava/lang/Object;)Z!org/biojava/bio/seq/FeatureHolderFEATURESLorg/biojava/utils/ChangeType;getChangeSupportA(Lorg/biojava/utils/ChangeType;)Lorg/biojava/utils/ChangeSupport;W(Ljava/lang/Object;Lorg/biojava/utils/ChangeType;Ljava/lang/Object;Ljava/lang/Object;)VfirePreChangeEvent"(Lorg/biojava/utils/ChangeEvent;)VfirePostChangeEventremovecontains! M**Y*5E67  !"U**Y*+=E>? !#$/*L  !%&4 *P  !'7 * T  !()T* *+ WA* M,YN»Y* +:,*+ W,-ç :-!ILLPL* ]^`a!b0f6gAhGiSk*0*+6,-T !T./0612345678)T* *+WA* M,YN»Y* +:,*+W,-ç :-!ILLPL* oprs!t0x6yAzG{S}*0*+6,-T !T./0612345679:? *+ ! ./;</*  !=>PK .*?:'1org/biojava/bio/seq/SimpleFeatureRealizer$1.class2   SourceFileSimpleFeatureRealizer.javaEnclosingMethod +org/biojava/bio/seq/SimpleFeatureRealizer$1 InnerClassesjava/lang/Object)org/biojava/bio/seq/SimpleFeatureRealizer  PK .*?: Ɣ <org/biojava/bio/seq/SimpleFeatureRealizer$TemplateImpl.class2 U VWXY Z [ \]^_ V` a bc d e fg hijkl mnptemplateLjava/lang/Class;consLjava/lang/reflect/Constructor;%(Ljava/lang/Class;Ljava/lang/Class;)VCodeLineNumberTableLocalVariableTableex!Ljava/lang/NoSuchMethodException;this TemplateImpl InnerClasses8Lorg/biojava/bio/seq/SimpleFeatureRealizer$TemplateImpl;impl signature[Ljava/lang/Class; StackMapTablepW-] ExceptionsacceptqTemplate)(Lorg/biojava/bio/seq/Feature$Template;)Ztemp&Lorg/biojava/bio/seq/Feature$Template;realize(Lorg/biojava/bio/seq/Sequence;Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;tLjava/lang/Throwable;Ljava/lang/Exception;seqLorg/biojava/bio/seq/Sequence;parent#Lorg/biojava/bio/seq/FeatureHolder;consArgs[Ljava/lang/Object;XYqDkkrsR(Ljava/lang/Class;Ljava/lang/Class;Lorg/biojava/bio/seq/SimpleFeatureRealizer$1;)Vx0x1x2-Lorg/biojava/bio/seq/SimpleFeatureRealizer$1; SourceFileSimpleFeatureRealizer.java ! tjava/lang/Classorg/biojava/bio/seq/Sequence!org/biojava/bio/seq/FeatureHolder  uv java/lang/NoSuchMethodExceptionorg/biojava/bio/BioExceptionjava/lang/StringBuilderClass wx yz# does not have suitable constructor {z | }~java/lang/Object org/biojava/bio/seq/Featurejava/lang/Exception+java/lang/reflect/InvocationTargetException Couldn't realize feature6org/biojava/bio/seq/SimpleFeatureRealizer$TemplateImpl$org/biojava/bio/seq/Feature$Templatejava/lang/Throwable+org/biojava/bio/seq/SimpleFeatureRealizer$1()VgetConstructor3([Ljava/lang/Class;)Ljava/lang/reflect/Constructor;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;getName()Ljava/lang/String;toString*(Ljava/lang/String;Ljava/lang/Throwable;)V isInstance(Ljava/lang/Object;)Zjava/lang/reflect/Constructor newInstance'([Ljava/lang/Object;)Ljava/lang/Object;getTargetException()Ljava/lang/Throwable;)org/biojava/bio/seq/SimpleFeatureRealizer  !"R*N-S-S-+S*+*,-*: Y Y  ,'* #. qr stuvy'|*z,{Q}$4,%%&R'*RR+ I,-.*/0012&3 47"= *+#$ '* 89:;"F:+S,S-S*:: : Y!"#*  "$(0:$H(<=$"%>F'*F?@FABF89@CD.$"/EFGHIJK3  N"O*+,#k$*'*OPQR3 ST)o( 56 LoPK .*?:d6L L /org/biojava/bio/seq/SimpleFeatureRealizer.class2{ DE D F GH I JK JL MN MO P Q RST DU V W XY Z [\]^_` InnerClasses TemplateImpltemplateToImplLjava/util/List;fallBack%Lorg/biojava/bio/seq/FeatureRealizer;()VCodeLineNumberTableLocalVariableTablethis+Lorg/biojava/bio/seq/SimpleFeatureRealizer;((Lorg/biojava/bio/seq/FeatureRealizer;)VaddImplementation%(Ljava/lang/Class;Ljava/lang/Class;)VtemplateLjava/lang/Class;implti8Lorg/biojava/bio/seq/SimpleFeatureRealizer$TemplateImpl; ExceptionsrealizeFeaturebTemplate(Lorg/biojava/bio/seq/Sequence;Lorg/biojava/bio/seq/FeatureHolder;Lorg/biojava/bio/seq/Feature$Template;)Lorg/biojava/bio/seq/Feature;iLjava/util/Iterator;seqLorg/biojava/bio/seq/Sequence;parent#Lorg/biojava/bio/seq/FeatureHolder;temp&Lorg/biojava/bio/seq/Feature$Template; StackMapTablec SourceFileSimpleFeatureRealizer.java $%java/util/ArrayList ! "#6org/biojava/bio/seq/SimpleFeatureRealizer$TemplateImpl $de fg hic jk lm no p7 47org/biojava/bio/BioExceptionjava/lang/StringBuilder7?@()*"#,-&gY+,N*-'U VW(*)*./0/ 12347&k* : $ :- +,- **+,-YY-'"^_!`*a3b6d=eJg(>!12 +89k)*k:;k<=k>?@  A'3BC 5a6 PK .*?:P]&org/biojava/bio/seq/StrandParser.class2R ,- ./012 345678 39:;<= 3>?@ ,A B C DEF()VCodeLineNumberTableLocalVariableTablethis"Lorg/biojava/bio/seq/StrandParser; parseStrandGStrand InnerClasses@(Ljava/lang/String;)Lorg/biojava/bio/seq/StrandedFeature$Strand;strandLjava/lang/String; StackMapTable SourceFileStrandParser.java +H IJ1plusPOSITIVEK 2L--1minusNEGATIVE 8L.0noneUNKNOWN =L"java/lang/IllegalArgumentExceptionjava/lang/StringBuilderNot a legal strand: MN OP Q org/biojava/bio/seq/StrandParserjava/lang/Object*org/biojava/bio/seq/StrandedFeature$Strandjava/lang/Stringequals(Ljava/lang/Object;)Z#org/biojava/bio/seq/StrandedFeature,Lorg/biojava/bio/seq/StrandedFeature$Strand;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/String;)V1/*  !"&*** ** * *  *  *** *YY*$$(%L+P,t2x5 '()$##*+% #3$PK .*?:OmG0org/biojava/bio/seq/StrandedFeature$Strand.class2O 3 4 5 6 7 89: ;< =>? @ ABCDtextLjava/lang/String;valueItokenC(Ljava/lang/String;IC)VCodeLineNumberTableLocalVariableTablethisStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;toString()Ljava/lang/String;getValue()IgetToken()Cflip.()Lorg/biojava/bio/seq/StrandedFeature$Strand; StackMapTable writeReplace()Ljava/lang/Object;nsfe Ljava/lang/NoSuchFieldException;> ExceptionsE SourceFileStrandedFeature.java F    G H )org/biojava/utils/StaticMemberPlaceHolder#org/biojava/bio/seq/StrandedFeatureI JK Ljava/lang/NoSuchFieldException java/io/NotSerializableException M" N*org/biojava/bio/seq/StrandedFeature$Strandjava/lang/Objectjava/io/Serializablejava/io/ObjectStreamException()VPOSITIVENEGATIVEjava/lang/ClassgetField-(Ljava/lang/String;)Ljava/lang/reflect/Field;(Ljava/lang/reflect/Field;)V getMessage(Ljava/lang/String;)V1l**+** * !"