jaligner-1.0\jaligner-1.0\api\allclasses-frame.html
............\............\...\allclasses-noframe.html
............\............\...\constant-values.html
............\............\...\deprecated-list.html
............\............\...\help-doc.html
............\............\...\index-all.html
............\............\...\index.html
............\............\...\jaligner\Alignment.html
............\............\...\........\Cell.html
............\............\...\........\class-use\Alignment.html
............\............\...\........\.........\Cell.html
............\............\...\........\.........\Directions.html
............\............\...\........\.........\Markups.html
............\............\...\........\.........\Sequence.html
............\............\...\........\.........\SmithWatermanGotoh.html
............\............\...\........\Directions.html
............\............\...\........\example\class-use\Example.html
............\............\...\........\.......\Example.html
............\............\...\........\.......\package-frame.html
............\............\...\........\.......\package-summary.html
............\............\...\........\.......\package-tree.html
............\............\...\........\.......\package-use.html
............\............\...\........\formats\class-use\CLUSTAL.html
............\............\...\........\.......\.........\FASTA.html
............\............\...\........\.......\.........\Format.html
............\............\...\........\.......\.........\FormatFactory.html
............\............\...\........\.......\.........\Pair.html
............\............\...\........\.......\CLUSTAL.html
............\............\...\........\.......\FASTA.html
............\............\...\........\.......\Format.html
............\............\...\........\.......\FormatFactory.html
............\............\...\........\.......\package-frame.html
............\............\...\........\.......\package-summary.html
............\............\...\........\.......\package-tree.html
............\............\...\........\.......\package-use.html
............\............\...\........\.......\Pair.html
............\............\...\........\Markups.html
............\............\...\........\matrix\class-use\MatricesCompartor.html
............\............\...\........\......\.........\Matrix.html
............\............\...\........\......\.........\MatrixLoader.html
............\............\...\........\......\.........\MatrixLoaderException.html
............\............\...\........\......\MatricesCompartor.html
............\............\...\........\......\Matrix.html
............\............\...\........\......\MatrixLoader.html
............\............\...\........\......\MatrixLoaderException.html
............\............\...\........\......\package-frame.html
............\............\...\........\......\package-summary.html
............\............\...\........\......\package-tree.html
............\............\...\........\......\package-use.html
............\............\...\........\package-frame.html
............\............\...\........\package-summary.html
............\............\...\........\package-tree.html
............\............\...\........\package-use.html
............\............\...\........\Sequence.html
............\............\...\........\SmithWatermanGotoh.html
............\............\...\........\test\AlignmentScoreChecker.html
............\............\...\........\....\class-use\AlignmentScoreChecker.html
............\............\...\........\....\.........\RandomSequenceGenerator.html
............\............\...\........\....\package-frame.html
............\............\...\........\....\package-summary.html
............\............\...\........\....\package-tree.html
............\............\...\........\....\package-use.html
............\............\...\........\....\RandomSequenceGenerator.html
............\............\...\........\ui\AlignCommandLine.html
............\............\...\........\..\AlignWindow.html