[med-svn] [brig] branch upstream updated (a8e6790 -> 50c473a)
Andreas Tille
tille at debian.org
Sun Nov 29 10:33:15 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository brig.
from a8e6790 Imported Upstream version 0.95+dfsg
new 50c473a Imported Upstream version 0.95+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:
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(-)
create mode 100644 HELP
create mode 100644 README_devel.txt
create mode 100644 TUV_500.fasta
create mode 100644 build-before-profiler.xml
create mode 100644 build.xml
delete mode 100644 cgview/README
delete mode 100644 cgview/ca/ualberta/stothard/cgview/Cgview.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/CgviewConstants.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/CgviewFactory$1.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/CgviewFactory$2.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/CgviewFactory$3.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/CgviewFactory$4.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/CgviewFactory$ElementDetails.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/CgviewFactory.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/CgviewFactoryPtt.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/CgviewFactoryTab.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/CgviewHTMLDocument.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/CgviewIO.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/Feature$SortFeatureRangesByStart.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/Feature.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/FeatureRange.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/FeatureSlot$SortFeaturesByStart.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/FeatureSlot.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/FileMover.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/InnerLabel.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/Label.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/LabelBounds.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/Legend.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/LegendItem.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/OuterLabel.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/Plasmid.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/SeriesImage.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/SortLabelsByForceLabel.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/SortLabelsByRadians.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/SortLabelsByRadiansShift.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/SortLabelsByRadius.class
delete mode 100644 cgview/ca/ualberta/stothard/cgview/SortSeriesImageByZoomCenter.class
delete mode 100644 cgview/cgview_xml_builder/README
delete mode 100644 cgview/cgview_xml_builder/cgview_xml_builder.pl
delete mode 100644 cgview/cgview_xml_builder/test.sh
delete mode 100644 cgview/includes/as_png.png
delete mode 100644 cgview/includes/as_svg.png
delete mode 100644 cgview/includes/expand_in.png
delete mode 100644 cgview/includes/expand_in_g.png
delete mode 100644 cgview/includes/expand_out.png
delete mode 100644 cgview/includes/expand_out_g.png
delete mode 100644 cgview/includes/full.png
delete mode 100644 cgview/includes/full_g.png
delete mode 100644 cgview/includes/help.html
delete mode 100644 cgview/includes/help.png
delete mode 100644 cgview/includes/help_png.html
delete mode 100644 cgview/includes/info.js
delete mode 100644 cgview/includes/move_back.png
delete mode 100644 cgview/includes/move_back_g.png
delete mode 100644 cgview/includes/move_forward.png
delete mode 100644 cgview/includes/move_forward_g.png
delete mode 100644 cgview/includes/overlib.js
delete mode 100644 cgview/includes/stylesheet.css
delete mode 100644 cgview/manifestinfo
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/Cgview.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/Cgview.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewConstants.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewConstants.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewFactory$1.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewFactory$2.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewFactory$3.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewFactory$4.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewFactory$ElementDetails.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewFactory.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewFactory.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewFactoryPtt.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewFactoryPtt.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewFactoryTab.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewFactoryTab.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewHTMLDocument.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewHTMLDocument.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewIO.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/CgviewIO.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/Feature$SortFeatureRangesByStart.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/Feature.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/Feature.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/FeatureRange.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/FeatureRange.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/FeatureSlot$SortFeaturesByStart.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/FeatureSlot.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/FeatureSlot.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/FileMover.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/FileMover.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/InnerLabel.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/InnerLabel.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/Label.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/Label.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/LabelBounds.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/LabelBounds.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/Legend.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/Legend.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/LegendItem.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/LegendItem.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/OuterLabel.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/OuterLabel.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/Plasmid.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/Plasmid.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/SeriesImage.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/SeriesImage.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/SortLabelsByForceLabel.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/SortLabelsByForceLabel.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/SortLabelsByRadians.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/SortLabelsByRadians.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/SortLabelsByRadiansShift.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/SortLabelsByRadiansShift.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/SortLabelsByRadius.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/SortLabelsByRadius.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/SortSeriesImageByZoomCenter.class
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/SortSeriesImageByZoomCenter.java
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/as_png.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/as_svg.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/expand_in.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/expand_in_g.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/expand_out.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/expand_out_g.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/full.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/full_g.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/help.html
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/help.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/help_png.html
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/info.js
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/move_back.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/move_back_g.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/move_forward.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/move_forward_g.png
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/overlib.js
delete mode 100644 cgview/src/ca/ualberta/stothard/cgview/includes/stylesheet.css
delete mode 100644 errorlog.xml
create mode 100644 manifest.mf
create mode 100644 nbproject/build-impl.xml
create mode 100644 nbproject/genfiles.properties
create mode 100644 nbproject/profiler-build-impl.xml
create mode 100644 nbproject/project.properties
create mode 100644 nbproject/project.xml
create mode 100644 src/brig/About.form
create mode 100644 src/brig/About.java
create mode 100644 src/brig/AnnoXML.java
create mode 100644 src/brig/BRIG.java
create mode 100644 src/brig/BRIGconsole.java
create mode 100644 src/brig/BRIGrun.java
create mode 100644 src/brig/CGHeader.form
create mode 100644 src/brig/CGHeader.java
create mode 100644 src/brig/Console.form
create mode 100644 src/brig/Console.java
create mode 100644 src/brig/CustomXML.form
create mode 100644 src/brig/CustomXML.java
create mode 100644 src/brig/FilterFVF.java
create mode 100644 src/brig/Genbank.form
create mode 100644 src/brig/Genbank.java
create mode 100644 src/brig/Graph.form
create mode 100644 src/brig/Graph.java
create mode 100644 src/brig/GraphFunctions.java
create mode 100644 src/brig/Main.java
create mode 100644 src/brig/One.form
create mode 100644 src/brig/One.java
create mode 100644 src/brig/Options.form
create mode 100644 src/brig/Options.java
create mode 100644 src/brig/QuickProfile.form
create mode 100644 src/brig/QuickProfile.java
create mode 100644 src/brig/SamCoverage.java
create mode 100644 src/brig/TextAreaOutputStream.java
create mode 100644 src/brig/Three2.form
create mode 100644 src/brig/Three2.java
create mode 100644 src/brig/Two.form
create mode 100644 src/brig/Two.java
create mode 100644 src/brig/backup.java
create mode 100644 src/brig/default-BRIG.xml
create mode 100644 src/brig/test.java
create mode 100644 src/brig/text.java
create mode 100644 src/brig/translateProtein.java
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