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 20 Nov 2020
1:04 pm

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

JAL-3779 apply properties to all groups with given name, not just first

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    • -105
    • +114
    /src/jalview/io/AnnotationFile.java
    • -5
    • +51
    /test/jalview/io/AnnotationFileIOTest.java
Thursday 29 Oct 2020
8:01 pm

Jim Procter

JAL-3766 what’s new and release notes for 2.11.1.3

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    • -5
    • +4
    /help/help/html/releases.html
    • -38
    • +14
    /help/help/html/whatsNew.html
3:35 pm

Jim Procter

JAL-3759 fix compilation error for test

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    • -1
    • +1
    /test/jalview/analysis/GroupingTest.java
3:20 pm

Jim Procter

JAL-3766 release notes for JAL-3759

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    • -0
    • +5
    /help/help/html/releases.html
3:17 pm

Jim Procter

JAL-3759 exclude hidden columns when processing column selection

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    • -3
    • +18
    /src/jalview/analysis/Grouping.java
    • -1
    • +2
    /src/jalview/controller/AlignViewController.java
3:13 pm

Jim Procter

Merge branch 'documentation/JAL-3766_relnotes' into releases/Release_2_11_1_Branch

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3:10 pm

Jim Procter

JAL-3766 release notes for JAL-3765 JAL-3763 JAL-3760 JAL-3751 JAL-3748 JAL-3725 JAL-3700 JAL-3611

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    • -3
    • +42
    /help/help/html/releases.html
2:24 pm

Jim Procter

Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_11_1_Branch

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2:19 pm

Ben Soares

JAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename

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    • -5
    • +6
    /doc/building.html
    • -5
    • +8
    /doc/building.md
11:30 am

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

JAL-3700 mapped sequence group includes short (or all gapped) sequences

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    • -13
    • +17
    /src/jalview/util/MappingUtils.java
    • -25
    • +24
    /test/jalview/util/MappingUtilsTest.java
Wednesday 28 Oct 2020
11:24 pm

Jim Procter

JAL-3725 fix tests for EMBLFlatFile parser when mapping doesn’t include stop codon

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    • -7
    • +8
    /test/jalview/io/EmblFlatFileTest.java
10:56 pm

Jim Procter

JAL-3725 patch EMBL flat file to exclude stop codon from the mapping (for 2.11.1.3 - needs cherry-pick to 2.11.2)

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    • -4
    • +2
    /src/jalview/io/EmblFlatFile.java
4:40 pm

Jim Procter

Merge branch 'bug/JAL-3760_protsTreatedAsNucleotides' into releases/Release_2_11_1_Branch

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12:18 pm

Ben Soares

JAL-3248 Added step to create the eclipse files before project import. Noted non-fatal NPEs during build with gradle 6.6+

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    • -139
    • +176
    /doc/building.html
    • -3
    • +11
    /doc/building.md
Tuesday 27 Oct 2020
12:58 pm

Jim Procter

update test for JAL-3763 redact shared DS sequences for contiguous CDS

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    • binary
    /examples/testdata/MN908947.jvp
11:02 am

Jim Procter

JAL-3768 noticed failure of test when run as part of suite via gradle - whilst patching JAL-3700 JAL-3748 JAL-3763 for 2.11.1.3

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    • -0
    • +2
    /test/jalview/structure/Mapping.java
10:54 am

Jim Procter

JAL-3700 JAL-3748 JAL-3763 don’t add stop codon via alignAs if guide peptide doesn’t include C terminus.

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    • -2
    • +2
    /src/jalview/analysis/AlignmentUtils.java
Thursday 22 Oct 2020
2:48 pm

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

JAL-3763 Javadoc, check for null, additional tests

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    • -3
    • +3
    /src/jalview/datamodel/AlignedCodonFrame.java
    • -1
    • +6
    /src/jalview/gui/PopupMenu.java
    • -0
    • +63
    /test/jalview/datamodel/AlignedCodonFrameTest.java
10:40 am

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

JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

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    • -1
    • +6
    /src/jalview/datamodel/AlignedCodonFrame.java
    • -2
    • +4
    /src/jalview/datamodel/SearchResults.java
    • -26
    • +129
    /test/jalview/datamodel/AlignedCodonFrameTest.java
Wednesday 21 Oct 2020
4:24 pm

Jim Procter

JAL-3766 release notes for JAL-3611 JAL-3765

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    • -0
    • +5
    /help/help/html/releases.html
4:21 pm

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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4:20 pm

Jim Procter

Merge branch 'bug/JAL-3765_Find_bugs_in_21112' into releases/Release_2_11_1_Branch

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4:20 pm

Jim Procter

JAL-3766 cut new patch release

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    • -1
    • +1
    /RELEASE
    • -0
    • +17
    /help/help/html/releases.html
    • -2
    • +2
    /help/help/html/whatsNew.html
Tuesday 20 Oct 2020
5:23 pm

Jim Procter

JAL-3765 fix test

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    • -10
    • +13
    /test/jalview/analysis/FinderTest.java
5:13 pm

Jim Procter

fix for JAL-3765

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    • -1
    • +1
    /src/jalview/analysis/Finder.java
Monday 19 Oct 2020
6:07 pm

Jim Procter

JAL-3765 simple test that findAll finds all matches for a pattern when it is present multiple times in a sequence

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    • -0
    • +10
    /test/jalview/analysis/FinderTest.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
3:29 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
    • +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