libbiojava-java-demos_1.7.1-5_all.deb


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Description

libbiojava-java-demos - Example programs for BioJava

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Main amd64
Package name libbiojava-java-demos
Package version 1.7.1
Package release 5
Package architecture all
Package type deb
Installed size 3.71 KB
Download size 2.71 MB
Official Mirror ftp.br.debian.org
The package comes with a wealth of use cases for BioJava. It is generated
together with the API documentation but because of its size of ~3.7MB it
was decided to distribute it separately.

Alternatives

Package Version Architecture Repository
libbiojava-java-demos_1.7.1-5_all.deb 1.7.1 all Debian Main
libbiojava-java-demos - - -

Download

Type URL
Binary Package libbiojava-java-demos_1.7.1-5_all.deb
Source Package biojava-live

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install libbiojava-java-demos deb package:
    # sudo apt-get install libbiojava-java-demos

Files

Path
/usr/share/doc/libbiojava-java-demos/changelog.Debian.gz
/usr/share/doc/libbiojava-java-demos/copyright
/usr/share/doc/libbiojava-java-demos/examples/ListChangeTypes.java
/usr/share/doc/libbiojava-java-demos/examples/RFetch.java
/usr/share/doc/libbiojava-java-demos/examples/CircLocTest/CircularLocationTester.java
/usr/share/doc/libbiojava-java-demos/examples/CircLocTest/TestFrame.java.gz
/usr/share/doc/libbiojava-java-demos/examples/annodb/CreateIndexDB.java
/usr/share/doc/libbiojava-java-demos/examples/biosql/DummyFromGFF.java
/usr/share/doc/libbiojava-java-demos/examples/biosql/LargeSequenceTest.java
/usr/share/doc/libbiojava-java-demos/examples/biosql/SeqDumper.java
/usr/share/doc/libbiojava-java-demos/examples/biosql/SeqEMBL.java
/usr/share/doc/libbiojava-java-demos/examples/biosql/SeqGFF.java
/usr/share/doc/libbiojava-java-demos/examples/biosql/SequenceTest.java.gz
/usr/share/doc/libbiojava-java-demos/examples/biosql/UploadFlat.java
/usr/share/doc/libbiojava-java-demos/examples/blastxml/BlastParser.java
/usr/share/doc/libbiojava-java-demos/examples/blastxml/input.xml.gz
/usr/share/doc/libbiojava-java-demos/examples/das/TestDAS.java
/usr/share/doc/libbiojava-java-demos/examples/das/TestDASG.java
/usr/share/doc/libbiojava-java-demos/examples/das/TestDASH.java
/usr/share/doc/libbiojava-java-demos/examples/das/TestDSN.java
/usr/share/doc/libbiojava-java-demos/examples/dist/TestDistribution.java
/usr/share/doc/libbiojava-java-demos/examples/dist/TestOrderNAlphabet.java
/usr/share/doc/libbiojava-java-demos/examples/dist/TestOrderNDistribution.java.gz
/usr/share/doc/libbiojava-java-demos/examples/dist/Tools.java
/usr/share/doc/libbiojava-java-demos/examples/dp/Dice.java.gz
/usr/share/doc/libbiojava-java-demos/examples/dp/PairwiseAlignment.java.gz
/usr/share/doc/libbiojava-java-demos/examples/dp/PatternFinder.java
/usr/share/doc/libbiojava-java-demos/examples/dp/SearchProfile.java.gz
/usr/share/doc/libbiojava-java-demos/examples/dp/ViterbiAlign.java.gz
