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share/examples/biojava/demos-1.4/ssaha/CreateDNAFastaHashTableCompact.java
share/examples/biojava/demos-1.4/ssaha/CreateDNAFastaHashTableLarge.java
share/examples/biojava/demos-1.4/ssaha/CreateDNAFastaHashTable.java
share/examples/biojava/demos-1.4/ssaha/CreateEmblHashTable.java
share/examples/biojava/demos-1.4/ssaha/CreateEmblHashTableLarge.java
share/examples/biojava/demos-1.4/ssaha/ResultPrinter.java
share/examples/biojava/demos-1.4/ssaha/SSAHA.java
share/examples/biojava/demos-1.4/ssaha/SSAHALarge.java
share/examples/biojava/demos-1.4/ssaha/SSAHASeq.java
share/examples/biojava/demos-1.4/ssaha/SSAHASeqLarge.java
share/examples/biojava/demos-1.4/unigene/CreateUnigeneFlat.java
share/examples/biojava/demos-1.4/unigene/ParseLibInfo.java
share/examples/biojava/demos-1.4/unigene/ParseUnigene.java
share/examples/biojava/demos-1.4/unigene/SearchUnigeneFlat.java
share/examples/biojava/demos-obsolete/bioseqdb/UploadSwissprot.java
share/examples/biojava/demos-obsolete/search/FastaSearchParse.java
share/examples/biojava/demos-obsolete/seq/TestSwissprotOrg.java
share/examples/biojava/demos-obsolete/symbol/TestPackedSymbolList.java
share/examples/biojava/demos/CircLocTest/CircularLocationTester.java
share/examples/biojava/demos/CircLocTest/TestFrame.java
share/examples/biojava/demos/ListChangeTypes.java
share/examples/biojava/demos/RFetch.java
share/examples/biojava/demos/biosql/DummyFromGFF.java
share/examples/biojava/demos/biosql/LargeSequenceTest.java
share/examples/biojava/demos/biosql/SeqDumper.java
share/examples/biojava/demos/biosql/SeqEMBL.java
share/examples/biojava/demos/biosql/SeqGFF.java
share/examples/biojava/demos/biosql/SequenceTest.java
share/examples/biojava/demos/biosql/UploadFlat.java
share/examples/biojava/demos/das/TestDAS.java
share/examples/biojava/demos/das/TestDASG.java
share/examples/biojava/demos/das/TestDASH.java
share/examples/biojava/demos/das/TestDSN.java
share/examples/biojava/demos/dist/TestDistribution.java
share/examples/biojava/demos/dist/TestOrderNAlphabet.java
share/examples/biojava/demos/dist/TestOrderNDistribution.java
share/examples/biojava/demos/dist/Tools.java
share/examples/biojava/demos/dp/Dice.java
share/examples/biojava/demos/dp/PairwiseAlignment.java
share/examples/biojava/demos/dp/SearchProfile.java
share/examples/biojava/demos/dp/ViterbiAlign.java
share/examples/biojava/demos/dp/fake.fasta
share/examples/biojava/demos/dp/fakepromoter.xml
share/examples/biojava/demos/dp/package.html
share/examples/biojava/demos/eventbasedparsing/Blast2HTML.java
share/examples/biojava/demos/eventbasedparsing/BlastLike2XML.java
share/examples/biojava/demos/eventbasedparsing/Fasta2XML.java
share/examples/biojava/demos/eventbasedparsing/Pdb2XML.java
share/examples/biojava/demos/eventbasedparsing/TutorialEx1.java
share/examples/biojava/demos/eventbasedparsing/TutorialEx1Handler.java
share/examples/biojava/demos/eventbasedparsing/stylesheets/copyall.xsl
share/examples/biojava/demos/eventbasedparsing/stylesheets/hitlisthtml.xsl
share/examples/biojava/demos/files/AL121903.embl
share/examples/biojava/demos/files/AL121903.genbank
share/examples/biojava/demos/files/ChrI.prom.fasta
share/examples/biojava/demos/files/GCG/blast.report
share/examples/biojava/demos/files/clustal/keratin.aln
share/examples/biojava/demos/files/fake.fasta
share/examples/biojava/demos/files/fakepromoter.xml
share/examples/biojava/demos/files/fp_demo.db
share/examples/biojava/demos/files/fp_demo.m10
share/examples/biojava/demos/files/fp_queries.db
share/examples/biojava/demos/files/hmmer/plus_tot.out
share/examples/biojava/demos/files/ncbiblast/Massive.out
share/examples/biojava/demos/files/ncbiblast/ReadMe
