jalview

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Commits this week: 8
Total Committers: 73
Last Commit:
Commits this week: 8

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Monday 26 Feb 2018
10:41 am

Kira Mourão

JAL-2909 Changes to htsjdk import control

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    • +2
    /utils/checkstyle/import-control.xml
10:41 am

Kira Mourão

JAL-2909 Cigar parsing tests

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    • -0
    • +130
    /test/jalview/datamodel/CigarParserTest.java
10:13 am

Jim Procter

Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

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    • -2
    • +0
    /build.xml
10:12 am

Jim Procter

JAL-984 remove all references to idwidth.gif - in build.xml too :)

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    • -2
    • +0
    /build.xml
Friday 23 Feb 2018
4:54 pm

Jim Procter

JAL-2885 release notes

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    • +3
    /help/html/releases.html
4:12 pm

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

JAL-2599 corrected case-insensitive symbol indexing

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    /src/jalview/datamodel/HiddenMarkovModel.java
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    • +2
    /test/jalview/datamodel/HiddenMarkovModelTest.java
4:01 pm

Jim Procter

Merge branch 'features/JAL-2885UniprotHttps' into releases/Release_2_10_4_Branch

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    • +24
    /src/jalview/ext/ensembl/EnsemblLookup.java
    • -4
    • +31
    /src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
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    • +2
    /test/jalview/ext/ensembl/EnsemblGeneTest.java
3:52 pm

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

JAL-2599 parser and datamodel use primitive double[] not List<Double>

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    • -5
    • +6
    /src/jalview/analysis/AAFrequency.java
    • -25
    • +31
    /src/jalview/datamodel/HMMNode.java
    • -497
    • +124
    /src/jalview/datamodel/HiddenMarkovModel.java
    • -342
    • +250
    /src/jalview/io/HMMFile.java
    • -2
    • +2
    /test/jalview/datamodel/HiddenMarkovModelTest.java
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    • +3
    /test/jalview/hmmer/HMMERTest.java
    • -176
    • +160
    /test/jalview/io/HMMFileTest.java
    • -1
    • +1
    /test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
11:40 am

Jim Procter

JAL-2885 xfam https

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    /src/jalview/ws/dbsources/Pfam.java
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    /src/jalview/ws/dbsources/Rfam.java
11:39 am

Jim Procter

JAL-2885 XFAM_DOMAIN->XFAM_BASEURL

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    • +4
    /src/jalview/ws/dbsources/Pfam.java
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    /src/jalview/ws/dbsources/Rfam.java
11:35 am

Jim Procter

JAL-2885 Ensembl* -> https

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    • -2
    • +2
    /src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
11:33 am

Jim Procter

JAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL

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    /src/jalview/ext/ensembl/EnsemblGenomes.java
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    • +5
    /src/jalview/ext/ensembl/EnsemblRestClient.java
    • -7
    • +10
    /src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
11:24 am

Jim Procter

JAL-2885 renamed base URL getter from getDomain..

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    • +1
    /src/jalview/ws/dbsources/Pfam.java
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    • +1
    /src/jalview/ws/dbsources/Rfam.java
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    • +7
    /src/jalview/ws/dbsources/Xfam.java
Thursday 22 Feb 2018
4:05 pm

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

JAL-2629 tidy tests, refactor hmmer node mapping slightly

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    • -87
    • +85
    /src/jalview/datamodel/HiddenMarkovModel.java
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    • +4
    /src/jalview/datamodel/Sequence.java
    • -0
    • +6
    /src/jalview/datamodel/SequenceI.java
    • -0
    • +5
    /src/jalview/hmmer/HMMAlignThread.java
    • -4
    • +4
    /src/jalview/hmmer/HMMBuildThread.java
    • -39
    • +57
    /src/jalview/io/HMMFile.java
    • -45
    • +57
    /test/jalview/hmmer/HMMERTest.java
    • -0
    • +88
    /test/jalview/hmmer/testProps.jvprops
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    • +40
    /test/jalview/io/HMMFileTest.java
3:15 pm

Jim Procter

Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

Options
3:14 pm

Jim Procter

JAL-984 ID width adjuster needs to be white !

