[med-svn] [artemis] 01/06: Merge tag 'upstream/16.0.17+dfsg'

[Sascha Steinbiss]

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satta pushed a commit to branch 6_0_17_fix
in repository artemis.

commit c586803f0fc9998acedcfd176f92a6a8ade6d1d8
Merge: 2a39317 30a81b9
Author: Sascha Steinbiss <satta at debian.org>
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(-)

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