jalview

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

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

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

JAL-3047 enable clover for testng

JAL-3047 ignore clover output dir

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

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

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

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

JAL-3035 remove DAS UI documentation

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    • +0
    /help/html/features/clarguments.html
    • -77
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    /help/html/features/dasfeatures.html
    • -74
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    /help/html/features/dassettings.html
    • -25
    • +21
    /help/html/menus/alignmentMenu.html
    • -12
    • +8
    /help/html/webServices/dbreffetcher.html
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

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

    • -864
    • +0
    /src/jalview/gui/DasSourceBrowser.java
    • -210
    • +0
    /src/jalview/gui/FeatureSettings.java
    • -50
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    /src/jalview/gui/JDatabaseTree.java
    • -22
    • +4
    /src/jalview/gui/SequenceFetcher.java
    • -10
    • +0
    /src/jalview/jbgui/GPreferences.java
    • -54
    • +11
    /src/jalview/ws/DBRefFetcher.java
    • -79
    • +7
    /src/jalview/ws/SequenceFetcher.java
  1. … 8 more files in changeset.
JAL-3035 (unrelated) random XML error in nbbuild.xml

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
JAL-3013 ensure Chimera as a symlink gets resolved

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

JAL-3019 correctly form toRange of 'traversed' MapList

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    /test/jalview/util/MapListTest.java
JAL-3018 updated REST versions to 6.3

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

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    /src/jalview/gui/FeatureTypeSettings.java
JAL-2808 pre-fill numeric inequality filter with min/max range value

    • -9
    • +35
    /src/jalview/gui/FeatureTypeSettings.java
Merge branch 'bug/JAL-797' into develop

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

Conflicts:

src/jalview/io/FeaturesFile.java

    • -2
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    /resources/lang/Messages_es.properties
    • -11
    • +29
    /src/jalview/gui/AlignFrame.java
    • -40
    • +146
    /src/jalview/gui/Desktop.java
    • -0
    • +20
    /test/jalview/gui/SeqCanvasTest.java
JAL-2999 release date for 2.10.4b1 set for 27th May 2018

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

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

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

JAL-2992 simpler heuristic for available height

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

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

JAL-1460 clarify release notes - and mention that shortcuts are now handled by Jalview