jalview

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Commits this week: 17
Total Committers: 73
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Commits this week: 17

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Sunday 27 Aug 2017
6:50 pm

Jim Procter

Merge branch 'develop' into features/JAL-250_hideredundantseqs

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    • -274
    • +130
    /src/jalview/analysis/AlignSeq.java
    • -103
    • +82
    /src/jalview/controller/AlignViewController.java
    • -9
    • +10
    /src/jalview/gui/RedundancyPanel.java
Friday 25 Aug 2017
9:27 am

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

JAL-2480 suppress debug timing output that got left in

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    • -6
    • +5
    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
Wednesday 23 Aug 2017
2:42 pm

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

JAL-2435 last lost commit e926a5d redone

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    • -9
    • +4
    /src/jalview/gui/FontChooser.java
11:48 am

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

JAL-2481 a smidgin more test coverage of findFeatures

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    • -0
    • +9
    /test/jalview/datamodel/SequenceTest.java
Tuesday 22 Aug 2017
4:03 pm

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

JAL-2680 remove all mappings in test teardown

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    • -2
    • +15
    /test/jalview/io/FeaturesFileTest.java
1:36 pm

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

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

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Monday 21 Aug 2017
3:20 pm

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

JAL-2680 clear down all mappings before test

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    • -6
    • +14
    /test/jalview/gui/AlignViewportTest.java
2:47 pm

Jim Procter

Merge branch 'documentation/JAL-2675_release2102b1' into develop

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2:46 pm

Jim Procter

JAL-2675 typo in what's new href

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    • -1
    • +1
    /help/html/whatsNew.html
2:06 pm

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

Merge branch 'develop' into features/JAL-2446NCList

Conflicts:

src/MCview/PDBChain.java

src/jalview/analysis/AlignmentSorter.java

src/jalview/analysis/AlignmentUtils.java

src/jalview/analysis/Dna.java

src/jalview/appletgui/AlignFrame.java

src/jalview/appletgui/FeatureRenderer.java

src/jalview/appletgui/Finder.java

src/jalview/appletgui/SeqPanel.java

src/jalview/commands/EditCommand.java

src/jalview/datamodel/AlignedCodonFrame.java

src/jalview/datamodel/Sequence.java

src/jalview/datamodel/SequenceFeature.java

src/jalview/datamodel/xdb/embl/EmblEntry.java

src/jalview/ext/ensembl/EnsemblGene.java

src/jalview/gui/AlignmentPanel.java

src/jalview/gui/AnnotationExporter.java

src/jalview/gui/CutAndPasteTransfer.java

src/jalview/gui/FeatureRenderer.java

src/jalview/gui/Finder.java

src/jalview/gui/PopupMenu.java

src/jalview/gui/SeqCanvas.java

src/jalview/gui/SeqPanel.java

src/jalview/io/FeaturesFile.java

src/jalview/io/JSONFile.java

src/jalview/io/gff/InterProScanHelper.java

src/jalview/io/vamsas/Datasetsequence.java

src/jalview/renderer/seqfeatures/FeatureRenderer.java

src/jalview/util/RangeComparator.java

src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java

src/jalview/ws/jws2/AADisorderClient.java

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    • -24
    • +22
    /src/MCview/PDBChain.java
    • -19
    • +20
    /src/jalview/analysis/AAFrequency.java
    • -31
    • +10
    /src/jalview/analysis/AlignmentSorter.java
    • -86
    • +91
    /src/jalview/analysis/AlignmentUtils.java
    • -15
    • +17
    /src/jalview/analysis/Conservation.java
    • -48
    • +48
    /src/jalview/analysis/CrossRef.java
    • -11
    • +14
    /src/jalview/analysis/Dna.java
    • -9
    • +11
    /src/jalview/analysis/Rna.java
    • -7
    • +7
    /src/jalview/analysis/SeqsetUtils.java
    • -2
    • +2
    /src/jalview/analysis/scoremodels/FeatureDistanceModel.java
    • -106
    • +116
    /src/jalview/appletgui/APopupMenu.java
    • -279
    • +277
    /src/jalview/appletgui/AlignFrame.java
    • -19
    • +21
    /src/jalview/appletgui/FeatureColourChooser.java
    • -12
    • +16
    /src/jalview/appletgui/FeatureRenderer.java
    • -28
    • +36
    /src/jalview/appletgui/FeatureSettings.java
  16. … 66 more files in changeset.
Friday 18 Aug 2017
2:15 pm

Jim Procter

JAL-2675 bump version for branch to 2.10.2b1

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    • -1
    • +1
    /RELEASE
2:13 pm

Jim Procter

JAL-1551 formatting

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    • -16
    • +17
    /help/html/releases.html
2:08 pm

Jim Procter

JAL-2675 release notes entry for 2.10.2b1, updated what’s new and link to latest notes in help.

