jalview

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Tuesday 29 Sep 2020
3:26 pm

Jim Procter

JAL-3760 refactor nucleotide proportion test to per-sequence and return false if any sequence appears protein-like

Options
    • -30
    • +39
    /src/jalview/util/Comparison.java
Monday 28 Sep 2020
4:57 pm

Ben Soares

JAL-3753 ensure correct dependencies for shadowJar task

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    • -24
    • +24
    /build.gradle
12:12 pm

Ben Soares

Merge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar

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    • -1
    • +1
    /build.gradle
    • -1
    • +2
    /gradle.properties
Friday 25 Sep 2020
9:39 am

Ben Soares

JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

Options
    • -1
    • +2
    /gradle.properties
9:39 am

Ben Soares

JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

Options
    • -1
    • +2
    /gradle.properties
9:39 am

Ben Soares

JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

Options
    • -1
    • +2
    /gradle.properties
8:16 am

Jim Procter

JAL-3758 tweak what’s new for 2.11.1.2!

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    • +6
    /help/help/html/whatsNew.html
8:05 am

Jim Procter

JAL-3758 release Fri 25th Sep

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    • +1
    /help/help/html/releases.html
7:45 am

Jim Procter

Merge branch 'releases/Release_2_11_1_Branch' of http://source.jalview.org/git/jalview into releases/Release_2_11_1_Branch

Options
Thursday 24 Sep 2020
6:16 pm

Ben Soares

JAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...

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    • -1
    • +1
    /build.gradle
6:16 pm

Ben Soares

JAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...

Options
    • -1
    • +1
    /build.gradle
6:16 pm

Ben Soares

JAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...

Options
    • -1
    • +1
    /build.gradle
2:38 pm

Jim Procter

JAL-3758 2.11.1.2 patch release notes and version bump

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    • -1
    • +1
    /RELEASE
    • -0
    • +18
    /help/help/html/releases.html
2:36 pm

Jim Procter

JAL-3757 JAL-3689 use AppletFormat.checkProtocol to resolve startup file’s retrieval protocol (sorry @benzoid for finessing you !)

Options
    • -6
    • +1
    /src/jalview/bin/Jalview.java
2:36 pm

Jim Procter

JAL-3757 JAL-3689 use AppletFormat.checkProtocol to resolve startup file’s retrieval protocol (sorry @benzoid for finessing you !)

Options
    • -6
    • +1
    /src/jalview/bin/Jalview.java
11:55 am

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

JAL-3751 only merge strictly contiguous ranges of mappings

Options
    • -58
    • +19
    /src/jalview/util/MapList.java
    • -112
    • +88
    /test/jalview/util/MapListTest.java
    • -10
    • +17
    /test/jalview/util/MappingUtilsTest.java
11:55 am

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

JAL-3751 only merge strictly contiguous ranges of mappings

Options
    • -58
    • +19
    /src/jalview/util/MapList.java
    • -112
    • +88
    /test/jalview/util/MapListTest.java
    • -10
    • +17
    /test/jalview/util/MappingUtilsTest.java
11:55 am

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

JAL-3751 only merge strictly contiguous ranges of mappings

Options
    • -58
    • +19
    /src/jalview/util/MapList.java
    • -112
    • +88
    /test/jalview/util/MapListTest.java
    • -0
    • +7
    /test/jalview/util/MappingUtilsTest.java
11:55 am

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

JAL-3751 only merge strictly contiguous ranges of mappings

Options
    • -58
    • +19
    /src/jalview/util/MapList.java
    • -112
    • +88
    /test/jalview/util/MapListTest.java
    • -0
    • +7
    /test/jalview/util/MappingUtilsTest.java
Wednesday 23 Sep 2020
11:41 pm

Ben Soares

JAL-3757 JAL-3689 Fixed checks for URLs by adding checks for https:// as well as http://

Options
    • -1
    • +1
    /src/jalview/bin/Jalview.java
11:41 pm

Ben Soares

JAL-3757 JAL-3689 Fixed checks for URLs by adding checks for https:// as well as http://

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    • -1
    • +2
    /src/jalview/bin/Jalview.java
5:34 pm

Jim Procter

JAL-3748 not testing for sequence’s containment in mapped range breaks CDS reconstruction but allows testAlignProteinAsDna_incompleteStartCodon to pass

Options
    • -1
    • +3
    /src/jalview/datamodel/AlignedCodonFrame.java
5:19 pm

Ben Soares

Merge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar

Options
5:17 pm

Jim Procter

JAL-3748 fix compilation error

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    • -1
    • +0
    /src/jalview/datamodel/AlignedCodonFrame.java
5:11 pm

Jim Procter

JAL-3748 maximal test for JAL-3748 using covid19 CDS/Protein

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    • -0
    • +34
    /test/jalview/gui/SplitFrameTest.java
4:49 pm

Ben Soares

JAL-3477 Added 10k leeway to amount of memory reserved for OS test for float rounding errors (needed to fix failing test)

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    • -11
    • +19
    /test/jalview/bin/MemorySettingTest.java
4:48 pm

Ben Soares

JAL-3753 Resources seen in tests and appropriate filters now being used as file opt-in rather than opt-out.

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    • -19
    • +28
    /build.gradle
4:39 pm

Jim Procter

JAL-3748 more tests verifying reconstruction of AlignemntView for linked CDS/Protein alignment and selected region

Options
    • -1
    • +6
    /test/jalview/gui/SplitFrameTest.java
4:38 pm

Jim Procter

JAL-3748 reusable assert to trace specific issues with recovering the correct Sequence/Mapping (highlights points of failure for AlignmentUtilsTests with patch

Options
    • -1
    • +44
    /test/jalview/analysis/AlignmentUtilsTests.java
4:35 pm

Jim Procter

JAL-3748 allow AlignedCodonFrame.covers to optionally only require coverage for either originating or mapped sequence.

Options
    • -16
    • +45
    /src/jalview/datamodel/AlignedCodonFrame.java