jalview

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Commits this week: 1
Total Committers: 72
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Commits this week: 1

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Thursday 24 Sep 2020
2:36 pm

Jim Procter

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

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    /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 !)

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    /src/jalview/bin/Jalview.java
11:55 am

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

JAL-3751 only merge strictly contiguous ranges of mappings

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    /src/jalview/util/MapList.java
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    /test/jalview/util/MapListTest.java
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    /test/jalview/util/MappingUtilsTest.java
11:55 am

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

JAL-3751 only merge strictly contiguous ranges of mappings

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    /src/jalview/util/MapList.java
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    /test/jalview/util/MapListTest.java
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    /test/jalview/util/MappingUtilsTest.java
11:55 am

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

JAL-3751 only merge strictly contiguous ranges of mappings

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    /src/jalview/util/MapList.java
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    /test/jalview/util/MapListTest.java
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    /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://

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    /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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    /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

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    /src/jalview/datamodel/AlignedCodonFrame.java
5:19 pm

Ben Soares

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

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5:17 pm

Jim Procter

JAL-3748 fix compilation error

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

Jim Procter

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

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    • +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

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    • +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.

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    /src/jalview/datamodel/AlignedCodonFrame.java
Tuesday 22 Sep 2020
3:30 pm

Jim Procter

JAL-3748 test data for SplitFrameTest

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    • binary
    /examples/testdata/MN908947.jvp
3:09 pm

Jim Procter

JAL-3748 don’t trash start/end on SequenceI reconstructed from a SeqCigar via SeqsetUtils.SeqCharacterUnhash

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    /src/jalview/analysis/SeqsetUtils.java
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    /src/jalview/datamodel/SeqCigar.java
2:45 pm

Jim Procter

JAL-3748 simple test for SeqCigar preservation of start/end and name for different ways of constructing SeqCigar and reconstructing alignment sequences

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    • +23
    /test/jalview/datamodel/SeqCigarTest.java
2:30 pm

Jim Procter

JAL-3748 additional asserts to verify start/end after reconstructing sequence from seqCigar

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    • -3
    • +11
    /test/jalview/datamodel/SeqCigarTest.java
Monday 21 Sep 2020
12:01 pm

Jim Procter

Merge branch 'merge_review/JAL-3490_2_11_2_develop' into develop

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    /src/jalview/gui/AlignFrame.java
Sunday 20 Sep 2020
8:33 pm

Ben Soares

JAL-3753 put resources in gradle run and test path

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    /.gitignore
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    /build.gradle
Friday 18 Sep 2020
6:18 pm

Ben Soares

JAL-3753 JAL-3754 first rejig

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    /build.gradle
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    /gradle.properties
12:09 pm

Ben Soares

JAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

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    /build.gradle
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    /gradle.properties
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    /resources/images/JalviewDevelopLogo_Huge.png
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    /utils/channels/develop_properties
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    /utils/channels/release_properties
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    /utils/getdown/Jalview-Logo.png
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    /utils/getdown/develop/jalview_logo_background_blur-640x480.xcf
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    /utils/getdown/develop/jalview_logo_background_getdown-progress.png
  16. … 31 more files in changeset.
12:09 pm

Ben Soares

JAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

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    /.gitignore
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    /build.gradle
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    /gradle.properties
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    /resources/images/JalviewDevelopLogo_Huge.png
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    /resources/images/Jalview_Develop_Logo.png
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    /resources/images/Jalview_Logo.png
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    /resources/images/jalview_logos.icns
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    /resources/images/jalview_logos.ico
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    /utils/channels/release_properties
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    /utils/getdown/Jalview-Logo.png
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    /utils/getdown/develop/Jalview-Logo.png
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    /utils/getdown/develop/jalview_logo_background_blur-640x480.xcf
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    /utils/getdown/develop/jalview_logo_background_getdown-progress.png
  16. … 31 more files in changeset.
Thursday 17 Sep 2020
6:47 pm

Jim Procter

Merge branch 'releases/Release_2_11_1_Branch'

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1:38 pm

Jim Procter

JAL-3675 release notes for JAL-3750 JAL-3751

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    /help/help/html/releases.html
12:28 pm

Jim Procter

Merge branch 'patch/JAL-3750_JAL-3741_https_patch' into releases/Release_2_11_1_Branch

Options
12:19 pm

Jim Procter

JAL-3741 http to https (and jar to jvp for exampleFile defaults!)

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    /help/help/html/features/commandline.html
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    /help/help/html/features/groovy.html
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    /help/help/html/groovy/featuresCounter.html
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    /help/help/html/index.html
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    /help/help/html/webServices/newsreader.html
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    /src/jalview/bin/Cache.java
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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/BlogReader.java
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    /src/jalview/gui/Preferences.java
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    /src/jalview/io/JSONFile.java
12:09 pm

Jim Procter

JAL-3750 parse protocol before checking if argument to -open can be opened as a file

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    /src/jalview/bin/Jalview.java