/*  #$/*  %&/*  '(\***   ) *+oY* L Y+   ,- )R./012 PK .*?:@YY2org/biojava/bio/seq/StrandedFeature$Template.class2 strandStrand InnerClasses,Lorg/biojava/bio/seq/StrandedFeature$Strand;()VCodeLineNumberTableLocalVariableTablethisTemplate.Lorg/biojava/bio/seq/StrandedFeature$Template; SourceFileStrandedFeature.java ,org/biojava/bio/seq/StrandedFeature$Template$org/biojava/bio/seq/Feature$Template*org/biojava/bio/seq/StrandedFeature$Strand#org/biojava/bio/seq/StrandedFeatureorg/biojava/bio/seq/Feature!  /* q   PK .*?:aa)org/biojava/bio/seq/StrandedFeature.class2:)*+ , -. / 0 1 234Strand InnerClasses5TemplateSTRANDLorg/biojava/utils/ChangeType;POSITIVE,Lorg/biojava/bio/seq/StrandedFeature$Strand;NEGATIVEUNKNOWN getStrand.()Lorg/biojava/bio/seq/StrandedFeature$Strand; setStrand/(Lorg/biojava/bio/seq/StrandedFeature$Strand;)V Exceptions6 getSymbols%()Lorg/biojava/bio/symbol/SymbolList;()VCodeLineNumberTable SourceFileStrandedFeature.javaorg/biojava/utils/ChangeTypeStrand has altered#org/biojava/bio/seq/StrandedFeature 78 *org/biojava/bio/seq/StrandedFeature$Strand 79   java/lang/Objectorg/biojava/bio/seq/Feature,org/biojava/bio/seq/StrandedFeature$Template%org/biojava/utils/ChangeVetoException8(Ljava/lang/String;Ljava/lang/Class;Ljava/lang/String;)V(Ljava/lang/String;IC)V !"#$%c?YY+ Y - Y . &2^ c/h'( PK .*?:ًorg/biojava/bio/seq/Up.class2  SourceFileUp.javaorg/biojava/bio/seq/Upjava/lang/Object!org/biojava/bio/seq/FeatureFilterPK .*?:1org/biojava/bio/seq/db/AbstractSequenceDB$1.class2B % & #' () * +, +-. #/012pIDLjava/util/Iterator;this$0+Lorg/biojava/bio/seq/db/AbstractSequenceDB;.(Lorg/biojava/bio/seq/db/AbstractSequenceDB;)VCodeLineNumberTableLocalVariableTablethis InnerClasses-Lorg/biojava/bio/seq/db/AbstractSequenceDB$1;hasNext()Z nextSequence ()Lorg/biojava/bio/seq/Sequence; Exceptions3 SourceFileAbstractSequenceDB.javaEnclosingMethod4 56  7 89: ;< =  >?java/lang/String @A+org/biojava/bio/seq/db/AbstractSequenceDB$1java/lang/Object$org/biojava/bio/seq/SequenceIteratororg/biojava/bio/BioException)org/biojava/bio/seq/db/AbstractSequenceDBsequenceIterator(()Lorg/biojava/bio/seq/SequenceIterator;()Vids()Ljava/util/Set; java/util/Setiterator()Ljava/util/Iterator;java/util/Iteratornext()Ljava/lang/Object; getSequence2(Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;   H*+*** 3 4 4 *7  >** ;  !"#$  PK .*?:s s /org/biojava/bio/seq/db/AbstractSequenceDB.class2g ?@ CD ? 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@A BCDEFGHI=7 **> ;<?  @AFGJI=4*> @A? @AFGKI=!L*+*+ *+*+ M Y N-Y- --,-W,>6 FGH,I>JIOQP\QgRmSsT{UV?*@ABCIELMQ=NQRS@nTU@FGVI=xL*+*+ *+*+ M,,M*+*+>& Z[\,]>_I`Sb]cwd? x@AuBCI/LMRS@6T@T @FGWI= L+ M*+*, *+*+ MN:::: Y :Y -,:   ,!",:   #  $,,%:  & '(:   6   )!* )* & '(:  . )*  # )!*   &,+Y,Y--.Y/Y0123:4:  & '(:   , 5,%:  & '(:    " 6  >6ij l$m.n@oKqNrRsVtZu^xgysz{|}~ &0<LQcr|&2KS[eq?@ABC LMNlXCRhYCVdZCZ`[C^\\CgSNQ$]^ _^ &`a <~b^ Lncd efR ST@ gSTSSSSSUh@@I gSTSSSSSUhhi gSTSSSSSUhhi@Gjh>@ @_k@l@FGlmP* (O +,./PK .*?:1  2org/biojava/bio/seq/db/AnnotatedSequenceDB$1.class29 $ % "& '# ( ) * "+,-.pi&Lorg/biojava/bio/seq/SequenceIterator;this$0,Lorg/biojava/bio/seq/db/AnnotatedSequenceDB;/(Lorg/biojava/bio/seq/db/AnnotatedSequenceDB;)VCodeLineNumberTableLocalVariableTablethis InnerClasses.Lorg/biojava/bio/seq/db/AnnotatedSequenceDB$1;hasNext()Z nextSequence ()Lorg/biojava/bio/seq/Sequence; Exceptions/ SourceFileAnnotatedSequenceDB.javaEnclosingMethod0 12  3 456   78,org/biojava/bio/seq/db/AnnotatedSequenceDB$1java/lang/Object$org/biojava/bio/seq/SequenceIteratororg/biojava/bio/BioException*org/biojava/bio/seq/db/AnnotatedSequenceDBsequenceIterator(()Lorg/biojava/bio/seq/SequenceIterator;()V access$000Q(Lorg/biojava/bio/seq/db/AnnotatedSequenceDB;)Lorg/biojava/bio/seq/db/SequenceDB;!org/biojava/bio/seq/db/SequenceDB doAnnotation>(Lorg/biojava/bio/seq/Sequence;)Lorg/biojava/bio/seq/Sequence;   H*+*** K L 4 *O  ;**S  !"#  PK .*?:{pЋ 0org/biojava/bio/seq/db/AnnotatedSequenceDB.class2p F G HI G J KL MNO N P Q RS V WXYZ[\ ]^ _`abcdparent#Lorg/biojava/bio/seq/db/SequenceDB; annotator'Lorg/biojava/bio/seq/SequenceAnnotator;M(Lorg/biojava/bio/seq/db/SequenceDB;Lorg/biojava/bio/seq/SequenceAnnotator;)VCodeLineNumberTableLocalVariableTablethis,Lorg/biojava/bio/seq/db/AnnotatedSequenceDB;a getParent%()Lorg/biojava/bio/seq/db/SequenceDB;getName()Ljava/lang/String; getSequence2(Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;idLjava/lang/String; Exceptionsids()Ljava/util/Set;sequenceIterator(()Lorg/biojava/bio/seq/SequenceIterator; doAnnotation>(Lorg/biojava/bio/seq/Sequence;)Lorg/biojava/bio/seq/Sequence;ex1Lorg/biojava/bio/symbol/IllegalAlphabetException;cve'Lorg/biojava/utils/ChangeVetoException;seqLorg/biojava/bio/seq/Sequence; StackMapTableY` access$000Q(Lorg/biojava/bio/seq/db/AnnotatedSequenceDB;)Lorg/biojava/bio/seq/db/SequenceDB;x0 SourceFileAnnotatedSequenceDB.java  !e  java/lang/StringBuilder +, fg (h i,) -. 