jalview

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Commits this week: 13
Total Committers: 69
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Commits this week: 13

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Today
2 hrs ago

Mungo Carstairs

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
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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4:04 pm

Jim Procter

Merge branch 'portforward/JAL-3765_patch_to_2112' into develop

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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
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+

Cherry pick from release, generated new building.html as it's a different process. Also added in a "**/*.md" into build.gradle (wasn't finding anything with "*.md")

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    • -1
    • +2
    /build.gradle
    • -3
    • +7
    /doc/building.html
    • -3
    • +11
    /doc/building.md
Tuesday 27 Oct
12:58 pm

Jim Procter

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

Options
    • 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
Monday 26 Oct
12:20 pm

Mateusz Warowny

JAL-3690 - introduce shutdown method that cleans up manager's resources.

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    • -0
    • +6
    /src/jalview/api/AlignCalcManagerI2.java
    • -0
    • +4
    /src/jalview/bin/Jalview.java
    • -0
    • +1
    /src/jalview/viewmodel/AlignmentViewport.java
    • -42
    • +108
    /src/jalview/workers/AlignCalcManager2.java
Thursday 22 Oct
2:48 pm

Mungo Carstairs

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
2:48 pm

Mungo Carstairs

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

Mungo Carstairs

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
10:40 am

Mungo Carstairs

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
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
4:14 pm

Jim Procter

Merge branch 'releases/Release_2_11_1_Branch'

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3:18 pm

Mateusz Warowny

JAL-3690 Documentation for AlignCalcListener

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    • -0
    • +27
    /src/jalview/api/AlignCalcListener.java
2:54 pm

Mateusz Warowny

JAL-3690 Catch and notify about worker cancellation separately.

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    • -0
    • +1
    /src/jalview/api/AlignCalcListener.java
    • -0
    • +17
    /src/jalview/workers/AlignCalcManager2.java
2:51 pm

Mateusz Warowny

JAL-3690 Fix concurrent modification exception when workers are cancelled

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    • -26
    • +32
    /src/jalview/workers/AlignCalcManager2.java
2:45 pm

Mateusz Warowny

JAL-3690 Documentation for AlignCalcManagerI2

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    • -0
    • +88
    /src/jalview/api/AlignCalcManagerI2.java
Tuesday 20 Oct
5:23 pm

Jim Procter

JAL-3765 fix test

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    • -0
    • +13
    /test/jalview/analysis/FinderTest.java
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
5:13 pm

Jim Procter

fix for JAL-3765

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    • -1
    • +1
    /src/jalview/analysis/Finder.java
Monday 19 Oct
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
11:59 am

Jim Procter

not related to JAL-3765 ! Actually related to JAL-3675!

not related to JAL-3765 ! Actually related to JAL-3675!