jalview

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Commits this week: 8
Total Committers: 73
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Commits this week: 8

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Friday 31 Aug 2018
11:39 am

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

JAL-3003 remove redundant call to drawSelectionGroup

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    • -4
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    /src/jalview/gui/SeqCanvas.java
Thursday 23 Aug 2018
1:28 pm

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

JAL-3059 use correct border colour for groups

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    • -2
    • +2
    /src/jalview/gui/SeqCanvas.java
1:27 pm

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

JAL-3003 draw selection group outline on main graphics context

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    • -171
    • +76
    /src/jalview/gui/SeqCanvas.java
Wednesday 15 Aug 2018
11:01 am

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

JAL-3080 remove tree partition if no groups created

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    • -1
    • +10
    /src/jalview/gui/TreeCanvas.java
Tuesday 14 Aug 2018
4:55 pm

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

JAL-3078 reset Tree font (only!) on Cancel

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    • -7
    • +12
    /src/jalview/gui/FontChooser.java
Thursday 19 Jul 2018
4:37 pm

Jim Procter

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

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4:36 pm

Jim Procter

JAL-3047 don't set classes unconditionally (forgot to delete it in earlier patch)

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    • -1
    • +0
    /build.xml
Thursday 12 Jul 2018
2:17 pm

Jim Procter

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

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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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    • +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
6:38 pm

Jim Procter

Merge branch 'task/JAL-3042_remove_SimpleDocument_dependency' into develop

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6:37 pm

Jim Procter

JAL-3042 remove mention of adjustable search box history length from docs

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    • -1
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    /help/html/editing/index.html
    • -1
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    /help/html/features/search.html
    • binary
    /help/html/features/searchclearhist.png
5:57 pm

Jim Procter

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

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    /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
    /RELEASE
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    • +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
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    /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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    /.classpath
    • binary
    /lib/jdas-1.0.4.jar
    • -18
    • +0
    /src/jalview/bin/Cache.java
    • -1
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    /src/jalview/bin/Jalview.java
    • -864
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    /src/jalview/gui/DasSourceBrowser.java
    • -210
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    /src/jalview/gui/FeatureSettings.java
    • -50
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    /src/jalview/gui/JDatabaseTree.java
    • -5
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    /src/jalview/gui/Preferences.java
    • -22
    • +4
    /src/jalview/gui/SequenceFetcher.java
    • -10
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    /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
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    /src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java
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    /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
3:37 pm

Jim Procter

JAL-3042 don't allow user to change default history length for an input box

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    • -77
    • +5
    /src/jalview/io/cache/JvCacheableInputBox.java
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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    /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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    /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
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    /test/jalview/analysis/AlignmentUtilsTests.java
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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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    /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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    /src/jalview/datamodel/features/FeatureAttributes.java
    • -1
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    /src/jalview/gui/FeatureTypeSettings.java