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data/jalview-2.7.dfsg/src/com/stevesoft/pat/Skipped.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/StringBufferLike.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/MultiMin.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/End.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/RBuffer.java: C++ source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Pthings.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/BackMatch.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Skip.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/oneChar.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Any.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Pattern.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/RuleHolder.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/parsePerl.java: C++ source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/RegexTokenizer.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/SkipBMH.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Backup.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/wrap/StringBufferWrap.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/wrap/StringWrap.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java: C source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/wrap/WriterWrap.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/wrap/CharArrayWrap.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/FileRegex.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/RegRes.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Range.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/patInf.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/StrPos.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/BasicStringBufferLike.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/WantMoreTextReplaceRule.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Transformer.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/SubMark.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Start.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/RegexReader.java: C source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/PatternSub.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Custom.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/PushRule.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/BackRefRule.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/SpecialRule.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Rthings.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/StringRule.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/FastBracket.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Ctrl.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/DirFileRegex.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/CaseMgr.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Multi.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/RegSyntax.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/UniValidator.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/PartialBuffer.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Prop.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Multi_stage2.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/OrMark.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/BackG.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/CustomEndpoint.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/RegOpt.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Skip2.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/DotMulti.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/FastMulti.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Regex.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Bracket.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/RegSyntaxError.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/Bits.java: C source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/LeftRule.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/AmpersandRule.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/lookAhead.java: Java source, ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/NonDirFileRegex.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/patInt.java: ASCII text data/jalview-2.7.dfsg/src/com/stevesoft/pat/NoPattern.java: Java source, ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/JpredResult_Helper.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/Object.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/Secstructpred.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/Alignment.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/Result.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/JpredResult.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/MsaResult.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/MsaResult_Helper.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/Sequence_Helper.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/Object_Helper.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/Msfalignment_Helper.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/Alignment_Helper.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/Msfalignment.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/Result_Helper.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/WsJobId.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/Secstructpred_Helper.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/SeqSearchResult.java: ASCII text, with CRLF line terminators data/jalview-2.7.dfsg/src/vamsas/objects/simple/Sequence.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/SequenceSet_Helper.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/WsJobId_Helper.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/objects/simple/SeqSearchResult_Helper.java: ASCII text, with CRLF line terminators data/jalview-2.7.dfsg/src/vamsas/objects/simple/SequenceSet.java: ASCII text data/jalview-2.7.dfsg/src/vamsas/IMsaWS.java: Perl5 module source, ASCII text data/jalview-2.7.dfsg/src/jalview/analysis/CrossRef.java: ASCII text, with CRLF line terminators data/jalview-2.7.dfsg/src/jalview/analysis/PCA.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/analysis/Finder.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/analysis/AAFrequency.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/analysis/SequenceIdMatcher.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/analysis/Grouping.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/analysis/ParseProperties.java: C source, ASCII text data/jalview-2.7.dfsg/src/jalview/analysis/NJTree.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/analysis/AlignmentSorter.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/analysis/Conservation.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/analysis/SeqsetUtils.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/analysis/Dna.java: ASCII text, with CRLF line terminators data/jalview-2.7.dfsg/src/jalview/binding/Property.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/jalview/binding/Viewport.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/jalview/binding/Features.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/jalview/binding/Pdbentry.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/jalview/binding/FeatureSettings.java: HTML document, ASCII text data/jalview-2.7.dfsg/src/jalview/binding/UserColours.java: 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data/jalview-2.7.dfsg/src/jalview/util/QuickSort.java: ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/Blosum62ColourScheme.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/ResidueColourScheme.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/HydrophobicColourScheme.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/ClustalxColourScheme.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/ZappoColourScheme.java: ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/ColourSchemeI.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/GraduatedColor.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/HelixColourScheme.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/ResidueProperties.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/AnnotationColourGradient.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/PIDColourScheme.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/Consensus.java: ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/TaylorColourScheme.java: ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/TurnColourScheme.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/ScoreMatrix.java: ASCII text, with CRLF line terminators data/jalview-2.7.dfsg/src/jalview/schemes/NucleotideColourScheme.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/BuriedColourScheme.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/StrandColourScheme.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/ScoreColourScheme.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/UserColourScheme.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/schemes/ColourSchemeProperty.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/javascript/MouseOverStructureListener.java: ASCII text, with CRLF, LF line terminators data/jalview-2.7.dfsg/src/jalview/javascript/JSFunctionExec.java: ASCII text, with CRLF, LF line terminators data/jalview-2.7.dfsg/src/jalview/javascript/JalviewLiteJsApi.java: Java source, ASCII text, with very long lines data/jalview-2.7.dfsg/src/jalview/javascript/JsSelectionSender.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/javascript/MouseOverListener.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/javascript/JsCallBack.java: ASCII text data/jalview-2.7.dfsg/src/jalview/structure/SequenceListener.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/structure/VamsasListener.java: ASCII text, with CRLF line terminators data/jalview-2.7.dfsg/src/jalview/structure/StructureListener.java: ASCII text data/jalview-2.7.dfsg/src/jalview/structure/StructureSelectionManager.java: Java source, ASCII text, with CRLF, LF line terminators data/jalview-2.7.dfsg/src/jalview/structure/SelectionListener.java: ASCII text data/jalview-2.7.dfsg/src/jalview/structure/SelectionSource.java: ASCII text data/jalview-2.7.dfsg/src/jalview/structure/AlignmentViewPanelListener.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/structure/StructureMappingcommandSet.java: ASCII text data/jalview-2.7.dfsg/src/jalview/structure/VamsasSource.java: ASCII text data/jalview-2.7.dfsg/src/jalview/structure/StructureMapping.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/io/FastaFile.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/io/AlignFile.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/io/VamsasAppDatastore.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/io/PIRFile.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/io/JPredFile.java: Java source, ASCII text data/jalview-2.7.dfsg/src/jalview/io/AnnotationFile.java: ASCII text, with CRLF line 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