67 23,org/biojava/bio/seq/db/AnnotatedSequenceDB$1 InnerClasses !jk l7/org/biojava/bio/symbol/IllegalAlphabetExceptionorg/biojava/bio/BioExceptionCouldn't apply annotator  to m n, !o%org/biojava/utils/ChangeVetoException*org/biojava/bio/seq/db/AnnotatedSequenceDB)org/biojava/bio/seq/db/AbstractSequenceDB!org/biojava/bio/seq/db/SequenceDBjava/io/Serializable()Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;java/lang/ObjecttoString/(Lorg/biojava/bio/seq/db/AnnotatedSequenceDB;)V%org/biojava/bio/seq/SequenceAnnotatorannotateorg/biojava/bio/seq/SequencegetURN*(Ljava/lang/String;Ljava/lang/Throwable;)V! !"#Y**+*,$01 23% &'( )*#/*$:% &'+,#U+Y**   $>% +&'-.#C**+  $C%&'/0123#4 *$G%  &'45#3 Y*$K%  &'67#m*+MYY* + ,MYY* + ,  <$_ ` a<b=c%* 089=0:;m&'m<=> K?p@1AB#/*$*% C'DEU PK .*?:'ҥ'org/biojava/bio/seq/db/BioIndex$1.class2"  ()VCodeLineNumberTableLocalVariableTablethis InnerClasses#Lorg/biojava/bio/seq/db/BioIndex$1;compare'(Ljava/lang/Object;Ljava/lang/Object;)IaLjava/lang/Object;b SourceFile BioIndex.javaEnclosingMethod java/lang/Comparable !!org/biojava/bio/seq/db/BioIndex$1java/lang/Objectjava/util/Comparatororg/biojava/bio/seq/db/BioIndex compareTo(Ljava/lang/Object;)I0 /* ;   I +, =     PK .*?:770org/biojava/bio/seq/db/BioIndex$Commitable.class2 commit()V Exceptionsrollback SourceFile BioIndex.java*org/biojava/bio/seq/db/BioIndex$Commitable Commitable InnerClassesjava/lang/Objectorg/biojava/bio/BioExceptionorg/biojava/bio/seq/db/BioIndex   PK .*?:6찒 0org/biojava/bio/seq/db/BioIndex$FileAsList.class2 "W #X "Y "Z "[\ X "] "^ _` _abcd e "f _gh "i _jk lm "n op "q _rst Xu v w xyz{ mappedFileLjava/io/RandomAccessFile;commitedRecordsIlastIndxlastRecLjava/lang/Object;buffer[Bthis$0!Lorg/biojava/bio/seq/db/BioIndex;?(Lorg/biojava/bio/seq/db/BioIndex;Ljava/io/RandomAccessFile;I)VCodeLineNumberTableLocalVariableTablethis FileAsList InnerClasses,Lorg/biojava/bio/seq/db/BioIndex$FileAsList; recordLengthget(I)Ljava/lang/Object;ioeLjava/io/IOException;indxoffsetJ StackMapTableybsize()Iadd(Ljava/lang/Object;)Zocommit()VrollbacktLjava/lang/Throwable;s parseRecord([B)Ljava/lang/Object;generateRecord([BLjava/lang/Object;)V getComparator()Ljava/util/Comparator; SourceFile BioIndex.java ./ 0J %& ,- DE#java/lang/IndexOutOfBoundsException )( *+} ~ java/io/IOExceptionorg/biojava/bio/BioErrorFailed to seek for record 0 OP Can't read file length QR Failed to write index ST '( java/lang/Throwablejava/lang/StringBuildereCould not roll back. The index store will be in an inconsistent state and should be discarded. 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"#-Failed to read full set of sequence IDs file $% ef2org/biojava/bio/seq/db/emblcd/EntryNamRandomAccess j&#Failed to close random access file *org/biojava/bio/seq/db/EmblCDROMIndexStorejava/lang/Object!org/biojava/bio/seq/db/IndexStoreorg/biojava/bio/seq/db/Index2org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader(Ljava/lang/String;)V3org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess findRecord'(Ljava/lang/String;)[Ljava/lang/Object;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString java/util/Mapget&(Ljava/lang/Object;)Ljava/lang/Object;#(Ljava/io/File;Ljava/lang/String;)V longValue()J%(Ljava/io/File;JILjava/lang/String;)V(I)V(Ljava/io/InputStream;)V readRecord()[Ljava/lang/Object; java/util/Setadd(Ljava/lang/Object;)Zjava/lang/SystemerrLjava/io/PrintStream;java/io/PrintStreamprintlnprintStackTracejava/util/CollectionsunmodifiableSet (Ljava/util/Set;)Ljava/util/Set;readRecordCount readDBNameput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;values()Ljava/util/Collection;addAll(Ljava/util/Collection;)ZreadRecordLength()I(Ljava/io/File;IIJ)V!OPQRSTSUSVWXYZ[\]^_`_abcdefgdhijklu*Y+,-m n>opRSTSVWXYZ[q$jrl***,*-** * *+ * m&   %)nH*op*US*RS*TS*VW*XY*Z[q$stl/* mn opuvl>*+ m nopUSwxl/* mn opyzl> Ymn op {|q}~l4 Ymn  opq~l+mn opl|M*+N-YY+YY* *-2 -2!"+#MNYY%+,[^$m&  +[^ _zn4 P_|op|bz{|+2ql*&*'Y*()&L*Y+Y*,-L.Y+/M B!*(!,0:*&21W! 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$! swiss-protpubmedabstract locuslinkGenbankGenpept6http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? ! Swiss-prot.http://us.expasy.org/cgi-bin/get-sprot-raw.pl? LocusLink1http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?java/lang/StringBuilderdb= [\ ]2rettype= &retmode=org/biojava/bio/seq/db/FetchURLjava/lang/Objectjava/lang/String()VtrimequalsIgnoreCase(Ljava/lang/String;)Zappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString! !"!#!$!%&'$*++ *++**, *, +  * + * * *, + *(B125"9:<@=E>J@VB\DhFnGtHyJLN) *+,!-!./0012'q*3*'***  *** ** **(R<UEVQWZXfYl[) q*+.<32'AY*(a) *+42'M#Y* * (g) #*+56PK .*?:Jh.org/biojava/bio/seq/db/GenbankSequenceDB.class2R V U U U  U       + U        % %     % % % % U 9  = = = B A U A A  +     M Rformat'Lorg/biojava/bio/seq/io/SequenceFormat;DBNameLjava/lang/String;IOExceptionFoundZExceptionFoundurlBatchSequences ConstantValue()VCodeLineNumberTableLocalVariableTablethis*Lorg/biojava/bio/seq/db/GenbankSequenceDB;getSequenceFormat)()Lorg/biojava/bio/seq/io/SequenceFormat; getAlphabet#()Lorg/biojava/bio/symbol/Alphabet; getAddress"(Ljava/lang/String;)Ljava/net/URL;iddefaultReturnFormatseqURL!Lorg/biojava/bio/seq/db/FetchURL;baseurldburl Exceptions4(Ljava/lang/String;Ljava/lang/String;)Ljava/net/URL; StackMapTablegetName()Ljava/lang/String; getSequence2(Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;queryURLLjava/net/URL;inLjava/io/DataInputStream;readerLjava/io/BufferedReader;seqI&Lorg/biojava/bio/seq/SequenceIterator;eLjava/lang/Exception;checkIOException()ZcheckExceptionmakeBatchRequest1(Ljava/net/URL;Ljava/util/Set;)Ljava/lang/String; idSequenceiLjava/util/Iterator;listLjava/util/Set;paramsLjava/lang/StringBuffer;bheaderrequest