This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch 6_0_17_fix in repository artemis.
commit c586803f0fc9998acedcfd176f92a6a8ade6d1d8 Merge: 2a39317 30a81b9 Author: Sascha Steinbiss <[email protected]> Date: Mon Dec 5 09:11:27 2016 +0000 Merge tag 'upstream/16.0.17+dfsg' Upstream version 16.0.17+dfsg .classpath | 2 + .travis.yml | 26 + AUTHORS | 3 + ChangeLog | 2 +- INSTALL | 48 +- LICENSE | 680 ++++++++++ Makefile | 213 +-- README => README.md | 12 +- act | 2 + art | 3 + docs/act_manual.sgml | 2 +- docs/act_start_chapter.sgml | 2 +- docs/feature_edit.gif | Bin 30763 -> 34452 bytes docs/jvm_options.sgml | 23 + docs/main_window_chapter.sgml | 1 + docs/manual.sgml | 3 +- docs/menus.sgml | 56 +- docs/qualifier_list.gif | Bin 0 -> 12357 bytes docs/qualifier_list2.gif | Bin 0 -> 15166 bytes docs/start_chapter.sgml | 2 +- docs/tick.png | Bin 0 -> 394 bytes docs/unix_args.sgml | 8 - docs/validation_report.png | Bin 0 -> 55887 bytes docs/validator.sgml | 181 +++ etc/feature_keys_gff | 6 +- etc/key_mapping | 7 +- etc/options | 14 +- etc/project.properties | 6 +- etc/qualifier_types | 4 +- etc/results_to_netscape | 15 +- etc/versions | 6 +- etc/writedb_entry | 9 +- gff2embl | 106 ++ install_dependencies.sh | 57 + test/data/MAL_8h.bam | Bin 0 -> 97476 bytes test/data/MAL_8h.bam.bai | Bin 0 -> 264 bytes .../components/alignment/MappedReadsTest.java | 143 ++ .../artemis/io/GFF3AttributeBuilderTest.java | 295 ++++ test/uk/ac/sanger/artemis/io/GFF3EncoderTest.java | 102 ++ uk/ac/sanger/artemis/AlignMatchVector.java | 16 +- uk/ac/sanger/artemis/FeatureVector.java | 2 +- uk/ac/sanger/artemis/chado/ArtemisUtils.java | 3 +- .../artemis/chado/ChadoTransactionManager.java | 14 +- uk/ac/sanger/artemis/components/EditMenu.java | 17 + uk/ac/sanger/artemis/components/EntryEdit.java | 2 +- uk/ac/sanger/artemis/components/FeatureEdit.java | 21 +- .../sanger/artemis/components/RunBlastAtNCBI.java | 4 +- .../artemis/components/RunPfamSearchThread.java | 4 +- uk/ac/sanger/artemis/components/SelectMenu.java | 68 +- uk/ac/sanger/artemis/components/Splash.java | 2 +- .../components/alignment/AbstractGraphPanel.java | 11 +- .../artemis/components/alignment/BamUtils.java | 208 ++- .../artemis/components/alignment/BamView.java | 68 +- .../alignment/CRAMReferenceSequenceFile.java | 7 +- .../components/alignment/CoveragePanel.java | 86 +- .../artemis/components/alignment/MappedReads.java | 359 ++--- .../artemis/components/alignment/ReadCount.java | 40 + .../components/alignment/ReadCountDialog.java | 7 +- .../components/genebuilder/GeneEditorPanel.java | 44 +- .../artemis/components/genebuilder/GeneUtils.java | 5 +- .../genebuilder/gff/PropertiesPanel.java | 24 +- uk/ac/sanger/artemis/io/DocumentEntryFactory.java | 15 +- .../sanger/artemis/io/GFF3AttributeAggregator.java | 38 + uk/ac/sanger/artemis/io/GFF3AttributeBuilder.java | 214 +++ uk/ac/sanger/artemis/io/GFF3Encoder.java | 38 + uk/ac/sanger/artemis/io/GFFStreamFeature.java | 1411 +++++++++----------- .../sanger/artemis/io/GenbankTblOutputStream.java | 96 +- uk/ac/sanger/artemis/io/GffToEMBL.java | 2 +- uk/ac/sanger/artemis/io/KeyVector.java | 26 +- uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java | 24 +- .../sanger/artemis/io/SimpleEntryInformation.java | 8 +- uk/ac/sanger/artemis/io/StreamQualifier.java | 16 +- uk/ac/sanger/artemis/plot/Algorithm.java | 2 +- uk/ac/sanger/artemis/plot/UserDataAlgorithm.java | 34 +- uk/ac/sanger/artemis/util/DatabaseDocument.java | 91 +- uk/ac/sanger/artemis/util/FastVector.java | 26 +- uk/ac/sanger/artemis/util/StringVector.java | 34 +- 77 files changed, 3545 insertions(+), 1581 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/artemis.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
