jalview

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-3402 suppress unmapped chains in View Chain menu

    • -0
    • +4
    /src/jalview/gui/StructureViewerBase.java
JAL-3400 include sequence name in View | Show Chain menu

    • -8
    • +0
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -2
    • +44
    /src/jalview/gui/StructureViewerBase.java
    • -1
    • +1
    /src/jalview/jbgui/GStructureViewer.java
JAL-3390 showSelectedChains pulled up to base class for Jmol/Chimera

    • -6
    • +9
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -14
    • +0
    /src/jalview/gui/ChimeraViewFrame.java
    • -2
    • +17
    /src/jalview/gui/StructureViewerBase.java
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

    • -1
    • +5
    /resources/lang/Messages_es.properties
    • -8
    • +27
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -24
    • +132
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
    • binary
    /utils/testnglibs/testng-sources.jar
JAL-3187 (fudge) look in both alignments for stored mappings

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

JAL-3390 first pass refactoring for JalviewJmolBinding.showStructures

    • -3
    • +3
    /src/jalview/appletgui/AppletJmol.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
    • -1
    • +1
    /src/jalview/gui/StructureViewerBase.java
JAL-3390 pull up of getShownResidues() to AAStructureBindingModel

    • -110
    • +35
    /src/jalview/ext/rbvi/chimera/AtomSpecModel.java
    • -76
    • +135
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
JAL-3390 redraw structures if alignment only and hidden regions change

    • -6
    • +0
    /src/jalview/gui/StructureViewerBase.java
JAL-3390 new View menu option to hide hidden regions in structure

    • -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
    • -1
    • +18
    /src/jalview/gui/StructureViewerBase.java
    • -0
    • +2
    /src/jalview/jbgui/GStructureViewer.java
JAL-3390 Chimera showStructures() respects visible/chain selections

    • -1
    • +2
    /src/jalview/appletgui/AppletJmol.java
    • -7
    • +6
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -14
    • +6
    /src/jalview/gui/ChimeraViewFrame.java
    • -1
    • +2
    /src/jalview/gui/StructureViewerBase.java
    • -0
    • +25
    /src/jalview/jbgui/GStructureViewer.java
JAL-3390 pull-up refactoring towards functional changes...

    • -0
    • +14
    /src/jalview/api/AlignmentViewPanel.java
    • -15
    • +0
    /src/jalview/gui/AppJmolBinding.java
    • -2
    • +3
    /src/jalview/gui/ChimeraViewFrame.java
    • -11
    • +15
    /src/jalview/gui/StructureViewerBase.java
    • -6
    • +7
    /src/jalview/gui/ViewSelectionMenu.java
JAL-3390 first draft of showing only visible alignment in Chimera

    • -0
    • +7
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -14
    • +14
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
    • -4
    • +2
    /src/jalview/gui/ChimeraViewFrame.java
    • -0
    • +12
    /src/jalview/gui/StructureViewerBase.java
    • -0
    • +3
    /src/jalview/jbgui/GStructureViewer.java
JAL-3389 add .py to restored Chimera session filename so it opens!

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

JAL-3198 more efficient Sequence.getDisplayId()

JAL-3388 correct class for column 0 Ref Sequence

    • -1
    • +2
    /src/jalview/fts/core/FTSRestResponse.java
JAL-3386 correct wrapped width calculation for headless image export

JAL-3377 more reused of SeqCanvas.computeWrappedGeometry

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

JAL-3377 Javadoc added for getWrappedHeight()

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

JAL-3377 corrected wrapped widths height for IdCanvas

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

Conflicts:

src/jalview/io/vcf/VCFLoader.java

test/jalview/io/vcf/VCFLoaderTest.java

    • -16
    • +177
    /src/jalview/io/vcf/VCFLoader.java
    • -71
    • +99
    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-1793 only decode specific special characters in VCF data

    • -10
    • +40
    /src/jalview/io/vcf/VCFLoader.java
    • -0
    • +13
    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-3376 capture VCF POS, ID, QUAL, FILTER as feature attributes

    • -2
    • +8
    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-3375 format validate VCF Integer and Float fields

    • -15
    • +102
    /src/jalview/io/vcf/VCFLoader.java
    • -3
    • +12
    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-3375 ignore '.' values for VCF data

    • -55
    • +95
    /test/jalview/io/vcf/VCFLoaderTest.java
Merge branch 'develop' into feature/JAL-3187linkedFeatures

JAL-2987 tolerate null double values when formatting JTable