jalview

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Commits this week: 10
Total Committers: 73
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Commits this week: 10

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Wednesday 16 Sep 2020
5:45 pm

Jim Procter

JAL-3748 recover complement alignment from complement alignmentView rather than let ‘alignAs’ to do the work

Options
    • -14
    • +18
    /src/jalview/ws/jws2/MsaWSThread.java
5:43 pm

Jim Procter

JAL-3748 make findAlignedSequence require mapped from/to to properly contain the given CDS or protein sequence

Options
    • -2
    • +6
    /src/jalview/datamodel/AlignedCodonFrame.java
5:39 pm

Jim Procter

JAL-3748 pass a list to findAlignedSequence to return mapping that relates CDS and the returned Peptide sequence to avoid searching twice

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    • -2
    • +3
    /src/jalview/analysis/AlignmentUtils.java
    • -0
    • +22
    /src/jalview/datamodel/AlignedCodonFrame.java
5:37 pm

Jim Procter

JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq,true) to select the protein that matches a CDS sequence

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    • -3
    • +2
    /src/jalview/datamodel/AlignedCodonFrame.java
5:33 pm

Jim Procter

JAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true) to verify mapping matches seq’s dataset sequence start/end rather than seq

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    • -2
    • +24
    /src/jalview/datamodel/AlignedCodonFrame.java
10:06 am

Jim Procter

Merge branch 'failingTest/JAL-3748_reconstructCDSafterProteinMSA' into cherry-pick/JAL-3700mapSequenceSelection

Options
7:02 am

Jim Procter

JAL-3748 store an AlignmentView for the complement within an viewport’s AlignView so it can be recovered after a web service operation

Options
    • -0
    • +9
    /src/jalview/api/AlignViewportI.java
    • -0
    • +31
    /src/jalview/datamodel/AlignmentView.java
    • -2
    • +20
    /src/jalview/viewmodel/AlignmentViewport.java
    • -0
    • +185
    /test/jalview/gui/SplitFrameTest.java
Tuesday 15 Sep 2020
6:05 pm

Jim Procter

JAL-3675 logged JAL-3748 as known defect

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    • -0
    • +6
    /help/help/html/releases.html
4:48 pm

Jim Procter

JAL-3765 JAL-3718 release notes

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    • -1
    • +8
    /help/help/html/releases.html

changeset discussion

  1. Jim Procter: not related to JAL-3765 ! Actually related to JAL-3675!
4:34 pm

Jim Procter

Merge branch 'patch/JAL-3718_fixed_getdown_patched_for_Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

Options
4:17 pm

Ben Soares

JAL-3718 Fixed getdown auto-update. This commit Getdown jars and version files.

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    • +1
    /getdown/lib/FJVL_VERSION
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    /getdown/lib/JVL_VERSION
    • binary
    /getdown/lib/getdown-core.jar
    • binary
    /getdown/lib/getdown-launcher-local.jar
    • binary
    /getdown/lib/getdown-launcher.jar
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar
4:09 pm

Ben Soares

JAL-3718 fixed getdown auto-update for future updates. Getdown Jars and version files.

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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
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    /getdown/src/getdown/core/pom.xml
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    /getdown/src/getdown/launcher/pom.xml
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    /getdown/src/getdown/pom.xml
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar
4:08 pm

Ben Soares

JAL-3718 fixed getdown auto-update for future updates. Getdown src files only

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    • -0
    • +2
    /getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
    • -1
    • +1
    /getdown/src/getdown/mvn_cmd
1:52 pm

Jim Procter

JAL-3675 typo in release notes :(

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    • -1
    • +0
    /help/help/html/releases.html
    • -2
    • +3
    /help/help/html/whatsNew.html
12:43 pm

Jim Procter

JAL-3675 update release date and release notes for JAL-3732

Options
    • -1
    • +5
    /help/help/html/releases.html
Monday 14 Sep 2020
11:24 pm

Ben Soares

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

Options
11:23 pm

Ben Soares

JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown jar and version files

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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
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar
11:23 pm

Ben Soares

JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown src files

Options
    • -1
    • +1
    /getdown/src/getdown/ant/pom.xml
    • -1
    • +1
    /getdown/src/getdown/core/pom.xml
    • -0
    • +2
    /getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
    • -1
    • +1
    /getdown/src/getdown/launcher/pom.xml
    • -1
    • +1
    /getdown/src/getdown/mvn_cmd
    • -1
    • +1
    /getdown/src/getdown/pom.xml
11:23 pm

Ben Soares

JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown src files

Options
    • -1
    • +1
    /getdown/src/getdown/ant/pom.xml
    • -1
    • +1
    /getdown/src/getdown/core/pom.xml
    • -0
    • +2
    /getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
    • -1
    • +1
    /getdown/src/getdown/launcher/pom.xml
    • -1
    • +1
    /getdown/src/getdown/mvn_cmd
    • -1
    • +1
    /getdown/src/getdown/pom.xml
6:11 pm

Ben Soares

Merge branch 'feature/JAL-3615gzipXfam' into develop

Options
Thursday 10 Sep 2020
5:41 pm

Jim Procter

JAL-3746 bump release version for 2.11.2 series (currently on develop)

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    • -2
    • +2
    /RELEASE
3:27 pm

Ben Soares

JAL-3744 this obvious attempt to detect/gunzip file input for jalviewjs fails

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    • -4
    • +13
    /src/jalview/io/FileParse.java
12:28 pm

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

JAL-2422 comments updated re ALTLOC handling

Options
    • -5
    • +8
    /src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
Saturday 05 Sep 2020
6:07 pm

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

JAL-3576 unit test for preserving order of colocated features

Options
    • -2
    • +22
    /test/jalview/datamodel/features/FeatureStoreTest.java
Friday 04 Sep 2020
6:29 pm

Ben Soares

JAL-3679 Added externally specified plugins dir to J2sPlugin check

Options
    • -5
    • +20
    /build.gradle
6:29 pm

Ben Soares

JAL-3679 Added externally specified plugins dir to J2sPlugin check

Options
    • -5
    • +20
    /build.gradle
6:29 pm

Ben Soares

JAL-3679 Added externally specified plugins dir to J2sPlugin check

Options
    • -5
    • +20
    /build.gradle
Thursday 03 Sep 2020
4:27 pm

Ben Soares

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

Options
2:04 pm

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

JAL-3576 IntervalStore updated to v1.2

Options
    • binary
    /j11lib/intervalstore-v1.1.jar
    • binary
    /j11lib/intervalstore-v1.2.jar
    • binary
    /j8lib/intervalstore-v1.1.jar
    • binary
    /j8lib/intervalstore-v1.2.jar
    • -59
    • +68
    /test/jalview/io/vcf/VCFLoaderTest.java
1:43 pm

Jim Procter

JAL-3675 update release date and release notes for JAL-3280

Options
    • -1
    • +5
    /help/help/html/releases.html