share/examples/biojava/demos/files/ncbiblast/blastn.out
share/examples/biojava/demos/files/ncbiblast/blastp.out
share/examples/biojava/demos/files/ncbiblast/blastx.out
share/examples/biojava/demos/files/ncbiblast/shortBlastn.out
share/examples/biojava/demos/files/ncbiblast/tblastn.out
share/examples/biojava/demos/files/ncbiblast/tblastx.out
share/examples/biojava/demos/files/ncbiblast/unsuppVersionBlastn.out
share/examples/biojava/demos/files/out.gff
share/examples/biojava/demos/files/pdb/12E8.pdb
share/examples/biojava/demos/files/pdb/hgh_ori.pdb
share/examples/biojava/demos/files/pdb/hmga_1.pdb
share/examples/biojava/demos/files/pdb/tnf.pdb
share/examples/biojava/demos/files/scoptest.fa
share/examples/biojava/demos/files/test.hmm
share/examples/biojava/demos/files/varC4-2.dna
share/examples/biojava/demos/files/varC4-2.gff
share/examples/biojava/demos/files/wublast/blastn.out
share/examples/biojava/demos/files/wublast/blastp.out
share/examples/biojava/demos/files/wublast/blastx.out
share/examples/biojava/demos/files/wublast/sh_blastn.out
share/examples/biojava/demos/files/wublast/sh_blastp.out
share/examples/biojava/demos/files/wublast/sh_blastx.out
share/examples/biojava/demos/files/wublast/sh_tblastx.out
share/examples/biojava/demos/files/wublast/tblastn.out
share/examples/biojava/demos/files/wublast/tblastx.out
share/examples/biojava/demos/game/AE002734.game
share/examples/biojava/demos/game/README.txt
share/examples/biojava/demos/game/SeqIOTatler.java
share/examples/biojava/demos/game/TestGAME.java
share/examples/biojava/demos/gff/AL121903.embl
share/examples/biojava/demos/gff/EmblToGffFasta.java
share/examples/biojava/demos/gff/GFFCompare.java
share/examples/biojava/demos/gff/GFFFilter.java
share/examples/biojava/demos/gff/GFFMask.java
share/examples/biojava/demos/gff/GFFToFeatures.java
share/examples/biojava/demos/gff/GenbankToGffFasta.java
share/examples/biojava/demos/gff/SwissprotToGffFasta.java
share/examples/biojava/demos/gff/XFF2GFF.java
share/examples/biojava/demos/gff/varC4-2.gff
share/examples/biojava/demos/indexing/CreateFAIndex.java
share/examples/biojava/demos/indexing/CreateIndex.java
share/examples/biojava/demos/indexing/CreateSPIndex.java
share/examples/biojava/demos/indexing/ListIDs.java
share/examples/biojava/demos/indexing/ReadRaw.java
share/examples/biojava/demos/indexing/ReadRawSecondary.java
share/examples/biojava/demos/nativeapps/BlastLike2XML.java
share/examples/biojava/demos/nativeapps/Pdb2XML.java
share/examples/biojava/demos/prot/TestDigestIO.java
share/examples/biojava/demos/ragbag/README
share/examples/biojava/demos/ragbag/SequenceDumper.java
share/examples/biojava/demos/ragbag/TestRagbagAssembly.java
share/examples/biojava/demos/ragbag/embldir.tgz
share/examples/biojava/demos/ragbag/seqdir.tgz
share/examples/biojava/demos/ragbag/testfeature.game
share/examples/biojava/demos/ragbag/virtdir.tgz
share/examples/biojava/demos/search/IndexFastaDB.java
share/examples/biojava/demos/seq/AL121903.embl
share/examples/biojava/demos/seq/AL121903.genbank
share/examples/biojava/demos/seq/FetchSeq.java
share/examples/biojava/demos/seq/GCContent.java
share/examples/biojava/demos/seq/MotifFinder2.java
share/examples/biojava/demos/seq/ReverseComplement.java
share/examples/biojava/demos/seq/SimpleAssemblyTest.java
share/examples/biojava/demos/seq/TestEmbl.java
share/examples/biojava/demos/seq/TestEmbl2.java
share/examples/biojava/demos/seq/TestGenbank.java
share/examples/biojava/demos/seq/TestRefSeqPrt.java
share/examples/biojava/demos/seq/TestSubSequence.java
share/examples/biojava/demos/seq/TestSwissprot.java
share/examples/biojava/demos/seq/TestTranslation.java
share/examples/biojava/demos/seq/db/AddFilesToIndex.java
share/examples/biojava/demos/seq/db/CreateIndex.java