getSequences4(Ljava/util/Set;)Lorg/biojava/bio/seq/db/SequenceDB;W(Ljava/util/Set;Lorg/biojava/bio/seq/db/SequenceDB;)Lorg/biojava/bio/seq/db/SequenceDB;lportIhostnamesLjava/net/Socket;sinLjava/io/InputStream; fromServersoutLjava/io/OutputStream;toServerLjava/io/PrintWriter; finEntete Ljava/net/MalformedURLException;Ljava/io/IOException;Lorg/biojava/bio/BioException;'Lorg/biojava/utils/ChangeVetoException;database#Lorg/biojava/bio/seq/db/SequenceDB;  SourceFileGenbankSequenceDB.java `a [\ ]\ WX textorg/biojava/bio/seq/db/FetchURL YZ ` !z "zjava/lang/StringBuilder #$&id= &rettype=gb %z java/net/URL `& '( kljava/io/DataInputStream )* `+java/io/BufferedReaderjava/io/InputStreamReader `,- ./ 01java/lang/Exception2 343Exception found in GenbankSequenceDB -- getSequence5 6&java/lang/StringBufferdb=nucleotide&rettype=gb&id= #7 89 :;java/lang/String <,POST =zC HTTP/1.0 Connection: close Accept: text/html, text/plain Host: >zj User-Agent: Biojava/GenbankSequenceDB Content-Type: application/x-www-form-urlencoded Content-Length: ?@ #A #B %org/biojava/bio/seq/db/HashSequenceDB8http://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi C@java/net/Socket `D E* FGjava/io/PrintWriterjava/io/OutputStreamWriter `H `I J& Ka Lz MN OPjava/net/MalformedURLExceptionorg/biojava/bio/BioException4Exception found in GenbankSequenceDB -- getSequences `Qjava/io/IOException%org/biojava/utils/ChangeVetoException$org/biojava/bio/seq/io/GenbankFormatGenbank(org/biojava/bio/seq/db/GenbankSequenceDBjava/lang/Objectjava/util/Iterator java/util/Set!org/biojava/bio/seq/db/SequenceDBjava/io/InputStreamjava/io/OutputStream$org/biojava/bio/seq/SequenceIteratororg/biojava/bio/seq/DNAToolsgetDNA)()Lorg/biojava/bio/symbol/FiniteAlphabet;'(Ljava/lang/String;Ljava/lang/String;)V getbaseURLgetDBappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString(Ljava/lang/String;)VequalsIgnoreCase(Ljava/lang/String;)Z openStream()Ljava/io/InputStream;(Ljava/io/InputStream;)V(Ljava/io/Reader;)V!org/biojava/bio/seq/io/SeqIOTools readGenbank@(Ljava/io/BufferedReader;)Lorg/biojava/bio/seq/SequenceIterator; nextSequence ()Lorg/biojava/bio/seq/Sequence;java/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln,(Ljava/lang/String;)Ljava/lang/StringBuffer;iterator()Ljava/util/Iterator;next()Ljava/lang/Object;hasNextgetPathgetHostlength()I(I)Ljava/lang/StringBuffer;2(Ljava/lang/StringBuffer;)Ljava/lang/StringBuffer;getPort(Ljava/lang/String;I)VgetInputStreamgetOutputStream()Ljava/io/OutputStream;(Ljava/io/OutputStream;)V(Ljava/io/Writer;)VprintflushreadLineequals(Ljava/lang/Object;)Z addSequence!(Lorg/biojava/bio/seq/Sequence;)V*(Ljava/lang/Throwable;Ljava/lang/String;)V!UV WX YZ[\]\^Z_; `abE***cB= >Cd efghb.cGd efijb.cLd efklbIMY, N- :- : Y +:YcUVWX[?]dHIefImZFnZ:op4qZ.rZ? sZtLkubVY, N- : - :- : Y +:Ycf ghi"j(mLodHVefVmZVWZ JopDqZ(.rZL sZv "wxtLyzb.ctd ef{|b[***+MY,NYY-::M!"#!,$#**;< c6 yz {-4<=EOTYdH,}~ -4=[ef[mZv|t b/*cd efb/*cd efb%Y&N-'(W6,):0*+:-(W, --(W6ѻ%Y&:.(W+/(W0(W+1(W2(W-34W5(W%Y&:6W-6W7cZ+2<FILU]goyd\ +Z2efs~\U\v+xb;*+8cdeftMb , 9Y:MY;N-<6-1:=Y>:?:YY:@: AYBY CD:  *-+EF G6 : HY:   I6 :  J, K3NMY-NONMY-NONMY-NONMY-NO, L P M Qcz "/6HOalqtw     dw Z s~"Z/6HpOi aW tD\     efvW j xxBKKK tMab,RYSTc ; <PK .*?:JE .org/biojava/bio/seq/db/GenpeptSequenceDB.class2 (` 'a 'b 'c defg 'h i j kl ` mno pq rs tu 'vw x yz{ y | }~  p  $`format'Lorg/biojava/bio/seq/io/SequenceFormat;DBNameLjava/lang/String;IOExceptionFoundZExceptionFound()VCodeLineNumberTableLocalVariableTablethis*Lorg/biojava/bio/seq/db/GenpeptSequenceDB;getSequenceFormat)()Lorg/biojava/bio/seq/io/SequenceFormat; getAlphabet#()Lorg/biojava/bio/symbol/Alphabet; getAddress"(Ljava/lang/String;)Ljava/net/URL;iddefaultReturnFormatseqURL!Lorg/biojava/bio/seq/db/FetchURL;baseurldburl Exceptions4(Ljava/lang/String;Ljava/lang/String;)Ljava/net/URL; StackMapTableggetName()Ljava/lang/String; getSequence2(Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;queryURLLjava/net/URL;inLjava/io/DataInputStream;readerLjava/io/BufferedReader;seqI&Lorg/biojava/bio/seq/SequenceIterator;eLjava/lang/Exception;checkIOException()ZcheckException SourceFileGenpeptSequenceDB.java 01 -. /. )* textorg/biojava/bio/seq/db/FetchURL +, 0 K Kjava/lang/StringBuilder &id= &rettype=gb K java/net/URL 0 ;<java/io/DataInputStream 0java/io/BufferedReaderjava/io/InputStreamReader 0  java/lang/Exception  $org/biojava/bio/seq/io/GenbankFormatGenpept(org/biojava/bio/seq/db/GenpeptSequenceDBjava/lang/Objectjava/net/MalformedURLExceptionjava/lang/Stringorg/biojava/bio/BioException org/biojava/bio/seq/ProteinTools getTAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;'(Ljava/lang/String;Ljava/lang/String;)V getbaseURLgetDBappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString(Ljava/lang/String;)VequalsIgnoreCase(Ljava/lang/String;)Z openStream()Ljava/io/InputStream;(Ljava/io/InputStream;)V(Ljava/io/Reader;)V!org/biojava/bio/seq/io/SeqIOTools readGenpept@(Ljava/io/BufferedReader;)Lorg/biojava/bio/seq/SequenceIterator;$org/biojava/bio/seq/SequenceIterator nextSequence ()Lorg/biojava/bio/seq/Sequence;java/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln!'( )* +,-./. 012A***3+. /4 56782.324 569:2.364 56;<2IMY, N- :- : Y +:Y3:;<=??A4HI56I=,F>,:?@4A,.B,? C,DE;F2VY, N- : - :- : Y +:Y3G HIJ"K(NLP4HV56V=,V), J?