/usr/share/doc/libbiojava-java-demos/examples/dp/fake.fasta.gz
/usr/share/doc/libbiojava-java-demos/examples/dp/fakepromoter.xml.gz
/usr/share/doc/libbiojava-java-demos/examples/dp/package.html
/usr/share/doc/libbiojava-java-demos/examples/eventbasedparsing/Blast2HTML.java.gz
/usr/share/doc/libbiojava-java-demos/examples/eventbasedparsing/BlastLike2XML.java.gz
/usr/share/doc/libbiojava-java-demos/examples/eventbasedparsing/Fasta2XML.java
/usr/share/doc/libbiojava-java-demos/examples/eventbasedparsing/Pdb2XML.java
/usr/share/doc/libbiojava-java-demos/examples/eventbasedparsing/TutorialEx1.java
/usr/share/doc/libbiojava-java-demos/examples/eventbasedparsing/TutorialEx1Handler.java
/usr/share/doc/libbiojava-java-demos/examples/eventbasedparsing/stylesheets/copyall.xsl
/usr/share/doc/libbiojava-java-demos/examples/eventbasedparsing/stylesheets/hitlisthtml.xsl
/usr/share/doc/libbiojava-java-demos/examples/files/ACTN_HUMAN.uniprot.gz
/usr/share/doc/libbiojava-java-demos/examples/files/AF438419.embl.gz
/usr/share/doc/libbiojava-java-demos/examples/files/AL121903.embl.gz
/usr/share/doc/libbiojava-java-demos/examples/files/AL121903.genbank.gz
/usr/share/doc/libbiojava-java-demos/examples/files/ChrI.prom.fasta.gz
/usr/share/doc/libbiojava-java-demos/examples/files/NP_001307.gp.gz
/usr/share/doc/libbiojava-java-demos/examples/files/fake.fasta.gz
/usr/share/doc/libbiojava-java-demos/examples/files/fakepromoter.xml.gz
/usr/share/doc/libbiojava-java-demos/examples/files/fp_demo.db.gz
/usr/share/doc/libbiojava-java-demos/examples/files/fp_demo.m10.gz
/usr/share/doc/libbiojava-java-demos/examples/files/fp_queries.db
/usr/share/doc/libbiojava-java-demos/examples/files/out.gff.gz
/usr/share/doc/libbiojava-java-demos/examples/files/scoptest.fa
/usr/share/doc/libbiojava-java-demos/examples/files/test.hmm.gz
/usr/share/doc/libbiojava-java-demos/examples/files/varC4-2.dna.gz
/usr/share/doc/libbiojava-java-demos/examples/files/varC4-2.gff.gz
/usr/share/doc/libbiojava-java-demos/examples/files/GCG/blast.report.gz
/usr/share/doc/libbiojava-java-demos/examples/files/clustal/keratin.aln.gz
/usr/share/doc/libbiojava-java-demos/examples/files/hmmer/plus_tot.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/Massive.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/ReadMe
/usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/blastn.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/blastp.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/blastx.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/shortBlastn.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/tblastn.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/tblastx.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/unsuppVersionBlastn.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/ontology/biosapiens.obo.gz
/usr/share/doc/libbiojava-java-demos/examples/files/ontology/evidence_code.obo.gz
/usr/share/doc/libbiojava-java-demos/examples/files/ontology/so.obo.gz
