jalview

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Tuesday 22 Sep 2020
2:30 pm

Jim Procter

JAL-3748 additional asserts to verify start/end after reconstructing sequence from seqCigar

Options
    • -3
    • +11
    /test/jalview/datamodel/SeqCigarTest.java
Monday 21 Sep 2020
12:01 pm

Jim Procter

Merge branch 'merge_review/JAL-3490_2_11_2_develop' into develop

Options
    • -3
    • +2
    /src/jalview/gui/AlignFrame.java
Sunday 20 Sep 2020
8:33 pm

Ben Soares

JAL-3753 put resources in gradle run and test path

Options
    • -1
    • +0
    /.gitignore
    • -64
    • +75
    /build.gradle
Friday 18 Sep 2020
6:18 pm

Ben Soares

JAL-3753 JAL-3754 first rejig

Options
    • -73
    • +90
    /build.gradle
    • -1
    • +0
    /gradle.properties
12:09 pm

Ben Soares

JAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

Options
    • -0
    • +2
    /.gitignore
    • -2
    • +30
    /build.gradle
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    • +13
    /gradle.properties
    • binary
    /resources/images/JalviewDevelopLogo_Huge.png
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    /resources/images/Jalview_Develop_Logo.png
    • binary
    /resources/images/Jalview_Logo.png
    • binary
    /resources/images/jalview_logos.icns
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    /resources/images/jalview_logos.ico
    • -0
    • +4
    /utils/channels/develop_properties
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    /utils/channels/release_properties
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    /utils/getdown/Jalview-Logo.png
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    /utils/getdown/develop/Jalview-Logo.png
    • binary
    /utils/getdown/develop/jalview_logo_background_blur-640x480.xcf
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    /utils/getdown/develop/jalview_logo_background_getdown-640x480.png
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    /utils/getdown/develop/jalview_logo_background_getdown-progress.png
  16. … 31 more files in changeset.
12:09 pm

Ben Soares

JAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

Options
    • -0
    • +1
    /.gitignore
    • -3
    • +39
    /build.gradle
    • -9
    • +13
    /gradle.properties
    • binary
    /resources/images/JalviewDevelopLogo_Huge.png
    • binary
    /resources/images/Jalview_Develop_Logo.png
    • binary
    /resources/images/Jalview_Logo.png
    • binary
    /resources/images/jalview_logos.icns
    • binary
    /resources/images/jalview_logos.ico
    • -0
    • +4
    /utils/channels/develop_properties
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    • +4
    /utils/channels/release_properties
    • binary
    /utils/getdown/Jalview-Logo.png
    • binary
    /utils/getdown/develop/Jalview-Logo.png
    • binary
    /utils/getdown/develop/jalview_logo_background_blur-640x480.xcf
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    /utils/getdown/develop/jalview_logo_background_getdown-640x480.png
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    /utils/getdown/develop/jalview_logo_background_getdown-progress.png
  16. … 31 more files in changeset.
Thursday 17 Sep 2020
6:47 pm

Jim Procter

Merge branch 'releases/Release_2_11_1_Branch'

Options
1:38 pm

Jim Procter

JAL-3675 release notes for JAL-3750 JAL-3751

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    • -0
    • +8
    /help/help/html/releases.html
12:28 pm

Jim Procter

Merge branch 'patch/JAL-3750_JAL-3741_https_patch' into releases/Release_2_11_1_Branch

Options
12:19 pm

Jim Procter

JAL-3741 http to https (and jar to jvp for exampleFile defaults!)

Options
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    /help/help/html/features/commandline.html
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    /help/help/html/features/groovy.html
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    /help/help/html/features/jvlfiles.html
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    /help/help/html/groovy/featuresCounter.html
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    /help/help/html/index.html
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    /help/help/html/memory.html
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    /help/help/html/webServices/newsreader.html
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    • +3
    /src/jalview/bin/Cache.java
    • -6
    • +9
    /src/jalview/bin/Jalview.java
    • -1
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    /src/jalview/gui/BlogReader.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/Preferences.java
    • -1
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    /src/jalview/io/JSONFile.java
12:09 pm

Jim Procter

JAL-3750 parse protocol before checking if argument to -open can be opened as a file

Options
    • -3
    • +5
    /src/jalview/bin/Jalview.java
11:35 am

Jim Procter

JAL-3675 patch release date 17th September 2020

Options
    • -1
    • +1
    /help/help/html/releases.html
11:19 am

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

JAL-3700 additions and corrections to unit tests (trivial) Conflicts: test/jalview/util/MappingUtilsTest.java

Options
    • -4
    • +4
    /src/jalview/datamodel/AlignedCodonFrame.java
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    /test/jalview/datamodel/AlignedCodonFrameTest.java
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    • +306
    /test/jalview/util/MappingUtilsTest.java
11:19 am

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

JAL-3700 additions and corrections to unit tests

Options
    • -4
    • +4
    /src/jalview/datamodel/AlignedCodonFrame.java
    • -3
    • +62
    /test/jalview/datamodel/AlignedCodonFrameTest.java
    • -172
    • +306
    /test/jalview/util/MappingUtilsTest.java
Wednesday 16 Sep 2020
5:46 pm

Jim Procter

JAL-3748 preserve sequence IDs from original alignment view when alignment returned by web service or analysis method.

Options
    • -0
    • +1
    /src/jalview/datamodel/SeqCigar.java
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

Options
    • -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

Options
    • -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

Options
    • -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

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

Jim Procter

JAL-3765 JAL-3718 release notes

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    • +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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    /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
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    /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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    /getdown/lib/FJVL_VERSION
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    /getdown/lib/JVL_VERSION
    • binary
    /getdown/lib/getdown-core.jar
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    /getdown/lib/getdown-launcher-local.jar
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    /getdown/lib/getdown-launcher.jar
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    /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
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    /j11lib/getdown-core.jar
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    /j8lib/getdown-core.jar
4:08 pm

Ben Soares

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

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

Jim Procter

JAL-3675 typo in release notes :(

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    • +0
    /help/help/html/releases.html
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    /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