jalview

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Wednesday 23 Sep 2020
4:39 pm

Jim Procter

JAL-3748 more tests verifying reconstruction of AlignemntView for linked CDS/Protein alignment and selected region

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    • +6
    /test/jalview/gui/SplitFrameTest.java
4:38 pm

Jim Procter

JAL-3748 reusable assert to trace specific issues with recovering the correct Sequence/Mapping (highlights points of failure for AlignmentUtilsTests with patch

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    • -1
    • +44
    /test/jalview/analysis/AlignmentUtilsTests.java
4:35 pm

Jim Procter

JAL-3748 allow AlignedCodonFrame.covers to optionally only require coverage for either originating or mapped sequence.

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    • -16
    • +45
    /src/jalview/datamodel/AlignedCodonFrame.java
Tuesday 22 Sep 2020
3:30 pm

Jim Procter

JAL-3748 test data for SplitFrameTest

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    • binary
    /examples/testdata/MN908947.jvp
3:09 pm

Jim Procter

JAL-3748 don’t trash start/end on SequenceI reconstructed from a SeqCigar via SeqsetUtils.SeqCharacterUnhash

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    • -3
    • +17
    /src/jalview/analysis/SeqsetUtils.java
    • -1
    • +1
    /src/jalview/datamodel/SeqCigar.java
2:45 pm

Jim Procter

JAL-3748 simple test for SeqCigar preservation of start/end and name for different ways of constructing SeqCigar and reconstructing alignment sequences

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    • -0
    • +23
    /test/jalview/datamodel/SeqCigarTest.java
2:30 pm

Jim Procter

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

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    • -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

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    • -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

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

Ben Soares

JAL-3753 JAL-3754 first rejig

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    • +90
    /build.gradle
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    /gradle.properties
12:09 pm

Ben Soares

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

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    /.gitignore
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    /build.gradle
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    /gradle.properties
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    /resources/images/JalviewDevelopLogo_Huge.png
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    /resources/images/Jalview_Develop_Logo.png
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    /resources/images/Jalview_Logo.png
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    /resources/images/jalview_logos.icns
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    /resources/images/jalview_logos.ico
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    /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
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    /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

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    /.gitignore
    • -3
    • +39
    /build.gradle
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    /gradle.properties
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    /resources/images/JalviewDevelopLogo_Huge.png
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    /resources/images/Jalview_Develop_Logo.png
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    /resources/images/Jalview_Logo.png
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    /resources/images/jalview_logos.icns
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    /resources/images/jalview_logos.ico
    • -0
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    /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
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    /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'

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1:38 pm

Jim Procter

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

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    • +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!)

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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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    /src/jalview/bin/Cache.java
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    /src/jalview/bin/Jalview.java
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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
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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

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    /src/jalview/bin/Jalview.java
11:35 am

Jim Procter

JAL-3675 patch release date 17th September 2020

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    • +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

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    /src/jalview/datamodel/AlignedCodonFrame.java
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    /test/jalview/datamodel/AlignedCodonFrameTest.java
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    /test/jalview/util/MappingUtilsTest.java
11:19 am

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

JAL-3700 additions and corrections to unit tests

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    • -4
    • +4
    /src/jalview/datamodel/AlignedCodonFrame.java
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    • +62
    /test/jalview/datamodel/AlignedCodonFrameTest.java
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    /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

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    • -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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    • +3
    /src/jalview/analysis/AlignmentUtils.java
    • -0
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    /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

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    • +9
    /src/jalview/api/AlignViewportI.java
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    /src/jalview/datamodel/AlignmentView.java
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    /src/jalview/viewmodel/AlignmentViewport.java
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    • +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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    /help/help/html/releases.html
4:48 pm

Jim Procter

JAL-3765 JAL-3718 release notes

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    /help/help/html/releases.html

changeset discussion

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