jalview

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Thursday 15 Oct 2020
3:01 pm

Ben Soares

Merge branch 'develop' into blocker/JAL-3611_space_character_in_jalview_install_path

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11:02 am

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

JAL-3763 unused method removed

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    • -34
    • +0
    /src/jalview/datamodel/AlignedCodonFrame.java
Thursday 08 Oct 2020
3:30 pm

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

JAL-3700 JAL-3763 create datasets for test sequences

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    • -4
    • +8
    /test/jalview/util/MappingUtilsTest.java
3:30 pm

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

JAL-3700 JAL-3763 create datasets for test sequences

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    • -4
    • +8
    /test/jalview/util/MappingUtilsTest.java
3:29 pm

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

JAL-3763 failsafe check for null

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    • -0
    • +4
    /src/jalview/datamodel/AlignedCodonFrame.java
3:29 pm

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

JAL-3763 failsafe check for null

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    • -0
    • +4
    /src/jalview/datamodel/AlignedCodonFrame.java
3:06 pm

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

JAL-3763 refactored getCoveringMapping for virtual feature discovery

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    • -25
    • +65
    /src/jalview/datamodel/AlignedCodonFrame.java
    • -7
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    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
3:06 pm

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

JAL-3763 refactored getCoveringMapping for virtual feature discovery

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    • -25
    • +65
    /src/jalview/datamodel/AlignedCodonFrame.java
    • -7
    • +7
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
3:05 pm

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

JAL-3763 always make a new dataset sequence for CDS sequence

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    • -55
    • +41
    /src/jalview/analysis/AlignmentUtils.java
3:05 pm

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

JAL-3763 always make a new dataset sequence for CDS sequence

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    • -55
    • +41
    /src/jalview/analysis/AlignmentUtils.java
8:40 am

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

JAL-3761 failing test, formatting, method renamed

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    • -18
    • +36
    /src/jalview/util/MapList.java
    • -8
    • +19
    /test/jalview/util/MapListTest.java
8:40 am

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

JAL-3761 failing test, formatting, method renamed

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    • -18
    • +36
    /src/jalview/util/MapList.java
    • -8
    • +19
    /test/jalview/util/MapListTest.java
Friday 02 Oct 2020
11:44 am

Jim Procter

JAL-3762 check for !args || args=="" before overwriting

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    • -1
    • +1
    /src/jalview/util/Platform.java
11:09 am

Jim Procter

JAL-3762 more typo fixing :q

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    • -3
    • +3
    /src/jalview/util/Platform.java
10:55 am

Jim Procter

JAL-3762 syntax error typo

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    • -1
    • +1
    /src/jalview/util/Platform.java
9:21 am

Jim Procter

JAL-3762 check if Info.args already defined before overwriting it with URL args. Also stashes URL args at Info.urlargs

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    • -11
    • +14
    /src/jalview/util/Platform.java
Thursday 01 Oct 2020
12:42 pm

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

JAL-3761 failing tests for locateInFrom/To with overlapping ranges

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    • -0
    • +53
    /test/jalview/util/MapListTest.java
12:42 pm

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

JAL-3761 failing tests for locateInFrom/To with overlapping ranges

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    • -0
    • +53
    /test/jalview/util/MapListTest.java
Tuesday 29 Sep 2020
4:41 pm

Jim Procter

JAL-3760 fix tests for changed behaviour

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    • -4
    • +4
    /test/jalview/util/ComparisonTest.java
4:41 pm

Jim Procter

JAL-3760 fix tests for changed behaviour

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    • -4
    • +4
    /test/jalview/util/ComparisonTest.java
3:26 pm

Jim Procter

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

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    • -30
    • +39
    /src/jalview/util/Comparison.java
3:26 pm

Jim Procter

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

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    • -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

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

Ben Soares

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

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

Ben Soares

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

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

Jim Procter

JAL-3758 tweak what’s new for 2.11.1.2!

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    /help/help/html/whatsNew.html
8:05 am

Jim Procter

JAL-3758 release Fri 25th Sep

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    /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

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