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commit d45bbb4fedb7bef62ef822e85580a4272debd9ff Merge: 6dd11e0 50c473a Author: Andreas Tille <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/brig.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