/usr/share/doc/libbiojava-java-demos/examples/files/pdb/12E8.pdb.gz
/usr/share/doc/libbiojava-java-demos/examples/files/pdb/hgh_ori.pdb.gz
/usr/share/doc/libbiojava-java-demos/examples/files/pdb/hmga_1.pdb.gz
/usr/share/doc/libbiojava-java-demos/examples/files/pdb/tnf.pdb.gz
/usr/share/doc/libbiojava-java-demos/examples/files/wublast/blastn.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/wublast/blastp.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/wublast/blastx.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/wublast/sh_blastn.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/wublast/sh_blastp.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/wublast/sh_blastx.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/wublast/sh_tblastx.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/wublast/tblastn.out.gz
/usr/share/doc/libbiojava-java-demos/examples/files/wublast/tblastx.out.gz
/usr/share/doc/libbiojava-java-demos/examples/game/AE002734.game.gz
/usr/share/doc/libbiojava-java-demos/examples/game/README.txt
/usr/share/doc/libbiojava-java-demos/examples/game/SeqIOTatler.java
/usr/share/doc/libbiojava-java-demos/examples/game/TestGAME.java
/usr/share/doc/libbiojava-java-demos/examples/gff/AL121903.embl.gz
/usr/share/doc/libbiojava-java-demos/examples/gff/EmblToGffFasta.java
/usr/share/doc/libbiojava-java-demos/examples/gff/GFFCompare.java.gz
/usr/share/doc/libbiojava-java-demos/examples/gff/GFFFilter.java.gz
/usr/share/doc/libbiojava-java-demos/examples/gff/GFFMask.java.gz
/usr/share/doc/libbiojava-java-demos/examples/gff/GFFToFeatures.java
/usr/share/doc/libbiojava-java-demos/examples/gff/GenbankToGffFasta.java
/usr/share/doc/libbiojava-java-demos/examples/gff/SwissprotToGffFasta.java
/usr/share/doc/libbiojava-java-demos/examples/gff/XFF2GFF.java
/usr/share/doc/libbiojava-java-demos/examples/gff/varC4-2.gff.gz
/usr/share/doc/libbiojava-java-demos/examples/indexing/CreateFAIndex.java
/usr/share/doc/libbiojava-java-demos/examples/indexing/CreateIndex.java
/usr/share/doc/libbiojava-java-demos/examples/indexing/CreateSPIndex.java
/usr/share/doc/libbiojava-java-demos/examples/indexing/ListIDs.java
/usr/share/doc/libbiojava-java-demos/examples/indexing/ReadRaw.java
/usr/share/doc/libbiojava-java-demos/examples/indexing/ReadRawSecondary.java
/usr/share/doc/libbiojava-java-demos/examples/nativeapps/BlastLike2XML.java.gz
/usr/share/doc/libbiojava-java-demos/examples/nativeapps/Pdb2XML.java
/usr/share/doc/libbiojava-java-demos/examples/ontology/obo/ParseBioSapiensOntology.java
/usr/share/doc/libbiojava-java-demos/examples/performance/AlignProteins.java.gz
/usr/share/doc/libbiojava-java-demos/examples/performance/ReadFasta.java
/usr/share/doc/libbiojava-java-demos/examples/performance/ReadFastaX.java
/usr/share/doc/libbiojava-java-demos/examples/performance/ReadFastaX2.java
/usr/share/doc/libbiojava-java-demos/examples/performance/ReverseComplement.java.gz
