[med-svn] [brig] 02/03: Merge tag 'upstream/0.95+dfsg'
Andreas Tille
tille at debian.org
Sun Nov 29 10:33:14 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository brig.
commit d45bbb4fedb7bef62ef822e85580a4272debd9ff
Merge: 6dd11e0 50c473a
Author: Andreas Tille <tille at debian.org>
Date: Sun Nov 29 11:27:06 2015 +0100
Merge tag 'upstream/0.95+dfsg'
Upstream version 0.95+dfsg
HELP | 69 +
README.txt | 112 +-
README_devel.txt | 35 +
TUV_500.fasta | 1 +
build-before-profiler.xml | 75 +
build.xml | 76 +
cgview/README | 155 -
cgview/ca/ualberta/stothard/cgview/Cgview.class | Bin 41377 -> 0 bytes
.../ualberta/stothard/cgview/CgviewConstants.class | Bin 1621 -> 0 bytes
.../ualberta/stothard/cgview/CgviewFactory$1.class | Bin 1334 -> 0 bytes
.../ualberta/stothard/cgview/CgviewFactory$2.class | Bin 1336 -> 0 bytes
.../ualberta/stothard/cgview/CgviewFactory$3.class | Bin 1334 -> 0 bytes
.../ualberta/stothard/cgview/CgviewFactory$4.class | Bin 1336 -> 0 bytes
.../cgview/CgviewFactory$ElementDetails.class | Bin 720 -> 0 bytes
.../ualberta/stothard/cgview/CgviewFactory.class | Bin 57036 -> 0 bytes
.../stothard/cgview/CgviewFactoryPtt.class | Bin 26400 -> 0 bytes
.../stothard/cgview/CgviewFactoryTab.class | Bin 24352 -> 0 bytes
.../stothard/cgview/CgviewHTMLDocument.class | Bin 9064 -> 0 bytes
cgview/ca/ualberta/stothard/cgview/CgviewIO.class | Bin 33567 -> 0 bytes
.../cgview/Feature$SortFeatureRangesByStart.class | Bin 798 -> 0 bytes
cgview/ca/ualberta/stothard/cgview/Feature.class | Bin 4588 -> 0 bytes
.../ca/ualberta/stothard/cgview/FeatureRange.class | Bin 14055 -> 0 bytes
.../cgview/FeatureSlot$SortFeaturesByStart.class | Bin 803 -> 0 bytes
.../ca/ualberta/stothard/cgview/FeatureSlot.class | Bin 3778 -> 0 bytes
cgview/ca/ualberta/stothard/cgview/FileMover.class | Bin 2242 -> 0 bytes
.../ca/ualberta/stothard/cgview/InnerLabel.class | Bin 6892 -> 0 bytes
cgview/ca/ualberta/stothard/cgview/Label.class | Bin 6459 -> 0 bytes
.../ca/ualberta/stothard/cgview/LabelBounds.class | Bin 1756 -> 0 bytes
cgview/ca/ualberta/stothard/cgview/Legend.class | Bin 5861 -> 0 bytes
.../ca/ualberta/stothard/cgview/LegendItem.class | Bin 4020 -> 0 bytes
.../ca/ualberta/stothard/cgview/OuterLabel.class | Bin 7016 -> 0 bytes
cgview/ca/ualberta/stothard/cgview/Plasmid.class | Bin 22469 -> 0 bytes
.../ca/ualberta/stothard/cgview/SeriesImage.class | Bin 2362 -> 0 bytes
.../stothard/cgview/SortLabelsByForceLabel.class | Bin 582 -> 0 bytes
.../stothard/cgview/SortLabelsByRadians.class | Bin 589 -> 0 bytes
.../stothard/cgview/SortLabelsByRadiansShift.class | Bin 706 -> 0 bytes
.../stothard/cgview/SortLabelsByRadius.class | Bin 844 -> 0 bytes
.../cgview/SortSeriesImageByZoomCenter.class | Bin 603 -> 0 bytes
cgview/cgview_xml_builder/README | 284 --
cgview/cgview_xml_builder/cgview_xml_builder.pl | 3757 --------------------
cgview/cgview_xml_builder/test.sh | 40 -
cgview/includes/as_png.png | Bin 2825 -> 0 bytes
cgview/includes/as_svg.png | Bin 2859 -> 0 bytes
cgview/includes/expand_in.png | Bin 2733 -> 0 bytes
cgview/includes/expand_in_g.png | Bin 1329 -> 0 bytes
cgview/includes/expand_out.png | Bin 2588 -> 0 bytes
cgview/includes/expand_out_g.png | Bin 1271 -> 0 bytes
cgview/includes/full.png | Bin 2565 -> 0 bytes
cgview/includes/full_g.png | Bin 1283 -> 0 bytes
cgview/includes/help.html | 153 -
cgview/includes/help.png | Bin 875 -> 0 bytes
cgview/includes/help_png.html | 135 -
cgview/includes/info.js | 73 -
cgview/includes/move_back.png | Bin 2375 -> 0 bytes
