[med-svn] [artemis] branch upstream updated (e4831b5 -> 30a81b9)

[Sascha Steinbiss]

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satta pushed a change to branch upstream
in repository artemis.

      from  e4831b5   Imported Upstream version 16.0.0+dfsg
       new  30a81b9   New upstream version 16.0.17+dfsg

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 +
 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 +-
 77 files changed, 3406 insertions(+), 1645 deletions(-)
 create mode 100644 .travis.yml
 create mode 100644 AUTHORS
 create mode 100644 LICENSE
 rename README => README.md (90%)
 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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