/usr/share/doc/libbiojava-java-demos/examples/performance/SmithWatermanExample.java.gz
/usr/share/doc/libbiojava-java-demos/examples/performance/UserDisplay.java
/usr/share/doc/libbiojava-java-demos/examples/performance/package.html
/usr/share/doc/libbiojava-java-demos/examples/process/ProcessToolsTest.java
/usr/share/doc/libbiojava-java-demos/examples/prot/TestDigestIO.java.gz
/usr/share/doc/libbiojava-java-demos/examples/search/IndexFastaDB.java
/usr/share/doc/libbiojava-java-demos/examples/seq/AL121903.embl.gz
/usr/share/doc/libbiojava-java-demos/examples/seq/AL121903.genbank.gz
/usr/share/doc/libbiojava-java-demos/examples/seq/FetchSeq.java
/usr/share/doc/libbiojava-java-demos/examples/seq/GCContent.java
/usr/share/doc/libbiojava-java-demos/examples/seq/MotifFinder2.java
/usr/share/doc/libbiojava-java-demos/examples/seq/ReverseComplement.java
/usr/share/doc/libbiojava-java-demos/examples/seq/SimpleAssemblyTest.java
/usr/share/doc/libbiojava-java-demos/examples/seq/TestEmbl.java
/usr/share/doc/libbiojava-java-demos/examples/seq/TestEmbl2.java
/usr/share/doc/libbiojava-java-demos/examples/seq/TestGenbank.java
/usr/share/doc/libbiojava-java-demos/examples/seq/TestRefSeqPrt.java
/usr/share/doc/libbiojava-java-demos/examples/seq/TestSubSequence.java
/usr/share/doc/libbiojava-java-demos/examples/seq/TestSwissprot.java
/usr/share/doc/libbiojava-java-demos/examples/seq/TestTranslation.java
/usr/share/doc/libbiojava-java-demos/examples/seq/UniProtDemo.java
/usr/share/doc/libbiojava-java-demos/examples/seq/utrs.fa
/usr/share/doc/libbiojava-java-demos/examples/seq/db/AddFilesToIndex.java
/usr/share/doc/libbiojava-java-demos/examples/seq/db/CreateIndex.java
/usr/share/doc/libbiojava-java-demos/examples/seq/db/FetchSequence.java
/usr/share/doc/libbiojava-java-demos/examples/seq/db/ListSeqsInIndex.java
/usr/share/doc/libbiojava-java-demos/examples/seqviewer/BeadDemo.java.gz
/usr/share/doc/libbiojava-java-demos/examples/seqviewer/CircularEmblViewer.java.gz
/usr/share/doc/libbiojava-java-demos/examples/seqviewer/EmblViewer.java.gz
/usr/share/doc/libbiojava-java-demos/examples/seqviewer/EmblViewer2.java.gz
/usr/share/doc/libbiojava-java-demos/examples/seqviewer/FastBeadDemo.java.gz
/usr/share/doc/libbiojava-java-demos/examples/seqviewer/GappedViewer.java
/usr/share/doc/libbiojava-java-demos/examples/seqviewer/TraceViewer.java
/usr/share/doc/libbiojava-java-demos/examples/seqviewer/test.fa
/usr/share/doc/libbiojava-java-demos/examples/ssaha/CreateDNAFastaHashTable.java
/usr/share/doc/libbiojava-java-demos/examples/ssaha/CreateDNAFastaHashTableCompact.java
/usr/share/doc/libbiojava-java-demos/examples/ssaha/CreateDNAFastaHashTableLarge.java
/usr/share/doc/libbiojava-java-demos/examples/ssaha/CreateEmblHashTable.java
/usr/share/doc/libbiojava-java-demos/examples/ssaha/CreateEmblHashTableLarge.java
/usr/share/doc/libbiojava-java-demos/examples/ssaha/ResultPrinter.java
/usr/share/doc/libbiojava-java-demos/examples/ssaha/SSAHA.java
