[med-svn] [artemis] branch master updated (2a39317 -> 5636cf8)
Andreas Tille
tille at debian.org
Thu Dec 8 08:22:10 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository artemis.
from 2a39317 artemis (16.0.0+dfsg-5) unstable; urgency=medium
adds 30a81b9 New upstream version 16.0.17+dfsg
adds c586803 Merge tag 'upstream/16.0.17+dfsg'
adds 7a7192c bump Changelog
adds ecf67fe use lang3
adds 02ace2c README is not Markdown
adds a1a0b2c refresh patches
adds 9738c5d update d/changelog
new 5636cf8 Cleanup patches and add DEP3 headers
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.classpath | 2 +
.travis.yml | 26 +
AUTHORS | 3 +
ChangeLog | 2 +-
INSTALL | 48 +-
LICENSE | 680 ++++
Makefile | 213 +-
README => README.md | 12 +-
act | 2 +
art | 3 +
debian/changelog | 13 +
debian/control | 1 +
debian/docs | 2 +-
debian/patches/CRAMReferenceSequenceFile.patch | 21 -
debian/patches/class-path.patch | 14 +-
debian/patches/htsjdk-api-change.patch | 3 +
debian/patches/jar-rules.patch | 20 +-
debian/patches/java-8-sort.patch | 57 -
debian/patches/picard-api-change.patch | 27 +-
debian/patches/samreader.patch | 3601 ++++++++++++++++++++
debian/patches/series | 4 +-
debian/patches/test-classpath.patch | 4 +-
debian/patches/use-lang3.patch | 15 +
debian/rules | 1 +
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 +-
dnaplotter => gff2embl | 35 +-
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 +-
.../alignment/ReadCount.java} | 38 +-
.../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 +-
...reamEvent.java => GFF3AttributeAggregator.java} | 38 +-
uk/ac/sanger/artemis/io/GFF3AttributeBuilder.java | 214 ++
.../io/{EntryStreamEvent.java => GFF3Encoder.java} | 36 +-
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 +-
91 files changed, 7070 insertions(+), 1764 deletions(-)
create mode 100644 .travis.yml
create mode 100644 AUTHORS
create mode 100644 LICENSE
rename README => README.md (90%)
delete mode 100644 debian/patches/CRAMReferenceSequenceFile.patch
delete mode 100644 debian/patches/java-8-sort.patch
create mode 100644 debian/patches/samreader.patch
create mode 100644 debian/patches/use-lang3.patch
create mode 100644 docs/qualifier_list.gif
create mode 100644 docs/qualifier_list2.gif
create mode 100644 docs/tick.png
create mode 100644 docs/validation_report.png
create mode 100644 docs/validator.sgml
copy dnaplotter => gff2embl (70%)
create mode 100644 install_dependencies.sh
create mode 100644 test/data/MAL_8h.bam
create mode 100644 test/data/MAL_8h.bam.bai
create mode 100644 test/uk/ac/sanger/artemis/components/alignment/MappedReadsTest.java
create mode 100644 test/uk/ac/sanger/artemis/io/GFF3AttributeBuilderTest.java
create mode 100644 test/uk/ac/sanger/artemis/io/GFF3EncoderTest.java
copy uk/ac/sanger/artemis/{circular/BlockComparator.java => components/alignment/ReadCount.java} (64%)
copy uk/ac/sanger/artemis/io/{EntryStreamEvent.java => GFF3AttributeAggregator.java} (61%)
create mode 100644 uk/ac/sanger/artemis/io/GFF3AttributeBuilder.java
copy uk/ac/sanger/artemis/io/{EntryStreamEvent.java => GFF3Encoder.java} (58%)
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