cgview/includes/move_back_g.png | Bin 1207 -> 0 bytes
cgview/includes/move_forward.png | Bin 2546 -> 0 bytes
cgview/includes/move_forward_g.png | Bin 1256 -> 0 bytes
cgview/includes/overlib.js | 1491 --------
cgview/includes/stylesheet.css | 19 -
cgview/manifestinfo | 6 -
.../src/ca/ualberta/stothard/cgview/Cgview.class | Bin 41371 -> 0 bytes
cgview/src/ca/ualberta/stothard/cgview/Cgview.java | 3693 -------------------
.../ualberta/stothard/cgview/CgviewConstants.class | Bin 1621 -> 0 bytes
.../ualberta/stothard/cgview/CgviewConstants.java | 208 --
.../ualberta/stothard/cgview/CgviewFactory$1.class | Bin 1334 -> 0 bytes
.../ualberta/stothard/cgview/CgviewFactory$2.class | Bin 1336 -> 0 bytes
.../ualberta/stothard/cgview/CgviewFactory$3.class | Bin 1334 -> 0 bytes
.../ualberta/stothard/cgview/CgviewFactory$4.class | Bin 1336 -> 0 bytes
.../cgview/CgviewFactory$ElementDetails.class | Bin 720 -> 0 bytes
.../ualberta/stothard/cgview/CgviewFactory.class | Bin 57036 -> 0 bytes
.../ca/ualberta/stothard/cgview/CgviewFactory.java | 2847 ---------------
.../stothard/cgview/CgviewFactoryPtt.class | Bin 26400 -> 0 bytes
.../ualberta/stothard/cgview/CgviewFactoryPtt.java | 1534 --------
.../stothard/cgview/CgviewFactoryTab.class | Bin 24352 -> 0 bytes
.../ualberta/stothard/cgview/CgviewFactoryTab.java | 1407 --------
.../stothard/cgview/CgviewHTMLDocument.class | Bin 9064 -> 0 bytes
.../stothard/cgview/CgviewHTMLDocument.java | 370 --
.../src/ca/ualberta/stothard/cgview/CgviewIO.class | Bin 33567 -> 0 bytes
.../src/ca/ualberta/stothard/cgview/CgviewIO.java | 1713 ---------
.../cgview/Feature$SortFeatureRangesByStart.class | Bin 798 -> 0 bytes
.../src/ca/ualberta/stothard/cgview/Feature.class | Bin 4588 -> 0 bytes
.../src/ca/ualberta/stothard/cgview/Feature.java | 461 ---
.../ca/ualberta/stothard/cgview/FeatureRange.class | Bin 14055 -> 0 bytes
.../ca/ualberta/stothard/cgview/FeatureRange.java | 1205 -------
.../cgview/FeatureSlot$SortFeaturesByStart.class | Bin 803 -> 0 bytes
.../ca/ualberta/stothard/cgview/FeatureSlot.class | Bin 3778 -> 0 bytes
.../ca/ualberta/stothard/cgview/FeatureSlot.java | 322 --
.../ca/ualberta/stothard/cgview/FileMover.class | Bin 2242 -> 0 bytes
.../src/ca/ualberta/stothard/cgview/FileMover.java | 61 -
.../ca/ualberta/stothard/cgview/InnerLabel.class | Bin 6892 -> 0 bytes
.../ca/ualberta/stothard/cgview/InnerLabel.java | 462 ---
cgview/src/ca/ualberta/stothard/cgview/Label.class | Bin 6459 -> 0 bytes
cgview/src/ca/ualberta/stothard/cgview/Label.java | 498 ---
.../ca/ualberta/stothard/cgview/LabelBounds.class | Bin 1756 -> 0 bytes
.../ca/ualberta/stothard/cgview/LabelBounds.java | 161 -
.../src/ca/ualberta/stothard/cgview/Legend.class | Bin 5861 -> 0 bytes
cgview/src/ca/ualberta/stothard/cgview/Legend.java | 447 ---
.../ca/ualberta/stothard/cgview/LegendItem.class | Bin 4020 -> 0 bytes
.../ca/ualberta/stothard/cgview/LegendItem.java | 290 --
.../ca/ualberta/stothard/cgview/OuterLabel.class | Bin 7016 -> 0 bytes
.../ca/ualberta/stothard/cgview/OuterLabel.java | 455 ---
.../src/ca/ualberta/stothard/cgview/Plasmid.class | Bin 22469 -> 0 bytes
.../src/ca/ualberta/stothard/cgview/Plasmid.java | 1237 -------
.../ca/ualberta/stothard/cgview/SeriesImage.class | Bin 2362 -> 0 bytes
.../ca/ualberta/stothard/cgview/SeriesImage.java | 194 -
.../stothard/cgview/SortLabelsByForceLabel.class | Bin 582 -> 0 bytes
.../stothard/cgview/SortLabelsByForceLabel.java | 26 -
.../stothard/cgview/SortLabelsByRadians.class | Bin 589 -> 0 bytes
.../stothard/cgview/SortLabelsByRadians.java | 26 -