@DA,(.B,L C,G "HIDEJK2.3T4 56LM2S***+MY,NYY-::M!,"#**;< 32 YZ [_`-a4c<e=fGgLhQi4H,NO PQ-RS4TU=VWS56S=,G|XDYZ[2/*3n4 56\[2/*3r4 56]12,$Y%&3 , -^_PK .*?:z g-org/biojava/bio/seq/db/HashSequenceDB$1.class2A # $ !% &' () * +, +-./01seqILjava/util/Iterator;this$0'Lorg/biojava/bio/seq/db/HashSequenceDB;*(Lorg/biojava/bio/seq/db/HashSequenceDB;)VCodeLineNumberTableLocalVariableTablethis InnerClasses)Lorg/biojava/bio/seq/db/HashSequenceDB$1;hasNext()Z nextSequence ()Lorg/biojava/bio/seq/Sequence; SourceFileHashSequenceDB.javaEnclosingMethod2 34  5 678 9:; <= >  ?@org/biojava/bio/seq/Sequence'org/biojava/bio/seq/db/HashSequenceDB$1java/lang/Object$org/biojava/bio/seq/SequenceIterator%org/biojava/bio/seq/db/HashSequenceDBsequenceIterator(()Lorg/biojava/bio/seq/SequenceIterator;()V access$0008(Lorg/biojava/bio/seq/db/HashSequenceDB;)Ljava/util/Map; java/util/Mapvalues()Ljava/util/Collection;java/util/Collectioniterator()Ljava/util/Iterator;java/util/Iteratornext()Ljava/lang/Object;   M*+*** T U 4 *V  7 * W   !"  PK .*?:<+org/biojava/bio/seq/db/HashSequenceDB.class2 "Z "[ \]^_` ab cd e f \gh k "l \m $n "opq r st su "v wx "y \z w{ "| #a} a~ sequenceByIDLjava/util/Map;idMaker Lorg/biojava/bio/seq/db/IDMaker;nameLjava/lang/String;getName()Ljava/lang/String;CodeLineNumberTableLocalVariableTablethis'Lorg/biojava/bio/seq/db/HashSequenceDB; getSequence2(Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;idseqLorg/biojava/bio/seq/Sequence; StackMapTable^ Exceptionsids()Ljava/util/Set;sequenceIterator(()Lorg/biojava/bio/seq/SequenceIterator; addSequence3(Ljava/lang/String;Lorg/biojava/bio/seq/Sequence;)VceLorg/biojava/utils/ChangeEvent; changeSupport!Lorg/biojava/utils/ChangeSupport;~q getIDMaker"()Lorg/biojava/bio/seq/db/IDMaker;!(Lorg/biojava/bio/seq/Sequence;)VremoveSequence(Ljava/lang/String;)V()V#(Lorg/biojava/bio/seq/db/IDMaker;)V5(Lorg/biojava/bio/seq/db/IDMaker;Ljava/lang/String;)V access$0008(Lorg/biojava/bio/seq/db/HashSequenceDB;)Ljava/util/Map;x0 SourceFileHashSequenceDB.java &' *+ org/biojava/bio/seq/Sequence)org/biojava/bio/seq/db/IllegalIDExceptionjava/lang/StringBuilder QRSequence with ID  could not be found - QO <'org/biojava/bio/seq/db/HashSequenceDB$1 InnerClasses Q org/biojava/utils/ChangeEventjava/lang/Object Q () ?@ ) QTjava/util/HashMap%org/biojava/bio/seq/db/HashSequenceDB)org/biojava/bio/seq/db/AbstractSequenceDB!org/biojava/bio/seq/db/SequenceDBjava/io/Serializablejava/lang/Stringorg/biojava/utils/ChangeSupportjava/lang/Throwable%org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioException java/util/Mapget&(Ljava/lang/Object;)Ljava/lang/Object;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toStringkeySet*(Lorg/biojava/bio/seq/db/HashSequenceDB;)V hasListeners()Zput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object; SEQUENCESLorg/biojava/utils/ChangeType;getChangeSupportA(Lorg/biojava/utils/ChangeType;)Lorg/biojava/utils/ChangeSupport;W(Ljava/lang/Object;Lorg/biojava/utils/ChangeType;Ljava/lang/Object;Ljava/lang/Object;)VfirePreChangeEvent"(Lorg/biojava/utils/ChangeEvent;)VfirePostChangeEventorg/biojava/bio/seq/db/IDMakercalcID2(Lorg/biojava/bio/seq/Sequence;)Ljava/lang/String;removebyName!"#$%&'()*+ ,-./*/B0 1234.4*+M,#YY +  ,/HIJ2L0 41245+&67829:;<.4 * /P0  12=>.3 Y*/T0  12?@.d**+,WP*N-Y:»Y*Y+SY,S:-*+,W-ç :#X[[`[/* degh#i=oCpOqUrct04=ABECDd12d5+d678DEF9GHI:JKL./*/|0 12?M.]*+M* *,+D*N-Y:»Y*,:-*,W-ç :(QTTYT/. #(7=HN\047AB#9CD]12]67 R5+8$F8E9FGHI:JNO.T**+WA*M,YN»Y*+:,*+W,-ç :-!ILLPL/* !06AGS0*0AB6CDT12T5+86EFGHI:PJQR.7 */ 0  12QS.?*+/ 012()QO.A *+/ 0 12 *+QT.h**+*,* Y!/ 0 12()*+UV./*/,0 W2XYj PK /*?:]/org/biojava/bio/seq/db/HashSequenceDBTest.class2/  !"# $ % &'((Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis+Lorg/biojava/bio/seq/db/HashSequenceDBTest;nameLjava/lang/String; getSequenceDB%()Lorg/biojava/bio/seq/db/SequenceDB; Exceptions)suite()Ljunit/framework/Test;main([Ljava/lang/String;)Vargs[Ljava/lang/String; SourceFileHashSequenceDBTest.java %org/biojava/bio/seq/db/HashSequenceDB *junit/framework/TestSuite)org/biojava/bio/seq/db/HashSequenceDBTest + , -.-org/biojava/bio/seq/db/AbstractSequenceDBTestjava/lang/Exception()V(Ljava/lang/Class;)Vjunit/textui/TestRunnerrun4(Ljunit/framework/Test;)Ljunit/framework/TestResult;! 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java/net/URL ) 45java/io/DataInputStream )java/io/BufferedReaderjava/io/InputStreamReader )  java/lang/Exception  %org/biojava/bio/seq/io/EmblLikeFormat swiss-prot*org/biojava/bio/seq/db/SwissprotSequenceDBjava/lang/Objectjava/net/MalformedURLExceptionorg/biojava/bio/BioException org/biojava/bio/seq/ProteinTools getTAlphabet)()Lorg/biojava/bio/symbol/FiniteAlphabet;'(Ljava/lang/String;Ljava/lang/String;)V getbaseURLappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString(Ljava/lang/String;)V openStream()Ljava/io/InputStream;(Ljava/io/InputStream;)V(Ljava/io/Reader;)V!org/biojava/bio/seq/io/SeqIOTools readSwissprot@(Ljava/io/BufferedReader;)Lorg/biojava/bio/seq/SequenceIterator;$org/biojava/bio/seq/SequenceIterator nextSequence ()Lorg/biojava/bio/seq/Sequence;java/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln!!" #$ %&'()*+8 **, ,0-  ./01+.,5- ./23+.,:- ./45+4MY,N- : Y  + :Y,?@AC*E->4./46&17&%89:&* ;&<=>?+.,J- ./@A+I**+MY,NYY-::M,*67,* QR ST(U/V7X8ZB[G\-H ,BC DE(FG/HI8JKI./I6&LwM<NOP+/*,b- ./Q*+,Y , . /RSPK .*?:SwP*org/biojava/bio/seq/db/TabIndexStore.class2     k !      !          #   '   5  - 5       ! 