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    • +2
    /src/jalview/appletgui/IdwidthAdjuster.java
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    • +5
    /src/jalview/gui/IdwidthAdjuster.java
3:05 pm

Jim Procter

JAL-2666 release notes

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    • +3
    /help/html/releases.html
2:48 pm

Jim Procter

Merge branch 'bug/JAL-2666' into releases/Release_2_10_4_Branch

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    • -29
    • +0
    /src/jalview/gui/AlignmentPanel.java
2:34 pm

Jim Procter

Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

Options
2:34 pm

Jim Procter

JAL-984 remove all references to idwidth.gif and use int constants in place of width/height of image when switching between margin adjustment active/inactive mouse cursor

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    /resources/images/idwidth.gif
    • -18
    • +12
    /src/jalview/appletgui/AnnotationLabels.java
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    • +0
    /src/jalview/appletgui/IdwidthAdjuster.java
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    • +9
    /src/jalview/gui/AnnotationLabels.java
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    • +0
    /src/jalview/gui/IdwidthAdjuster.java
2:16 pm

Jim Procter

JAL-2906 typo fixes

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    • +1
    /help/html/features/splitView.html
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    • +1
    /help/html/releases.html
2:15 pm

Jim Procter

JAL-984 release notes

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    • +1
    /help/html/releases.html
2:08 pm

Jim Procter

Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

Options
2:08 pm

Jim Procter

JAL-294 remove unneeded paint() method

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    • -16
    • +0
    /src/jalview/appletgui/IdwidthAdjuster.java
2:07 pm

Jim Procter

JAL-984 remove commented/unnecessary if clause

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    • -8
    • +2
    /src/jalview/appletgui/AnnotationLabels.java
    • -5
    • +1
    /src/jalview/gui/AnnotationLabels.java
1:43 pm

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

JAL-2629 tidy unit tests, constants etc

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    • +72
    /src/jalview/analysis/AAFrequency.java
    • -1
    • +1
    /src/jalview/datamodel/AlignmentAnnotation.java
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    • +40
    /src/jalview/datamodel/HiddenMarkovModel.java
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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceGroup.java
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    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/io/HMMFile.java
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    /src/jalview/renderer/AnnotationRenderer.java
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    /src/jalview/viewmodel/AlignmentViewport.java
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    /src/jalview/workers/InformationThread.java
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    /test/jalview/analysis/AAFrequencyTest.java
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    • +108
    /test/jalview/datamodel/HiddenMarkovModelTest.java
Wednesday 21 Feb 2018
5:40 pm

Jim Procter

JAL-2906 release notes for 2.10.4

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    • +23
    /help/html/releases.html
5:19 pm

Jim Procter

Merge branch 'bug/JAL-2778again' into releases/Release_2_10_4_Branch

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    /src/jalview/datamodel/Alignment.java
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    /src/jalview/gui/AnnotationPanel.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/IdCanvas.java
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    /src/jalview/gui/ScalePanel.java
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    /src/jalview/gui/SeqCanvas.java
4:28 pm

Jim Procter

JAL-2778 reinstate transparent windows to avoid ugly borders on OSX

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    /src/jalview/gui/Desktop.java
4:18 pm

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

JAL-2629 simplifying method signatures in Hmmer command classes

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/hmmer/HMMAlignThread.java
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    /src/jalview/hmmer/HMMBuildThread.java
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    /src/jalview/hmmer/HMMERParamStore.java
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    /src/jalview/hmmer/HMMSearchThread.java
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    /src/jalview/hmmer/HmmerCommand.java
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    /test/jalview/hmmer/HMMERTest.java