jalview

Clone Tools

Stats

Commits this week: 0
Total Committers: 73
Last Commit:
Commits this week: 0

Lines of code count not available

Commit Activity

Commits By Day In Week
52 week commits volume
Commits By Day In Week
Commits by day
Commits By Day In Week
Commits by hour
Commits By Hour In Day
Commit calendar
 

Most active committers (90 days)

loading
loading
  • last updated a few seconds ago
All Commits Reviews
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
Thursday 08 Aug 2019
10:18 am

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

JAL-3402 suppress unmapped chains in View Chain menu

Options
    • -0
    • +4
    /src/jalview/gui/StructureViewerBase.java
10:16 am

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

JAL-3400 include sequence name in View | Show Chain menu

Options
    • -8
    • +0
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -14
    • +0
    /src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
    • -2
    • +44
    /src/jalview/gui/StructureViewerBase.java
    • -1
    • +1
    /src/jalview/jbgui/GStructureViewer.java
    • -0
    • +22
    /src/jalview/structure/StructureSelectionManager.java
    • -7
    • +13
    /src/jalview/structures/models/AAStructureBindingModel.java
    • -6
    • +0
    /test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
    • -13
    • +0
    /test/jalview/structures/models/AAStructureBindingModelTest.java
Wednesday 07 Aug 2019
4:56 pm

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

JAL-3390 showSelectedChains pulled up to base class for Jmol/Chimera

Options
    • -6
    • +9
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -7
    • +0
    /src/jalview/gui/AppJmol.java
    • -14
    • +0
    /src/jalview/gui/ChimeraViewFrame.java
    • -2
    • +17
    /src/jalview/gui/StructureViewerBase.java
    • -1
    • +1
    /src/jalview/structures/models/AAStructureBindingModel.java
2:19 pm

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

Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/ext/rbvi/chimera/ChimeraCommands.java

test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java

Options
    • -2
    • +2
    /gradle.properties
    • -1
    • +5
    /resources/lang/Messages.properties
    • -1
    • +5
    /resources/lang/Messages_es.properties
    • -8
    • +27
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -24
    • +132
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
    • -1
    • +2
    /src/jalview/gui/JalviewChimeraBindingModel.java
    • -3
    • +4
    /src/jalview/structures/models/AAStructureBindingModel.java
    • -21
    • +23
    /test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
    • binary
    /utils/testnglibs/testng-sources.jar
10:25 am

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

JAL-3187 (fudge) look in both alignments for stored mappings

Options
    • -0
    • +10
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
9:42 am

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

Merge branch 'develop' into feature/JAL-3187linkedFeatures

Options
    • -8
    • +8
    /src/jalview/project/Jalview2XML.java
Tuesday 06 Aug 2019
7:58 pm

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

JAL-3390 first pass refactoring for JalviewJmolBinding.showStructures

Options
    • -3
    • +3
    /src/jalview/appletgui/AppletJmol.java
    • -1
    • +1
    /src/jalview/appletgui/AppletJmolBinding.java
    • -14
    • +41
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -1
    • +78
    /src/jalview/ext/jmol/JmolCommands.java
    • -23
    • +10
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
    • -11
    • +11
    /src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
    • -1
    • +1
    /src/jalview/gui/StructureViewerBase.java
    • -6
    • +130
    /src/jalview/structures/models/AAStructureBindingModel.java
    • -24
    • +21
    /test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
    • -8
    • +5
    /test/jalview/structures/models/AAStructureBindingModelTest.java
1:05 pm

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

JAL-3390 pull up of getShownResidues() to AAStructureBindingModel

Options
    • -110
    • +35
    /src/jalview/ext/rbvi/chimera/AtomSpecModel.java
    • -76
    • +135
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
    • -101
    • +13
    /src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
    • -0
    • +96
    /src/jalview/structures/models/AAStructureBindingModel.java
    • -39
    • +0
    /test/jalview/ext/rbvi/chimera/AtomSpecModelTest.java
    • -9
    • +153
    /test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
Monday 05 Aug 2019
4:32 pm

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

JAL-3390 redraw structures if alignment only and hidden regions change

Options
    • -8
    • +0
    /src/jalview/api/structures/JalviewStructureDisplayI.java
    • -4
    • +6
    /src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
    • -6
    • +0
    /src/jalview/gui/StructureViewerBase.java
    • -3
    • +11
    /src/jalview/structures/models/AAStructureBindingModel.java
3:24 pm

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

JAL-3390 new View menu option to hide hidden regions in structure

Options
    • -0
    • +2
    /resources/lang/Messages.properties
    • -1
    • +4
    /resources/lang/Messages_es.properties
    • -4
    • +2
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -2
    • +12
    /src/jalview/ext/jmol/JmolCommands.java
    • -9
    • +40
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
    • -5
    • +3
    /src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
    • -1
    • +18
    /src/jalview/gui/StructureViewerBase.java
    • -0
    • +2
    /src/jalview/jbgui/GStructureViewer.java
    • -6
    • +30
    /src/jalview/structures/models/AAStructureBindingModel.java
    • -6
    • +8
    /test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
    • -2
    • +2
    /test/jalview/structures/models/AAStructureBindingModelTest.java
1:00 pm

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

JAL-3390 Chimera showStructures() respects visible/chain selections

Options
    • -1
    • +2
    /src/jalview/appletgui/AppletJmol.java
    • -7
    • +6
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -48
    • +22
    /src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
    • -1
    • +1
    /src/jalview/gui/AlignFrame.java
    • -15
    • +2
    /src/jalview/gui/AppJmol.java
    • -14
    • +6
    /src/jalview/gui/ChimeraViewFrame.java
    • -1
    • +2
    /src/jalview/gui/StructureViewerBase.java
    • -0
    • +25
    /src/jalview/jbgui/GStructureViewer.java
    • -1
    • +41
    /src/jalview/structures/models/AAStructureBindingModel.java
10:34 am

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

JAL-3390 pull-up refactoring towards functional changes...