.../stothard/cgview/SortLabelsByRadiansShift.class | Bin 706 -> 0 bytes
.../stothard/cgview/SortLabelsByRadiansShift.java | 27 -
.../stothard/cgview/SortLabelsByRadius.class | Bin 844 -> 0 bytes
.../stothard/cgview/SortLabelsByRadius.java | 44 -
.../cgview/SortSeriesImageByZoomCenter.class | Bin 603 -> 0 bytes
.../cgview/SortSeriesImageByZoomCenter.java | 26 -
.../ualberta/stothard/cgview/includes/as_png.png | Bin 2825 -> 0 bytes
.../ualberta/stothard/cgview/includes/as_svg.png | Bin 2859 -> 0 bytes
.../stothard/cgview/includes/expand_in.png | Bin 2733 -> 0 bytes
.../stothard/cgview/includes/expand_in_g.png | Bin 1329 -> 0 bytes
.../stothard/cgview/includes/expand_out.png | Bin 2588 -> 0 bytes
.../stothard/cgview/includes/expand_out_g.png | Bin 1271 -> 0 bytes
.../ca/ualberta/stothard/cgview/includes/full.png | Bin 2565 -> 0 bytes
.../ualberta/stothard/cgview/includes/full_g.png | Bin 1283 -> 0 bytes
.../ca/ualberta/stothard/cgview/includes/help.html | 153 -
.../ca/ualberta/stothard/cgview/includes/help.png | Bin 875 -> 0 bytes
.../stothard/cgview/includes/help_png.html | 135 -
.../ca/ualberta/stothard/cgview/includes/info.js | 73 -
.../stothard/cgview/includes/move_back.png | Bin 2375 -> 0 bytes
.../stothard/cgview/includes/move_back_g.png | Bin 1207 -> 0 bytes
.../stothard/cgview/includes/move_forward.png | Bin 2546 -> 0 bytes
.../stothard/cgview/includes/move_forward_g.png | Bin 1256 -> 0 bytes
.../ualberta/stothard/cgview/includes/overlib.js | 1491 --------
.../stothard/cgview/includes/stylesheet.css | 19 -
default-BRIG.xml | 16 +-
errorlog.xml | 760 ----
manifest.mf | 3 +
nbproject/build-impl.xml | 891 +++++
nbproject/genfiles.properties | 11 +
nbproject/profiler-build-impl.xml | 131 +
nbproject/project.properties | 73 +
nbproject/project.xml | 15 +
profiles/Eight_rings.xml | 16 +-
profiles/Fifteen_rings.xml | 16 +-
profiles/Five_rings.xml | 16 +-
profiles/Four_rings.xml | 16 +-
profiles/Nine_rings.xml | 16 +-
profiles/One_ring.xml | 16 +-
profiles/Seven_rings.xml | 16 +-
profiles/Six_rings.xml | 16 +-
profiles/Ten_rings.xml | 16 +-
profiles/Three_rings.xml | 16 +-
profiles/Twenty_rings.xml | 16 +-
profiles/Two_ring.xml | 16 +-
profiles/Two_rings.xml | 16 +-
proteins.txt | 126 +-
src/brig/About.form | 102 +
src/brig/About.java | 142 +
src/brig/AnnoXML.java | 253 ++
src/brig/BRIG.java | 2286 ++++++++++++
src/brig/BRIGconsole.java | 102 +
src/brig/BRIGrun.java | 47 +
src/brig/CGHeader.form | 2023 +++++++++++
src/brig/CGHeader.java | 1646 +++++++++
src/brig/Console.form | 79 +
src/brig/Console.java | 132 +
src/brig/CustomXML.form | 541 +++
src/brig/CustomXML.java | 1203 +++++++
src/brig/FilterFVF.java | 51 +
src/brig/Genbank.form | 103 +
src/brig/Genbank.java | 151 +
src/brig/Graph.form | 276 ++
src/brig/Graph.java | 1285 +++++++
src/brig/GraphFunctions.java | 312 ++
src/brig/Main.java | 43 +
src/brig/One.form | 362 ++
src/brig/One.java | 942 +++++
src/brig/Options.form | 486 +++
src/brig/Options.java | 660 ++++
src/brig/QuickProfile.form | 95 +
src/brig/QuickProfile.java | 218 ++
src/brig/SamCoverage.java | 112 +
src/brig/TextAreaOutputStream.java | 117 +
src/brig/Three2.form | 218 ++
src/brig/Three2.java | 380 ++
src/brig/Two.form | 720 ++++
src/brig/Two.java | 1598 +++++++++
src/brig/backup.java | 279 ++
src/brig/default-BRIG.xml | 4 +
src/brig/test.java | 110 +
src/brig/text.java | 52 +
src/brig/translateProtein.java | 55 +
191 files changed, 18796 insertions(+), 26689 deletions(-)
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