/usr/share/doc/libbiojava-java-demos/examples/ssaha/SSAHALarge.java
/usr/share/doc/libbiojava-java-demos/examples/ssaha/SSAHASeq.java
/usr/share/doc/libbiojava-java-demos/examples/ssaha/SSAHASeqLarge.java
/usr/share/doc/libbiojava-java-demos/examples/ssbind/AlignmentBuilder.java
/usr/share/doc/libbiojava-java-demos/examples/ssbind/CountHits.java
/usr/share/doc/libbiojava-java-demos/examples/ssbind/CountSubHits.java
/usr/share/doc/libbiojava-java-demos/examples/ssbind/Echoer.java
/usr/share/doc/libbiojava-java-demos/examples/ssbind/FilterByValue.java
/usr/share/doc/libbiojava-java-demos/examples/ssbind/ListQueries.java
/usr/share/doc/libbiojava-java-demos/examples/ssbind/ListSubjects.java
/usr/share/doc/libbiojava-java-demos/examples/ssbind/ProcessBlastReport.java.gz
/usr/share/doc/libbiojava-java-demos/examples/ssbind/PropertyEchoer.java
/usr/share/doc/libbiojava-java-demos/examples/ssbind/SubHitBuilder.java
/usr/share/doc/libbiojava-java-demos/examples/ssbind/SubHitFilter.java
/usr/share/doc/libbiojava-java-demos/examples/structure/LoadStructure.java
/usr/share/doc/libbiojava-java-demos/examples/structure/PDBView.java
/usr/share/doc/libbiojava-java-demos/examples/structure/PhiPsiCalculation.java
/usr/share/doc/libbiojava-java-demos/examples/structure/SuperimposeStructures.java
/usr/share/doc/libbiojava-java-demos/examples/symbol/MatrixValue.java
/usr/share/doc/libbiojava-java-demos/examples/symbol/PatternDemo.java.gz
/usr/share/doc/libbiojava-java-demos/examples/symbol/TestAlphabetIndexers.java
/usr/share/doc/libbiojava-java-demos/examples/symbol/TestAmbiguity.java.gz
/usr/share/doc/libbiojava-java-demos/examples/symbol/TestGappedSymbolList.java
/usr/share/doc/libbiojava-java-demos/examples/symbol/TestIndexedIntegers.java
/usr/share/doc/libbiojava-java-demos/examples/symbol/TestLocation.java
/usr/share/doc/libbiojava-java-demos/examples/symbol/TestOrderNSymbolList.java
/usr/share/doc/libbiojava-java-demos/examples/symbol/TestSimpleAlignment.java
/usr/share/doc/libbiojava-java-demos/examples/symbol/TestWindowedSymbolList.java
/usr/share/doc/libbiojava-java-demos/examples/symbol/Tools.java
/usr/share/doc/libbiojava-java-demos/examples/symbol/WindowCount.java.gz
/usr/share/doc/libbiojava-java-demos/examples/tagvalue/Grep.java
/usr/share/doc/libbiojava-java-demos/examples/tagvalue/Index.java
/usr/share/doc/libbiojava-java-demos/examples/tagvalue/Parse.java
/usr/share/doc/libbiojava-java-demos/examples/tagvalue/ParseEmbl.java
/usr/share/doc/libbiojava-java-demos/examples/tagvalue/ParseSwissprot.java
/usr/share/doc/libbiojava-java-demos/examples/tagvalue/PrintFormat.java
/usr/share/doc/libbiojava-java-demos/examples/unigene/CreateUnigeneFlat.java
/usr/share/doc/libbiojava-java-demos/examples/unigene/ParseLibInfo.java
/usr/share/doc/libbiojava-java-demos/examples/unigene/ParseUnigene.java
/usr/share/doc/libbiojava-java-demos/examples/unigene/SearchUnigeneFlat.java
/usr/share/doc/libbiojava-java-demos/examples/xff/TestXFFStreaming.java