Options
    • -0
    • +14
    /src/jalview/api/AlignmentViewPanel.java
    • -0
    • +2
    /src/jalview/api/structures/JalviewStructureDisplayI.java
    • -0
    • +12
    /src/jalview/appletgui/AlignmentPanel.java
    • -8
    • +8
    /src/jalview/gui/AlignFrame.java
    • -0
    • +6
    /src/jalview/gui/AlignmentPanel.java
    • -2
    • +3
    /src/jalview/gui/AppJmol.java
    • -15
    • +0
    /src/jalview/gui/AppJmolBinding.java
    • -2
    • +3
    /src/jalview/gui/ChimeraViewFrame.java
    • -15
    • +0
    /src/jalview/gui/JalviewChimeraBindingModel.java
    • -11
    • +15
    /src/jalview/gui/StructureViewerBase.java
    • -6
    • +7
    /src/jalview/gui/ViewSelectionMenu.java
    • -5
    • +30
    /src/jalview/structures/models/AAStructureBindingModel.java
Friday 02 Aug 2019
4:51 pm

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

JAL-3390 first draft of showing only visible alignment in Chimera

Options
    • -0
    • +7
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -14
    • +14
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
    • -10
    • +122
    /src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
    • -4
    • +2
    /src/jalview/gui/ChimeraViewFrame.java
    • -0
    • +12
    /src/jalview/gui/StructureViewerBase.java
    • -0
    • +3
    /src/jalview/jbgui/GStructureViewer.java
    • -4
    • +38
    /src/jalview/structures/models/AAStructureBindingModel.java
Wednesday 31 Jul 2019
12:59 pm

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

JAL-3389 add .py to restored Chimera session filename so it opens!

Options
    • -8
    • +8
    /src/jalview/project/Jalview2XML.java
9:10 am

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

Merge branch 'bug/JAL-3388structureChooserSorting' into develop

Options
Tuesday 30 Jul 2019
6:45 pm

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

JAL-3198 more efficient Sequence.getDisplayId()

Options
    • -5
    • +6
    /src/jalview/datamodel/Sequence.java
5:51 pm

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

JAL-3388 correct class for column 0 Ref Sequence

Options
    • -1
    • +2
    /src/jalview/fts/core/FTSRestResponse.java
Monday 29 Jul 2019
3:48 pm

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

JAL-3386 correct wrapped width calculation for headless image export

Options
    • -2
    • +3
    /src/jalview/gui/AlignmentPanel.java
3:35 pm

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

JAL-3377 more reused of SeqCanvas.computeWrappedGeometry

Options
    • -0
    • +2
    /src/jalview/gui/AlignmentPanel.java
    • -20
    • +7
    /src/jalview/gui/IdCanvas.java
    • -27
    • +18
    /src/jalview/gui/SeqCanvas.java
11:44 am

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

JAL-3377 add seq-annotations gap to cheight not to hgap

Options
    • -2
    • +2
    /src/jalview/gui/IdCanvas.java
11:34 am

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

JAL-3377 Javadoc added for getWrappedHeight()

Options
    • -0
    • +6
    /src/jalview/gui/AlignmentPanel.java
11:20 am

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

JAL-3377 include seq-annotation spacing in getWrappedHeight()

Options
    • -0
    • +1
    /src/jalview/gui/AlignmentPanel.java
Sunday 28 Jul 2019
11:05 am

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

JAL-3377 corrected wrapped widths height for IdCanvas

Options
    • -7
    • +8
    /src/jalview/gui/IdCanvas.java
Friday 26 Jul 2019
7:42 pm

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

Merge branch 'features/JAL-3375vcfValidation' into feature/JAL-3187linkedFeatures

Conflicts:

src/jalview/io/vcf/VCFLoader.java

test/jalview/io/vcf/VCFLoaderTest.java

Options
    • -1
    • +1
    /src/jalview/io/SequenceAnnotationReport.java
    • -16
    • +177
    /src/jalview/io/vcf/VCFLoader.java
    • -71
    • +99
    /test/jalview/io/vcf/VCFLoaderTest.java
5:52 pm

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

JAL-1793 only decode specific special characters in VCF data

Options
    • -10
    • +40
    /src/jalview/io/vcf/VCFLoader.java
    • -0
    • +13
    /test/jalview/io/vcf/VCFLoaderTest.java
4:58 pm

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

JAL-3376 capture VCF POS, ID, QUAL, FILTER as feature attributes

Options
    • -3
    • +75
    /src/jalview/io/vcf/VCFLoader.java
    • -2
    • +8
    /test/jalview/io/vcf/VCFLoaderTest.java
2:40 pm

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

JAL-3375 format validate VCF Integer and Float fields

Options
    • -15
    • +102
    /src/jalview/io/vcf/VCFLoader.java
    • -3
    • +12
    /test/jalview/io/vcf/VCFLoaderTest.java
Thursday 25 Jul 2019
11:48 am

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

JAL-3375 ignore '.' values for VCF data

Options
    • -0
    • +23
    /src/jalview/datamodel/features/FeatureAttributes.java
    • -1
    • +3
    /src/jalview/io/vcf/VCFLoader.java
    • -55
    • +95
    /test/jalview/io/vcf/VCFLoaderTest.java
Tuesday 16 Jul 2019
5:13 pm

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

Merge branch 'develop' into feature/JAL-3187linkedFeatures

Options
11:23 am

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

JAL-2987 tolerate null double values when formatting JTable

Options
    • -6
    • +5
    /src/jalview/fts/core/DecimalFormatTableCellRenderer.java