jalview

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Commits this week: 4
Total Committers: 73
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Commits this week: 4

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Monday 03 Apr 2017
4:51 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2314 made non-test method non-public

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    /test/jalview/ws/jabaws/RNAStructExportImport.java
2:13 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

Merge branch 'develop' into bug/JAL-2314

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12:56 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

Merge branch 'develop' into bug/JAL-2461

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Friday 31 Mar 2017
12:26 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2405 additional checks for circular reference in context or dataset

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    • +4
    /src/jalview/datamodel/Alignment.java
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    /src/jalview/datamodel/SequenceGroup.java
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    • +9
    /test/jalview/datamodel/AlignmentTest.java
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    • +17
    /test/jalview/datamodel/SequenceGroupTest.java
12:09 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2472 PrivilegedAccessor added

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    • +331
    /test/junit/extensions/PA.java
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    • +647
    /test/junit/extensions/PrivilegedAccessor.java
10:59 am

gmungoc <g.m.carstairs@dundee.ac.uk>

Merge branch 'develop' into bug/JAL-2431splitFrameNewView

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
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    • +46
    /src/jalview/viewmodel/AlignmentViewport.java
10:40 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2430 code tidy, unit test for Jmol hidden column colours

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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    • +79
    /test/jalview/ext/jmol/JmolCommandsTest.java
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    /test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
Thursday 30 Mar 2017
3:11 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

Merge branch 'develop' into bug/JAL-1608createGroups

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    • +1
    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/jbgui/GAlignFrame.java
3:10 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1608 leave Create Group, Remove Group menu items enabled

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    /src/jalview/gui/AlignFrame.java
    • -23
    • +2
    /src/jalview/jbgui/GAlignFrame.java
2:40 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2401 code and help tidy for review comments

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    /help/html/colourSchemes/user.html
    • binary
    /help/html/colourSchemes/userDefined_java6.gif
    • binary
    /help/html/colourSchemes/userDefined_java7.gif
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    /src/jalview/gui/UserDefinedColours.java
12:48 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2401 don't apply lower case colour to upper case

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    • +8
    /src/jalview/gui/UserDefinedColours.java
12:20 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

Merge branch 'develop' into bug/JAL-2399textColour

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
12:16 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2346 JAL-1933 test updated to include Occupancy

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    • +5
    /test/jalview/gui/AnnotationRowFilterTest.java
12:11 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2346 always run setup!

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    /test/jalview/schemes/AnnotationColourGradientTest.java
11:59 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2346 more test coverage for AnnotationColourGradient

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    • +153
    /test/jalview/schemes/AnnotationColourGradientTest.java
11:01 am

gmungoc <g.m.carstairs@dundee.ac.uk>

Merge branch 'develop' into bug/JAL-2346annotationChoice

Conflicts:

src/jalview/gui/AnnotationRowFilter.java

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    • +6
    /src/jalview/datamodel/AlignmentAnnotation.java
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    /src/jalview/gui/AnnotationRowFilter.java
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    /src/jalview/gui/Jalview2XML.java
Wednesday 29 Mar 2017
4:36 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

Merge branch 'develop' into bug/JAL-1608createGroups

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    • +28
    /resources/lang/Messages.properties
    • -3
    • +20
    /resources/lang/Messages_es.properties
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    • +36
    /src/jalview/appletgui/AlignFrame.java
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    • +18
    /src/jalview/gui/AlignFrame.java
Friday 24 Mar 2017
3:28 pm

Jim Procter

JAL-2360 fix applet build by separating castor XML dependency from jalview.schemes.ColourSchemes to jalview.schemes.ColourSchemeLoader

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    • -1
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    /src/jalview/bin/Cache.java
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    /src/jalview/gui/ColourMenuHelper.java
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    /src/jalview/gui/UserDefinedColours.java
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    /src/jalview/schemes/ColourSchemeLoader.java
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    /src/jalview/schemes/ColourSchemes.java
9:44 am

Kira Mourão

Merge remote-tracking branch 'origin/develop' into bug/JAL-2314

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9:43 am

Kira Mourão

JAL-2314 Tidy up

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    /src/jalview/gui/Desktop.java
9:35 am

Kira Mourão

JAL-2314 Fixes to DisorderAnnotExportImport test

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    • +8
    /test/jalview/ws/jabaws/DisorderAnnotExportImport.java
Thursday 23 Mar 2017
8:40 pm

Kira Mourão

Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

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8:39 pm

Kira Mourão

JAL-2388 unit test initialisation fix for running full suite

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    • +1
    /test/jalview/gui/AlignmentPanelTest.java
6:47 pm

Kira Mourão

JAL-2314 Tweaks to stop thread sync issues

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    • +2
    /src/jalview/gui/Desktop.java
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    • +27
    /src/jalview/ws/jws2/Jws2Discoverer.java
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    • +6
    /test/jalview/ws/jabaws/RNAStructExportImport.java
3:10 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2464 fix cancel tree print behaviour

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    • +10
    /src/jalview/gui/TreeCanvas.java
3:10 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2464 fix cancel tree print behaviour

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    /src/jalview/gui/TreeCanvas.java
2:56 pm

Kira Mourão

JAL-2314 Tidies

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    /src/jalview/gui/Desktop.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
2:17 pm

Kira Mourão

JAL-2314 Re-annotated unit tests using Jws2Discoverer

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    /test/jalview/ws/jabaws/DisorderAnnotExportImport.java
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    /test/jalview/ws/jabaws/RNAStructExportImport.java
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    /test/jalview/ws/jws2/ParameterUtilsTest.java
Wednesday 22 Mar 2017
2:21 pm

Kira Mourão

JAL-2461 Removed DAS error stack trace, updated message

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    /src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
2:12 pm

Kira Mourão

JAL-2388 Reinstated original overview checks for annotation display

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    /src/jalview/appletgui/OverviewPanel.java
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    /src/jalview/gui/OverviewPanel.java