jalview

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Commits this week: 2
Total Committers: 72
Last Commit:
Commits this week: 2

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Friday 20 Nov 2020
11:58 am

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

JAL-3761 debugged and working (but not tidied) locateInFrom2/To2

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    • -33
    • +98
    /src/jalview/util/MapList.java
    • -102
    • +281
    /test/jalview/util/MapListTest.java
Thursday 19 Nov 2020
5:58 pm

Ben Soares

JAL-3521 removed unnecessary parts of the ext project in build.gradle

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    • -327
    • +6
    /build.gradle
4:17 pm

Ben Soares

JAL-3521 Minimal plugins and tasks needed to run tests and build jalview.jar

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    • -1034
    • +5
    /build.gradle
Friday 13 Nov 2020
6:10 pm

Ben Soares

JAL-3775 Re-compiled Getdown jars

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    • -1
    • +1
    /getdown/lib/FJVL_VERSION
    • -1
    • +1
    /getdown/lib/JVL_VERSION
    • binary
    /getdown/lib/getdown-core.jar
    • binary
    /getdown/lib/getdown-launcher-local.jar
    • binary
    /getdown/lib/getdown-launcher.jar
    • -1
    • +1
    /getdown/src/getdown/ant/pom.xml
    • -1
    • +1
    /getdown/src/getdown/core/pom.xml
    • -1
    • +1
    /getdown/src/getdown/launcher/pom.xml
    • -1
    • +1
    /getdown/src/getdown/mvn_cmd
    • -1
    • +1
    /getdown/src/getdown/pom.xml
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar
6:09 pm

Ben Soares

JAL-3775 Eclipse re-formatting commit

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    • -3
    • +2
    /src/jalview/gui/AlignFrame.java
    • -79
    • +82
    /src/jalview/gui/Desktop.java
    • -24
    • +20
    /src/jalview/gui/Preferences.java
    • -6
    • +6
    /src/jalview/io/BackupFiles.java
    • -29
    • +26
    /src/jalview/jbgui/GPreferences.java
    • -155
    • +157
    /src/jalview/project/Jalview2XML.java
3:51 pm

Mateusz Warowny

JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker

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    • -1
    • +1
    /src/jalview/api/PollableAlignCalcWorkerI.java
    • -0
    • +6
    /src/jalview/gui/AlignFrame.java
    • -0
    • +7
    /src/jalview/gui/Desktop.java
    • -0
    • +7
    /src/jalview/gui/IProgressIndicator.java
    • -0
    • +6
    /src/jalview/gui/PCAPanel.java
    • -0
    • +17
    /src/jalview/gui/ProgressBar.java
    • -0
    • +6
    /src/jalview/gui/StructureChooser.java
    • -0
    • +6
    /src/jalview/gui/WebserviceInfo.java
    • -1
    • +1
    /src/jalview/workers/AlignCalcManager.java
    • -8
    • +11
    /src/jalview/workers/AlignCalcManager2.java
    • -179
    • +122
    /src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
Thursday 12 Nov 2020
3:13 pm

Mateusz Warowny

JAL-3690 - fixed state inconsistency when restarting the calcworker

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    • -54
    • +22
    /src/jalview/workers/AlignCalcManager2.java
2:36 pm

Jim Procter

Merge branch 'feature/JAL-3469clinvarVCF' into spike/clinvar

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    • -7
    • +24
    /src/jalview/io/vcf/VCFLoader.java
    • -2
    • +8
    /test/jalview/io/vcf/VCFLoaderTest.java
2:27 pm

Ben Soares

JAL-3628 Error when saving alert box has been moved in develop for JS, adding Platform.isHeadless test to new isSaveAlignmentSuccessful method.

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    • -18
    • +14
    /src/jalview/gui/AlignFrame.java
10:03 am

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

JAL-3761 locateInFrom2 work in progress commit

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    • -10
    • +254
    /src/jalview/util/MapList.java
    • -16
    • +35
    /src/jalview/util/MappingUtils.java
    • -22
    • +128
    /test/jalview/util/MapListTest.java
Wednesday 11 Nov 2020
6:42 pm

Mateusz Warowny

JAL-3690 partially reworked AlignCalcManager

todo:

- modify SeqAnnotationServiceCalcWorker to implement PollableAlignCalcWorkerI

- fix race condition where worker state gets overriden by the old job (QUEUED to IDLE)

Options
    • -14
    • +3
    /src/jalview/api/AlignCalcWorkerI.java
    • -0
    • +18
    /src/jalview/api/PollableAlignCalcWorkerI.java
    • -183
    • +304
    /src/jalview/workers/AlignCalcManager2.java
Friday 06 Nov 2020
5:05 pm

Ben Soares

JAL-3609 formatting save after cherry-picks

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    • -46
    • +46
    /getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java
    • -46
    • +46
    /src/jalview/bin/MemorySetting.java
Thursday 05 Nov 2020
4:01 pm

Ben Soares

JAL-3608 cherry pick of 92cb745e7

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    • -35
    • +64
    /src/jalview/bin/Cache.java
    • -104
    • +141
    /src/jalview/bin/Jalview.java
Thursday 29 Oct 2020
9:34 pm

Jim Procter

Merge branch 'releases/Release_2_11_1_Branch'

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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
3:50 pm

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

JAL-3761 unit test for MapList.countPos()

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    • -0
    • +64
    /test/jalview/util/MapListTest.java
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
2:26 pm

Ben Soares

JAL-3248 Added mention of version 'TEST' in shadow jar filename in building.md/html since develop branch currently uses this by default.

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    • -1
    • +1
    /doc/building.html
    • -1
    • +1
    /doc/building.md
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
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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4:04 pm

Jim Procter

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

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