8 7       5  7  7     !"# O$ Q% Q& Q' O () (* +, !-./ Z01 ^ ]2 ]34 b b5 67 89: g; < =>?@ idToIndexLjava/util/Map;commited uncommited storeFileLjava/io/File; indexFilenameLjava/lang/String;filesLjava/util/Set; seqFileIndex[Ljava/io/File;format'Lorg/biojava/bio/seq/io/SequenceFormat; sbFactory/Lorg/biojava/bio/seq/io/SequenceBuilderFactory; symbolParser+Lorg/biojava/bio/seq/io/SymbolTokenization;open6(Ljava/io/File;)Lorg/biojava/bio/seq/db/TabIndexStore;CodeLineNumberTableLocalVariableTablefisLjava/io/FileInputStream;pLjava/io/ObjectInputStream; indxStore&Lorg/biojava/bio/seq/db/TabIndexStore;cnfe"Ljava/lang/ClassNotFoundException; StackMapTable Exceptions(Ljava/io/File;Ljava/io/File;Ljava/lang/String;Lorg/biojava/bio/seq/io/SequenceFormat;Lorg/biojava/bio/seq/io/SequenceBuilderFactory;Lorg/biojava/bio/seq/io/SymbolTokenization;)VthisABCDstore!(Lorg/biojava/bio/seq/db/Index;)VindxLorg/biojava/bio/seq/db/Index;fetch2(Ljava/lang/String;)Lorg/biojava/bio/seq/db/Index;id commit()ViLjava/util/Iterator;outLjava/io/PrintWriter;ioeLjava/io/IOException; ErollbackgetName()Ljava/lang/String;getIDs()Ljava/util/Set;getFiles getFormat)()Lorg/biojava/bio/seq/io/SequenceFormat; getSBFactory1()Lorg/biojava/bio/seq/io/SequenceBuilderFactory;getSymbolParser-()Lorg/biojava/bio/seq/io/SymbolTokenization; commitStorefosLjava/io/FileOutputStream;Ljava/io/ObjectOutputStream;addFile(Ljava/io/File;)VlenIsfif getFileIndex(Ljava/io/File;)Iposfile initializestokLjava/util/StringTokenizer;fileNumstartJindex$Lorg/biojava/bio/seq/db/SimpleIndex;linereaderLjava/io/BufferedReader;0 readObject(Ljava/io/ObjectInputStream;)Vin SourceFileTabIndexStore.javajava/io/FileInputStream java/io/ObjectInputStream F G$org/biojava/bio/seq/db/TabIndexStore H java/lang/ClassNotFoundException"org/biojava/utils/AssertionFailure'Assertion Failure: How did we get here? 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Sequences may not be removed from a biofetch databaseembl genbankswiss swissprotrefseqorg/biojava/bio/BioExceptionjava/lang/StringBuilderSequence database  is not supported Ojava/lang/StringBuffer  style=raw; format=;db=;id= java/net/URL java/net/HttpURLConnection java/io/BufferedReaderjava/io/InputStreamReader G G OContent- java/util/StringTokenizer OERROR )org/biojava/bio/seq/db/IllegalIDException No such ID  in database NOError fetching from BioFetch:   java/io/IOException Error reading data from BioFetch G2org/biojava/bio/seq/db/biofetch/BioFetchSequenceDBorg/biojava/utils/Unchangeable%org/biojava/bio/seq/db/SequenceDBLitejava/lang/String$org/biojava/bio/seq/SequenceIterator()Vequals(Ljava/lang/Object;)Zappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString(C)Ljava/lang/StringBuffer;,(Ljava/lang/String;)Ljava/lang/StringBuffer; substring(I)Ljava/lang/String;openConnection()Ljava/net/URLConnection;connectgetInputStream()Ljava/io/InputStream;(Ljava/io/InputStream;)V(Ljava/io/Reader;)Vmark(I)VreadLine startsWith(Ljava/lang/String;)Z nextTokenjava/lang/IntegerparseInt(Ljava/lang/String;)Ireset!org/biojava/bio/seq/io/SeqIOToolsreadEmbl@(Ljava/io/BufferedReader;)Lorg/biojava/bio/seq/SequenceIterator; readGenbank readSwissprot nextSequence ()Lorg/biojava/bio/seq/Sequence;*(Ljava/lang/String;Ljava/lang/Throwable;)V!ABCDEFEGHIY**+*,JBC DEK LMDEFENOI/*JHK LMPQI> YJLK LM RSTUVI> YJRK LM WETXYIq M*  M*  MD*  M2* &YY*Y*N-?W-W-W-,W-W-*W-W-+WY- !"#:$%Y&Y'():*+:,-+W+:.Y/:0:1 V026  *3YY4+5*67YY89:: * :: ,* ;: * <:  =:Y?@>J,Z\]^_$`0a6bBcegqhxijklmnortuwyz{|#)PlqxKz #IZ[ \]^_`EabcExGde  fgLMWEhEq\ijkR l.mllnoplRql!rmllnsT3tuPK .*?:y::@org/biojava/bio/seq/db/biofetch/BioFetchSequenceDBProvider.class2; &' ()*+, -./0 1234()VCodeLineNumberTableLocalVariableTablethis+M, Y+ N- Y  Y,- 2 348&9*:4>*>> 2& !!"#$%PK /*?:RC,org/biojava/bio/seq/db/biofetch/package.html Client for the OBDA BioFetch protocol.

For more information about this protocol, see the OBDA website.

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and term.term_id = bioentry_qualifier_value.term_id        java/util/Collectionjava/util/ArrayList  cjava/sql/SQLException#org/biojava/bio/BioRuntimeExceptionError fetching annotations `%org/biojava/utils/ChangeVetoExceptionorg/biojava/bio/BioError ` 4select taxon_id from bioentry where bioentry_id = ? !" #$ %&' (i )* )+&Couldn't manipulate in-memory taxonomy#Error fetching taxonomy annotations bc ,-org/biojava/utils/ChangeEvent . `/ 01 21  java/util/NoSuchElementExceptionjava/lang/StringBuilder$Annotation doesn't contain property 34 5 `6 78 9: ;c <cError adding to BioSQL tables (rolled back successfully) = >?@ A BC DC6org/biojava/bio/seq/db/biosql/BioSQLSequenceAnnotationjava/lang/Objectorg/biojava/bio/Annotationjava/sql/Connectionjava/sql/PreparedStatementjava/sql/ResultSetjava/lang/Stringjava/lang/Throwable?*0M,YN»1Y*2+3:,4*+@*+7,6-ç :-Bnqquq\6  6>BPV`flx]*Py^_yhg>;u *:}zz#[N*N-A*-*+,B-C-M:6--D6:-: Y9Y:E<FG<>"25>GJLRU\B&,257:>DGLW]RLpWop:E7Hqp^_hgjg~stu~5}zzv|}zzv~|H|}zzv~WW}zzv~WWy #[[**/*+\ ]^_hgu [P**/*H\ ] ^_u [S**/*IJ\  ] ^_u [A *+KL\ ] ^_ [Z*0 Y* +,M\ ] ^_[A *+KN\ ] ^_ [Z*0 Y* +,O\  !] ^_[6\$]^_PK /*?:h6org/biojava/bio/seq/db/biosql/BioSQLSequenceDB$1.class2B % & #' () * +, +-. #/012pIDLjava/util/Iterator;this$00Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB;3(Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB;)VCodeLineNumberTableLocalVariableTablethis InnerClasses2Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$1;hasNext()Z nextSequence ()Lorg/biojava/bio/seq/Sequence; Exceptions3 SourceFileBioSQLSequenceDB.javaEnclosingMethod4 56  7 89: ;< =  >?java/lang/String @A0org/biojava/bio/seq/db/biosql/BioSQLSequenceDB$1java/lang/Object$org/biojava/bio/seq/SequenceIteratororg/biojava/bio/BioException.org/biojava/bio/seq/db/biosql/BioSQLSequenceDBsequenceIterator(()Lorg/biojava/bio/seq/SequenceIterator;()Vids()Ljava/util/Set; java/util/Setiterator()Ljava/util/Iterator;java/util/Iteratornext()Ljava/lang/Object; getSequence2(Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;   H*+***   4 *  >**   !"