jalview

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Friday 06 Jul 2018
12:31 pm

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

JAL-3059 use the right colour for group border

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    • -1
    • +1
    /src/jalview/gui/SeqCanvas.java
Monday 02 Jul 2018
10:24 am

Jim Procter

Merge branch 'task/JAL-3047_clovercoverage' into develop

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10:24 am

Jim Procter

JAL-3047 don’t let the makedist task complete if a clover build was performed

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    • -0
    • +3
    /build.xml
10:20 am

Jim Procter

JAL-3047 ‘cloverclasses’ build directory for instrumented classes (allow incremental compile and avoid releasing instrumented classes in production builds)

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    • -0
    • +2
    /build.xml
Wednesday 27 Jun 2018
6:17 pm

Jim Procter

JAL-3047 enable clover for testng

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    • -0
    • +4
    /build.xml
6:17 pm

Jim Procter

JAL-3047 ignore clover output dir

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    • +2
    /.gitignore
6:02 pm

Jim Procter

JAL-3047 ant -Dclover.jar=../path/to/clover/lib/clover.jar to enable clover for testng ant task

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    • -0
    • +1
    /build.xml
Tuesday 26 Jun 2018
5:57 pm

Jim Procter

JAL-3035 removed jdas in libs documentation and noted spring modules as candidates for removal

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    • +2
    /THIRDPARTYLIBS
5:07 pm

Jim Procter

Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

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5:06 pm

Jim Procter

JAL-3035 documentation in 2.11 release notes (and 2.11 fictional release date)

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    • -2
    • +2
    /RELEASE
    • -0
    • +24
    /help/html/releases.html
5:06 pm

Jim Procter

JAL-3035 remove DAS UI documentation

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    • +0
    /help/help.jhm
    • -4
    • +1
    /help/helpTOC.xml
    • -24
    • +0
    /help/html/features/clarguments.html
    • -77
    • +0
    /help/html/features/dasfeatures.html
    • -74
    • +0
    /help/html/features/dassettings.html
    • -4
    • +0
    /help/html/features/preferences.html
    • -4
    • +1
    /help/html/features/seqfeatures.html
    • -26
    • +4
    /help/html/features/seqfetch.html
    • -25
    • +21
    /help/html/menus/alignmentMenu.html
    • -2
    • +1
    /help/html/menus/alwview.html
    • -9
    • +8
    /help/html/menus/wsmenu.html
    • -12
    • +8
    /help/html/webServices/dbreffetcher.html
    • -9
    • +5
    /help/html/webServices/index.html
4:40 pm

Jim Procter

Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

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4:16 pm

Jim Procter

JAL-3035 - jalview-das is no more ! - jsdas lib removed - DAS settings panel deleted (Feature settings pane has no tabs now) - all code for wrapping DAS sources and retrieving sequences and features from them is gone - test methods/main methods have been de-dasified or removed if their only purpose was to test DAS source discovery - fancy sorting code to account for DAS sequence source names has been removed

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    • +0
    /.classpath
    • binary
    /lib/jdas-1.0.4.jar
    • -18
    • +0
    /src/jalview/bin/Cache.java
    • -1
    • +0
    /src/jalview/bin/Jalview.java
    • -864
    • +0
    /src/jalview/gui/DasSourceBrowser.java
    • -210
    • +0
    /src/jalview/gui/FeatureSettings.java
    • -50
    • +0
    /src/jalview/gui/JDatabaseTree.java
    • -5
    • +0
    /src/jalview/gui/Preferences.java
    • -22
    • +4
    /src/jalview/gui/SequenceFetcher.java
    • -10
    • +0
    /src/jalview/jbgui/GPreferences.java
    • -54
    • +11
    /src/jalview/ws/DBRefFetcher.java
    • -925
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    /src/jalview/ws/DasSequenceFeatureFetcher.java
    • -79
    • +7
    /src/jalview/ws/SequenceFetcher.java
    • -57
    • +0
    /src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java
    • -87
    • +0
    /src/jalview/ws/dbsources/das/api/jalviewSourceI.java
  16. … 8 more files in changeset.
4:09 pm

Jim Procter

JAL-3035 (unrelated) random XML error in nbbuild.xml

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    /nbbuild.xml
Thursday 07 Jun 2018
3:40 pm

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

JAL-2755 correct Javadoc and error handling

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    /src/jalview/ext/ensembl/EnsemblLookup.java
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    /src/jalview/ext/ensembl/EnsemblMap.java
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    /src/jalview/ext/ensembl/EnsemblRestClient.java
Wednesday 06 Jun 2018
3:16 pm

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

JAL-3013 ensure Chimera as a symlink gets resolved

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    • -21
    • +24
    /src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
Monday 04 Jun 2018
8:42 pm

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

JAL-2808 update test for revised treatment of 'mixed type' attribute values

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    • -2
    • +4
    /test/jalview/datamodel/features/FeatureAttributesTest.java
8:40 pm

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

JAL-3019 correctly form toRange of 'traversed' MapList

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    /src/jalview/util/MapList.java
    • -6
    • +6
    /test/jalview/analysis/AlignmentUtilsTests.java
    • -31
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    /test/jalview/util/MapListTest.java
3:06 pm

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

JAL-3018 updated REST versions to 6.3

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    • +2
    /src/jalview/ext/ensembl/EnsemblRestClient.java
Thursday 31 May 2018
2:20 pm

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

JAL-2808 don't capture or report min-max for mixed text/numeric attribute

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    • -18
    • +32
    /src/jalview/datamodel/features/FeatureAttributes.java
    • -1
    • +1
    /src/jalview/gui/FeatureTypeSettings.java
11:43 am

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

JAL-2808 pre-fill numeric inequality filter with min/max range value

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    • -9
    • +35
    /src/jalview/gui/FeatureTypeSettings.java
Monday 28 May 2018
9:23 am

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

Merge branch 'bug/JAL-797' into develop

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    • +42
    /src/jalview/gui/Desktop.java
9:19 am

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

Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into develop

Conflicts:

src/jalview/io/FeaturesFile.java

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    /build.xml
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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
    • -11
    • +29
    /src/jalview/gui/AlignFrame.java
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    • +146
    /src/jalview/gui/Desktop.java
    • -2
    • +0
    /src/jalview/io/FeaturesFile.java
    • -0
    • +20
    /test/jalview/gui/SeqCanvasTest.java
    • -0
    • +20
    /test/jalview/renderer/seqfeatures/FeatureRendererTest.java
Saturday 26 May 2018
1:36 pm

Jim Procter

JAL-2999 release date for 2.10.4b1 set for 27th May 2018

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    • -1
    • +1
    /help/html/releases.html
Friday 25 May 2018
1:58 pm

Jim Procter

Merge branch 'documentation/JAL-2999_r2104b1' into releases/Release_2_10_4_Branch

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1:58 pm

Jim Procter

Merge branch 'bug/JAL-2992panelHeight' into releases/Release_2_10_4_Branch

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1:56 pm

Jim Procter

Merge branch 'bug/JAL-1460_dragndropWindows' into releases/Release_2_10_4_Branch

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1:49 pm

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

JAL-2992 simpler heuristic for available height

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    /src/jalview/gui/AlignmentPanel.java
11:19 am

Jim Procter

Merge branch 'bug/JAL-2991_exporttosvgwrapview' into releases/Release_2_10_4_Branch

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11:10 am

Jim Procter

Merge branch 'feature/JAL-2994chimeraPath' into releases/Release_2_10_4_Branch

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