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%%PORTDOCS%%%%DOCSDIR%%/LICENSE
%%PORTDOCS%%%%DOCSDIR%%/README
%%INSTEX%%%%EXAMPLESDIR%%/demos/CircLocTest/CircularLocationTester.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/CircLocTest/TestFrame.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ListChangeTypes.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/RFetch.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/annodb/CreateIndexDB.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/DummyFromGFF.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/LargeSequenceTest.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/SeqDumper.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/SeqEMBL.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/SeqGFF.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/SequenceTest.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/UploadFlat.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/blastxml/BlastParser.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/blastxml/input.xml
%%INSTEX%%%%EXAMPLESDIR%%/demos/das/TestDAS.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/das/TestDASG.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/das/TestDASH.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/das/TestDSN.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/dist/TestDistribution.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/dist/TestOrderNAlphabet.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/dist/TestOrderNDistribution.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/dist/Tools.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/Dice.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/PairwiseAlignment.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/PatternFinder.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/SearchProfile.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/ViterbiAlign.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/fake.fasta
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/fakepromoter.xml
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/package.html
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/Blast2HTML.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/BlastLike2XML.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/Fasta2XML.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/Pdb2XML.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/TutorialEx1.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/TutorialEx1Handler.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/stylesheets/copyall.xsl
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/stylesheets/hitlisthtml.xsl
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ACTN_HUMAN.uniprot
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/AF438419.embl
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/AL121903.embl
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/AL121903.genbank
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ChrI.prom.fasta
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/GCG/blast.report
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/NP_001307.gp
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/clustal/keratin.aln
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fake.fasta
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fakepromoter.xml
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fp_demo.db
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fp_demo.m10
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fp_queries.db
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/hmmer/plus_tot.out
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/Massive.out
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/ReadMe
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/blastn.out
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/blastp.out
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%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/tblastx.out
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/unsuppVersionBlastn.out
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/out.gff
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/pdb/12E8.pdb
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/pdb/hgh_ori.pdb
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/pdb/hmga_1.pdb
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/pdb/tnf.pdb
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/scoptest.fa
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/test.hmm
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/varC4-2.dna
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/varC4-2.gff
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/blastn.out
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/blastp.out
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/blastx.out
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/sh_blastn.out
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%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/sh_blastx.out
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/sh_tblastx.out
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/tblastn.out
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/tblastx.out
%%INSTEX%%%%EXAMPLESDIR%%/demos/game/AE002734.game
%%INSTEX%%%%EXAMPLESDIR%%/demos/game/README.txt
%%INSTEX%%%%EXAMPLESDIR%%/demos/game/SeqIOTatler.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/game/TestGAME.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/AL121903.embl
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/EmblToGffFasta.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GFFCompare.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GFFFilter.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GFFMask.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GFFToFeatures.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GenbankToGffFasta.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/SwissprotToGffFasta.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/XFF2GFF.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/varC4-2.gff
%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/CreateFAIndex.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/CreateIndex.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/CreateSPIndex.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/ListIDs.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/ReadRaw.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/ReadRawSecondary.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/nativeapps/BlastLike2XML.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/nativeapps/Pdb2XML.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/process/ProcessToolsTest.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/prot/TestDigestIO.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/search/IndexFastaDB.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/AL121903.embl
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/AL121903.genbank
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/FetchSeq.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/GCContent.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/MotifFinder2.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/ReverseComplement.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/SimpleAssemblyTest.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestEmbl.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestEmbl2.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestGenbank.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestRefSeqPrt.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestSubSequence.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestSwissprot.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestTranslation.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/UniProtDemo.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/db/AddFilesToIndex.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/db/CreateIndex.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/db/FetchSequence.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/db/ListSeqsInIndex.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/utrs.fa
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/BeadDemo.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/CircularEmblViewer.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/EmblViewer.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/EmblViewer2.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/FastBeadDemo.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/GappedViewer.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/TraceViewer.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/test.fa
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateDNAFastaHashTable.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateDNAFastaHashTableCompact.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateDNAFastaHashTableLarge.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateEmblHashTable.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateEmblHashTableLarge.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/ResultPrinter.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/SSAHA.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/SSAHALarge.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/SSAHASeq.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/SSAHASeqLarge.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/AlignmentBuilder.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/CountHits.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/CountSubHits.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/Echoer.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/FilterByValue.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/ListQueries.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/ListSubjects.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/ProcessBlastReport.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/PropertyEchoer.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/SubHitBuilder.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/SubHitFilter.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/MatrixValue.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/PatternDemo.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestAlphabetIndexers.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestAmbiguity.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestGappedSymbolList.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestIndexedIntegers.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestLocation.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestOrderNSymbolList.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestSimpleAlignment.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestWindowedSymbolList.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/Tools.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/WindowCount.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/Grep.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/Index.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/Parse.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/ParseEmbl.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/ParseSwissprot.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/PrintFormat.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/unigene/CreateUnigeneFlat.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/unigene/ParseLibInfo.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/unigene/ParseUnigene.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/unigene/SearchUnigeneFlat.java
%%INSTEX%%%%EXAMPLESDIR%%/demos/xff/TestXFFStreaming.java
%%JAVAJARDIR%%/apps-%%VER%%.jar
%%JAVAJARDIR%%/biojava.jar
%%JAVAJARDIR%%/bytecode.jar
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/xff
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/unigene
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/tagvalue
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/symbol
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/ssbind
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/ssaha
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/seqviewer
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/seq/db
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/seq
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/search
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/prot
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/process
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/nativeapps
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/indexing
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/gff
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/game
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/wublast
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/pdb
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/ncbiblast
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/hmmer
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/clustal
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/GCG
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/eventbasedparsing/stylesheets
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/eventbasedparsing
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/dp
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/dist
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/das
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/blastxml
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/biosql
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/annodb
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/CircLocTest
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos
%%INSTEX%%@dirrm %%EXAMPLESDIR%%
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