#$  PK /*?:_Gorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$FilterByInternalID.class2+    ! "$%&idIthis$00Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB;4(Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB;I)VCodeLineNumberTableLocalVariableTablethisFilterByInternalID InnerClassesCLorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$FilterByInternalID;accept (Lorg/biojava/bio/seq/Feature;)ZfLorg/biojava/bio/seq/Feature;intID StackMapTable SourceFileBioSQLSequenceDB.java ' +org/biojava/bio/seq/db/biosql/BioSQLFeature ()*Aorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$FilterByInternalIDjava/lang/Object!org/biojava/bio/seq/FeatureFilter()V_getInternalID()I.org/biojava/bio/seq/db/biosql/BioSQLSequenceDB    K*+**  x++=*     @ #PK /*?:vJorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$SingleFeatureReceiver.class22 & ' & ()* +-.featureLorg/biojava/bio/seq/Feature;this$00Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB;3(Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB;)VCodeLineNumberTableLocalVariableTablethisSingleFeatureReceiver InnerClassesFLorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$SingleFeatureReceiver;deliverTopLevelFeature (Lorg/biojava/bio/seq/Feature;)Vf StackMapTable Exceptions getFeature()Lorg/biojava/bio/seq/Feature;/e(Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB;Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$1;)Vx0x12Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$1; SourceFileBioSQLSequenceDB.java  %org/biojava/bio/seq/io/ParseExceptionExpecting only a single feature 01Dorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$SingleFeatureReceiver3org/biojava/bio/seq/db/biosql/BioSQLFeatureReceiver0org/biojava/bio/seq/db/biosql/BioSQLSequenceDB$1(Ljava/lang/String;)V.org/biojava/bio/seq/db/biosql/BioSQLSequenceDB    = *+*+$% &  d* *+ Y+,.0  /*3  D*+! ! "#$%,PK /*?:&VBorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$SqlizedFilter.class2 7r 8st s 7u 7v 7w 7x 7y{ }~ s   7 7    2 $ )s )   )tablesLjava/util/List;filterLjava/lang/String;used_otIused_sfsthis$00Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB;V(Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB;Lorg/biojava/bio/seq/FeatureFilter;)VCodeLineNumberTableLocalVariableTablethis SqlizedFilter InnerClasses>Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$SqlizedFilter;ff#Lorg/biojava/bio/seq/FeatureFilter; sqlizeFilter8(Lorg/biojava/bio/seq/FeatureFilter;Z)Ljava/lang/String;type tableNamesourceandAnd'Lorg/biojava/bio/seq/FeatureFilter$And;ff1ff2filter1filter2childnegateZ StackMapTableeq(Z)Ljava/lang/String;qw&(Ljava/lang/String;)Ljava/lang/String;wordgetQuery()Ljava/lang/String;iLjava/util/Iterator;queryLjava/lang/StringBuffer; SourceFileBioSQLSequenceDB.java @A Bjava/util/ArrayList 9: => ?> MN ;<(org/biojava/bio/seq/FeatureFilter$ByTypeByType ijava/lang/StringBuilderot_ iterm as  .name cd ef and seqfeature.type_term_id = .term_id*org/biojava/bio/seq/FeatureFilter$BySourceBySource isfs_! and seqfeature.source_term_id = .org/biojava/bio/seq/FeatureFilter$ByAnnotation ByAnnotation%org/biojava/bio/seq/FeatureFilter$And  and %org/biojava/bio/seq/FeatureFilter$NotNot  <> ='java/lang/StringBuffer4select bioentry.accession, seqfeature.seqfeature_id  from seqfeature, bioentry  , java/lang/String4 where bioentry.bioentry_id = seqfeature.bioentry_id" and bioentry.biodatabase_id = ? order by bioentry.accession ?>@ABCDq)*+**Y****, ED >@AE(FF)GJ)KLMND+ |+ N Y *YZ`:* Y W Y **-+|+N Y *YZ`:* Y W Y **-++a+N- :-!:*:*:"(" Y #"+$+$%N*-EvIJK.LLMNOPQRSU xyz{"|+}4~<D^ailov~F qO<.RP<qQ<RP<YRTSUL"MVL+DW<4;X<~YLGJKLZ[\h  S]^_^^`` ]^]^^ab]^^abcdDO &'EF GJ Z[\efDM Y (+(EFGJg<hiDv)Y*L++,W+-,W*.M,/+0,W+,12,W+3,W+4,W* "+#,W+* ,W+5,W+6E6 )0AHOY`ipF  !jkvGJnlm\ no 'pqI27HzS z|zz$zPK /*?:E4org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.class2 (H (I (J (K (L (M (N )O (PR O (TU O (V (W (XY Z ([ (\ (] (^ (_ (` (a (b (c (d (e (f (g hijkl #m (n op qr stu *vw ,xy .xz 0{ |} ~  ( ~ # ( <v  ( ~     (    ~ (s  QO Q Q 7    * \ ( ( (  t ~ jm ( Q        j ~     (     ( <        ( t (  Z    Q    (   (d   "    (   O     !"