Changelog

2014-05-20 - Olivier Sallou <osallou@debian.org>
biojava-live (1:1.7.1-5) unstable; urgency=medium
* d/control: use libcommons-collections3 instead of 
libcommons-collection in runtime deps (Closes: #748473).
2014-01-31 - Olivier Sallou <osallou@debian.org>
biojava-live (1:1.7.1-4) unstable; urgency=low
[ Andreas Tille ]
* debian/upstream:
- Author conform to BibTeX syntax
- Add eprint
[ Olivier Sallou ]
* Fix watch file to follow biojava v1, not v3
2013-09-10 - Olivier Sallou <osallou@debian.org>
biojava-live (1:1.7.1-3) unstable; urgency=low
* Use libcommons-collections3-java instead of libcommons-collections-java 
2012-04-18 - Andreas Tille <tille@debian.org>
biojava-live (1:1.7.1-2) unstable; urgency=low
[ Jari Aalto ]
* Remove quilt and upgrade to packaging format "3.0 quilt" which
includes patch management built-in.
* Update buildxml.patch to DEP-3 and run "quilt refresh" to make it
apply cleanly.
* Update to Standards-Version to 3.9.3 (no changes needed) and debhelper 9.
* Update obsolete depends default-jdk-builddep to default-jdk.
Closes: #669122
* Fix wrong-section-according-to-package-name (Lintian) by changing
section from science to java.
* Fix needless-dependency-on-jre (Lintian) by removing jre dependencies.
* Fix duplicate-short-description (Lintian).
* Fix extended-description-is-probably-too-short (Lintian).
[ Andreas Tille ]
* debian/control:
- Short-Desc: Java 1.7 API is missleading regarding JDK version - rather
add the version at the end and declare the version-less metapackage as
default version
- Dropped default-jre-headless from Depends according to Java policy
- Fixed Vcs fields
* debian/watch: enable detecting new versions
* debian/{control,upstream}: Moved citations from long description to
upstream file
* libbiojava*.lintian: removed because now useless
* debian/compat: 9
* debian/copyright: Rewritten to be compliant with DEP5 and verified
using `cme fix dpkg-copyright`
* debian/rules: s/dh_clean -k/dh_prep/
2010-01-20 - Steffen Moeller <moeller@debian.org>
biojava-live (1:1.7.1-1) unstable; urgency=low
* New upstream version.
* New epoch
- because of an unfortunate versioning of previous upload
- to indicate the now happening BioJava Hackathon in Cambridge, UK
2009-06-26 - Andreas Tille <tille@debian.org>
biojava-live (1.7.svn.20090419-3) unstable; urgency=low
* debian/control:
- Conflicts: libbiojava1.6-java
- Replaces: libbiojava1.6-java
- Enhanced long description of libbiojava-java-doc
Closes: #522269
* debian/rules: set JAVA_HOME to enable proper clean target
2009-06-22 - Andreas Tille <tille@debian.org>
biojava-live (1.7.svn.20090419-2) unstable; urgency=low
* Add Build Depends: ant-optional
Closes: #533896
* Standards-Version: 3.8.2 (no changes needed)
2009-04-19 - Steffen Moeller <moeller@debian.org>
biojava-live (1.7.svn.20090419-1) unstable; urgency=low
* New upstream version, addressing structures.
* Removed dependency on libjgrapht, so biojava can go to main.
* Conformance to 3.8.1 (no changes required).
2009-03-09 - Andreas Tille <tille@debian.org>
biojava-live (1.6.1.svn.20090306-1) experimental; urgency=low
[ Andreas Tille ]
* Initial release (Closes:#491025).
[ Steffen Moeller ]
* Added dependency to quilt.
* Moved -doc to section doc.
* Added symlinks to jar file with pseudo-soname
* Need to be placed in contrib section as a start because of dependency
to libjgrapht that is still in contrib.
2008-07-13 - Steffen Moeller <moeller@debian.org>
biojava-live (1.6.0.svn.20080716-1) UNRELEASED; urgency=low
* Renamed to biojava-live in analogy to upstream's name
and to keep the opportunity to add a biojava meta package
later on.
* License issue fixed that led to previous rejection of biojava.

See Also

Package Description
libbiojava-java-doc_1.7.1-5_all.deb [Biology] Documentation for BioJava
libbiojava-java_1.7.1-5_all.deb Java API to biological data and applications (default version)
libbiojava1.7-java_1.7.1-5_all.deb Java API to biological data and applications (version 1.7)
libbiojava3-java-doc_3.1.0+dfsg-2_all.deb [Biology] Documentation for BioJava
libbiojava3-java_3.1.0+dfsg-2_all.deb Java API to biological data and applications (default version)
libbiojava3.0-java_3.1.0+dfsg-2_all.deb Java API to biological data and applications (version 3)
libbiosig-dev_1.3.0-2+b2_amd64.deb I/O library for biomedical data - development files
libbiosig1_1.3.0-2+b2_amd64.deb I/O library for biomedical data - dynamic library
libbisho-common-dev_0.27.2+git20111122.9e68ef3d-2_amd64.deb Meego web services settings library (development files)
libbisho-common0_0.27.2+git20111122.9e68ef3d-2_amd64.deb Meego web services settings library
libbison-dev_3.0.2.dfsg-2_amd64.deb YACC-compatible parser generator - development library
libbit-vector-minimal-perl_1.3-4_all.deb object-oriented wrapper around vec()
libbit-vector-perl_7.3-1+b2_amd64.deb Perl module for bit vectors and more
libbitcoin-dev_2.0-2.2_amd64.deb Bitcoin toolkit library for asynchronous apps - development headers
libbitcoin0_2.0-2.2_amd64.deb Bitcoin toolkit library for asynchronous apps
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