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    • -1
    • +1
    /help/help.jhm
    • -0
    • +18
    /help/html/releases.html
    • -6
    • +14
    /help/html/whatsNew.html
Thursday 17 Aug 2017
1:07 pm

Jim Procter

JAL-2418 ahem - correct year for what's new

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    • -1
    • +1
    /help/html/whatsNew.html
12:37 pm

Jim Procter

JAL-2418 JAL-2116 use single j2se 7+ argumant with java 9 add-modules - seems to work on java 8 (windows, osx, linux) without 'use latest version' popup and also on java 9

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    • -1
    • +1
    /build.xml
11:41 am

Jim Procter

JAL-2418 JAL-2116 make sure java 8,7 vm args are also listed

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    • -2
    • +1
    /build.xml
Wednesday 16 Aug 2017
11:24 pm

Jim Procter

Merge branch 'develop' into releases/Release_2_10_2_Branch

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11:24 pm

Jim Procter

Merge branch 'documentation/JAL-2418_release2102' into develop

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11:23 pm

Jim Procter

JAL-2418 formatting

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    • -8
    • +12
    /help/html/whatsNew.html
11:23 pm

Jim Procter

JAL-2418 occupancy row in What’s New

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    • -0
    • +9
    /help/html/whatsNew.html
10:37 pm

Jim Procter

Merge branch 'develop' into releases/Release_2_10_2_Branch

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10:30 pm

Jim Procter

JAL-2418 add GPL to main sources

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    • -0
    • +20
    /src/jalview/analysis/AverageDistanceTree.java
    • -0
    • +20
    /src/jalview/analysis/TreeBuilder.java
    • -0
    • +20
    /src/jalview/analysis/scoremodels/DistanceScoreModel.java
    • -0
    • +20
    /src/jalview/analysis/scoremodels/PIDModel.java
    • -0
    • +20
    /src/jalview/analysis/scoremodels/ScoreModels.java
    • -0
    • +20
    /src/jalview/analysis/scoremodels/SimilarityParams.java
    • -0
    • +20
    /src/jalview/analysis/scoremodels/SimilarityScoreModel.java
    • -0
    • +20
    /src/jalview/api/AlignmentColsCollectionI.java
    • -0
    • +20
    /src/jalview/api/AlignmentRowsCollectionI.java
    • -0
    • +20
    /src/jalview/api/analysis/PairwiseScoreModelI.java
    • -0
    • +20
    /src/jalview/api/analysis/ScoreModelI.java
    • -0
    • +20
    /src/jalview/api/analysis/SimilarityParamsI.java
    • -0
    • +20
    /src/jalview/ext/rbvi/chimera/AtomSpecModel.java
    • -0
    • +20
    /src/jalview/gui/ColourMenuHelper.java
    • -0
    • +20
    /src/jalview/gui/ComboBoxTooltipRenderer.java
  16. … 23 more files in changeset.
10:22 pm

Jim Procter

JAL-2418 source formatting

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    • -25
    • +36
    /src/MCview/AppletPDBCanvas.java
    • -10
    • +10
    /src/MCview/AppletPDBViewer.java
    • -24
    • +35
    /src/MCview/PDBCanvas.java
    • -21
    • +24
    /src/MCview/PDBChain.java
    • -7
    • +5
    /src/MCview/PDBfile.java
    • -19
    • +20
    /src/jalview/analysis/AAFrequency.java
    • -21
    • +26
    /src/jalview/analysis/AlignSeq.java
    • -5
    • +4
    /src/jalview/analysis/AlignmentAnnotationUtils.java
    • -26
    • +24
    /src/jalview/analysis/AlignmentSorter.java
    • -95
    • +101
    /src/jalview/analysis/AlignmentUtils.java
    • -5
    • +8
    /src/jalview/analysis/AnnotationSorter.java
    • -2
    • +2
    /src/jalview/analysis/AverageDistanceTree.java
    • -15
    • +17
    /src/jalview/analysis/Conservation.java
    • -48
    • +48
    /src/jalview/analysis/CrossRef.java
    • -14
    • +18
    /src/jalview/analysis/Dna.java
  16. … 450 more files in changeset.
9:52 pm

Jim Procter

Merge branch 'develop' into releases/Release_2_10_2_Branch

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9:52 pm

Jim Procter

Merge branch 'documentation/JAL-2418_release2102' into develop

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9:52 pm

Jim Procter

JAL-2418 mirror fonts option doc tweak

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    • -6
    • +5
    /help/html/features/splitView.html
8:17 pm

Jim Procter

Merge branch 'documentation/JAL-2418_release2102' into develop

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8:17 pm

Jim Procter

JAL-2418 whats new for 2.10.2

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    • -47
    • +67
    /help/html/whatsNew.html
8:16 pm

Jim Procter

JAL-2418 reclassify some issues to features/bugs resolved

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    • -9
    • +9
    /help/html/releases.html
7:23 pm

Jim Procter

JAL-2418 typos in release notes

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