#$%&' O(  )*+ ,- q./ 012 q3 7 (45 (678 9 : ; <= <> ? <@ABC 7D E FtG HIJKLMN jOP QR ST  OU . (VW X  YZ [  \]^ m_` v \a (b c cde "f <g "hijklmSingleFeatureReceiver InnerClassesFilterByInternalID SqlizedFilter dataSourceLjavax/sql/DataSource;dbidInameLjava/lang/String;idmaker Lorg/biojava/bio/seq/db/IDMaker;sequencesByName*Lorg/biojava/utils/cache/WeakValueHashMap; sequencesByIDhelper(Lorg/biojava/bio/seq/db/biosql/DBHelper; featuresSQL+Lorg/biojava/bio/seq/db/biosql/FeaturesSQL; ontologySQL+Lorg/biojava/bio/seq/db/biosql/OntologySQL;entryChangeHub4Lorg/biojava/bio/seq/db/biosql/BioSQLEntryChangeHub;entryAnnotationChangeHub>Lorg/biojava/bio/seq/db/biosql/BioSQLEntryAnnotationChangeHub;featureChangeHub6Lorg/biojava/bio/seq/db/biosql/BioSQLFeatureChangeHub;featureAnnotationChangeHub@Lorg/biojava/bio/seq/db/biosql/BioSQLFeatureAnnotationChangeHub; featuresByID tileCacheLorg/biojava/utils/cache/Cache;hierarchyCheckedZhierarchySupportedassemblyCheckedassemblySupportedbioentryPropertyCheckedbioentryPropertySupporteddbSchemaCheckeddbSchemaSupportedcommentTableNameCheckedcommentTableName spaChecked spaSupported getDataSource()Ljavax/sql/DataSource;CodeLineNumberTableLocalVariableTablethis0Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB; 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description getOntology3(Ljava/lang/String;)Lorg/biojava/ontology/Ontology; addOntology@(Lorg/biojava/ontology/Ontology;)Lorg/biojava/ontology/Ontology;ontoLorg/biojava/ontology/Ontology;getName()Ljava/lang/String;createDummySequence7(Ljava/lang/String;Lorg/biojava/bio/symbol/Alphabet;I)VcevLorg/biojava/utils/ChangeEvent;idalphabet!Lorg/biojava/bio/symbol/Alphabet;lengthrst_createDummySequencecreate_bioentry bioentry_id create_dummyex2 rolledbackseqAlphaversion addSequence!(Lorg/biojava/bio/seq/Sequence;)VseqLorg/biojava/bio/seq/Sequence; _addSequencecreate_biosequenceseqstrretrieve_biosequenceodh.Lorg/biojava/bio/seq/db/biosql/OracleDBHelper;meEntryLjava/util/Map$Entry;keyLjava/lang/Object;valueiLjava/util/Iterator;annLorg/biojava/bio/Annotation;bsuBioSequenceStyle9Lorg/biojava/bio/seq/db/biosql/DBHelper$BioSequenceStyle;features#Lorg/biojava/bio/seq/FeatureHolder;numseqNameseqToke+Lorg/biojava/bio/seq/io/SymbolTokenization;vwuxy getSequence2(Ljava/lang/String;)Lorg/biojava/bio/seq/Sequence;!(I)Lorg/biojava/bio/seq/Sequence;3(Ljava/lang/String;I)Lorg/biojava/bio/seq/Sequence; get_bioentry get_accessionmoleculeget_biosequence assembly_id get_assemblyremoveSequence(Ljava/lang/String;)V_removeSequencedelete_comment delete_locssfid get_seqfeatssfids delete_fqv delete_reldelete_reference delete_qv generic_idsLjava/util/ArrayList;delete_featuresdelete_biosequencedstylez DeleteStyle4Lorg/biojava/bio/seq/db/biosql/DBHelper$DeleteStyle; delete_entrystatus get_sequenceexistszids()Ljava/util/Set;_idsLjava/util/Set;st{persistBioentryProperty?(Ljava/sql/Connection;ILjava/lang/Object;Ljava/lang/Object;ZZ)V set_taxontaxon_idremove_old_valuecnt insert_newtermID keyString removeFirstsilentintern_ontology_term*(Ljava/sql/Connection;Ljava/lang/String;)Islegacyts|getOntologyTerm(I)Ljava/lang/String;termIdisHierarchySupported()ZisAssemblySupportedisBioentryPropertySupportedisDbSchemaSupportedgetCommentTableNameisSPASupportedlevelpsfilterH(Lorg/biojava/bio/seq/FeatureFilter;)Lorg/biojava/bio/seq/FeatureHolder; accessionfid hereFeaturefLorg/biojava/bio/seq/Feature;sqf>Lorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$SqlizedFilter; get_featureslastAccfh)Lorg/biojava/bio/seq/SimpleFeatureHolder;'Lorg/biojava/utils/ChangeVetoException;Lorg/biojava/bio/BioException;ff#Lorg/biojava/bio/seq/FeatureFilter;}PT]]kksequenceIterator(()Lorg/biojava/bio/seq/SequenceIterator;firePreChangeEvent"(Lorg/biojava/utils/ChangeEvent;)VfirePostChangeEventcanonicalizeFeature](Lorg/biojava/bio/seq/db/biosql/BioSQLFeature;I)Lorg/biojava/bio/seq/db/biosql/BioSQLFeature;-Lorg/biojava/bio/seq/db/biosql/BioSQLFeature; feature_idLjava/lang/Integer; oldFeaturedgetFeatureByID0(I)Lorg/biojava/bio/seq/db/biosql/BioSQLFeature;receiverFLorg/biojava/bio/seq/db/biosql/BioSQLSequenceDB$SingleFeatureReceiver;e getTileCache!()Lorg/biojava/utils/cache/Cache; SourceFileBioSQLSequenceDB.java Deprecated /0 :; <= @A BC DE FG k~ 12%org/biojava/bio/seq/db/IDMaker$ByNameByName 56(org/biojava/utils/cache/WeakValueHashMap 78 98 H8&org/biojava/utils/cache/FixedSizeCache k IJ KL ML NL OL PL QL RL SL TL U4 VL WL Xjava/lang/Exceptionorg/biojava/bio/BioExceptionError getting datasource k  s  2org/biojava/bio/seq/db/biosql/BioSQLEntryChangeHub korg/biojava/bio/seq/db/biosql/BioSQLFeatureAnnotationChangeHub k o  _  ~java/sql/SQLExceptionThis database appears to be an old (pre-Singapore) BioSQL. If you need to access it, try an older BioJava snapshot (1.3pre1 or earlier) k rThis database appears to be an old (pre-Cape-Town) BioSQL. If you need to access it, try an older BioJava snapshot)org/biojava/bio/seq/db/biosql/FeaturesSQL  >?Error accessing ontologies5select biodatabase_id from biodatabase where name = ? p  q   34+insert into biodatabase (name) values ( ? )  ~ _`biodatabase_id java/lang/StringBuilder Biodatabase  doesn't exist %Error connecting to BioSQL database:    org/biojava/utils/ChangeEvent  k 34  54`insert into bioentry (biodatabase_id, name, accession, version, division) values (?, ?, ?, ?, ?) ?bioentry[insert into biosequence (bioentry_id, version, alphabet, length) values (?, ?, ?, ?)r ~#org/biojava/bio/BioRuntimeExceptionError adding dummy sequence (rolled back successfully)   token QCan't store sequences in BioSQL unless they can be sensibly tokenized/detokenized   ginsert into biosequence (bioentry_id, version, length, seq, alphabet) values (?, ?, ?, empty_clob(), ?) v 

The data structures and interfaces included in this package define an interoperable framework for bibliographic searches. A reference implementation was developed at European Bioinformatics Institute as an open source project OpenBQS, providing an access to the MEDLINE, a major bibliographic repository in the life sciences research domain, but not limited to it.