share/examples/biojava/demos/seq/db/FetchSequence.java
share/examples/biojava/demos/seq/db/ListSeqsInIndex.java
share/examples/biojava/demos/seq/utrs.fa
share/examples/biojava/demos/seqviewer/BeadDemo.java
share/examples/biojava/demos/seqviewer/EmblViewer.java
share/examples/biojava/demos/seqviewer/EmblViewer2.java
share/examples/biojava/demos/seqviewer/FastBeadDemo.java
share/examples/biojava/demos/seqviewer/TraceViewer.java
share/examples/biojava/demos/seqviewer/test.fa
share/examples/biojava/demos/ssbind/AlignmentBuilder.java
share/examples/biojava/demos/ssbind/CountHits.java
share/examples/biojava/demos/ssbind/CountSubHits.java
share/examples/biojava/demos/ssbind/Echoer.java
share/examples/biojava/demos/ssbind/FilterByValue.java
share/examples/biojava/demos/ssbind/ListQueries.java
share/examples/biojava/demos/ssbind/ListSubjects.java
share/examples/biojava/demos/ssbind/ProcessBlastReport.java
share/examples/biojava/demos/ssbind/PropertyEchoer.java
share/examples/biojava/demos/ssbind/SubHitBuilder.java
share/examples/biojava/demos/ssbind/SubHitFilter.java
share/examples/biojava/demos/symbol/MatrixValue.java
share/examples/biojava/demos/symbol/PatternDemo.java
share/examples/biojava/demos/symbol/TestAlphabetIndexers.java
share/examples/biojava/demos/symbol/TestAmbiguity.java
share/examples/biojava/demos/symbol/TestGappedSymbolList.java
share/examples/biojava/demos/symbol/TestIndexedIntegers.java
share/examples/biojava/demos/symbol/TestLocation.java
share/examples/biojava/demos/symbol/TestOrderNSymbolList.java
share/examples/biojava/demos/symbol/TestSimpleAlignment.java
share/examples/biojava/demos/symbol/TestWindowedSymbolList.java
share/examples/biojava/demos/symbol/Tools.java
share/examples/biojava/demos/symbol/WindowCount.java
share/examples/biojava/demos/tagvalue/ParseEmbl.java
share/examples/biojava/demos/tagvalue/ParseSwissprot.java
share/examples/biojava/demos/xff/TestXFFStreaming.java
share/java/classes/biojava.jar
share/java/classes/bytecode.jar
@dirrm share/examples/biojava/demos/xff
@dirrm share/examples/biojava/demos/tagvalue
@dirrm share/examples/biojava/demos/symbol
@dirrm share/examples/biojava/demos/ssbind
@dirrm share/examples/biojava/demos/seqviewer
@dirrm share/examples/biojava/demos/seq/db
@dirrm share/examples/biojava/demos/seq
@dirrm share/examples/biojava/demos/search
@dirrm share/examples/biojava/demos/ragbag
@dirrm share/examples/biojava/demos/prot
@dirrm share/examples/biojava/demos/nativeapps
@dirrm share/examples/biojava/demos/indexing
@dirrm share/examples/biojava/demos/gff
@dirrm share/examples/biojava/demos/game
@dirrm share/examples/biojava/demos/files/wublast
@dirrm share/examples/biojava/demos/files/pdb
@dirrm share/examples/biojava/demos/files/ncbiblast
@dirrm share/examples/biojava/demos/files/hmmer
@dirrm share/examples/biojava/demos/files/clustal
@dirrm share/examples/biojava/demos/files/GCG
@dirrm share/examples/biojava/demos/files
@dirrm share/examples/biojava/demos/eventbasedparsing/stylesheets
@dirrm share/examples/biojava/demos/eventbasedparsing
@dirrm share/examples/biojava/demos/dp
@dirrm share/examples/biojava/demos/dist
@dirrm share/examples/biojava/demos/das
@dirrm share/examples/biojava/demos/biosql
@dirrm share/examples/biojava/demos/CircLocTest
@dirrm share/examples/biojava/demos-obsolete/symbol
@dirrm share/examples/biojava/demos-obsolete/seq
@dirrm share/examples/biojava/demos-obsolete/search
@dirrm share/examples/biojava/demos-obsolete/bioseqdb
@dirrm share/examples/biojava/demos-obsolete
@dirrm share/examples/biojava/demos-1.4/unigene
@dirrm share/examples/biojava/demos-1.4/ssaha
@dirrm share/examples/biojava/demos-1.4
@dirrm share/examples/biojava/demos
@dirrm share/examples/biojava