jalview

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
Merge branch 'develop' into features/JAL-2446NCList

Conflicts:

src/jalview/datamodel/Sequence.java

src/jalview/gui/OverviewPanel.java

Merge branch 'features/JAL-2388OverviewWindow' into develop

JAL-2446 FeatureStore with NCList - work in progress

    • -0
    • +15
    /src/jalview/datamodel/Sequence.java
    • -0
    • +11
    /src/jalview/datamodel/SequenceI.java
    • -0
    • +8
    /src/jalview/datamodel/features/ContiguousI.java
    • -0
    • +10
    /src/jalview/datamodel/features/FeatureLocationI.java
    • -0
    • +445
    /src/jalview/datamodel/features/FeatureStore.java
    • -0
    • +324
    /src/jalview/datamodel/features/NCList.java
    • -0
    • +124
    /src/jalview/datamodel/features/NCNode.java
    • -0
    • +69
    /src/jalview/datamodel/features/RangeComparator.java
    • -0
    • +60
    /src/jalview/datamodel/features/SequenceFeatures.java
    • -0
    • +27
    /src/jalview/datamodel/features/SubList.java
    • -0
    • +232
    /test/jalview/datamodel/features/FeatureStoreTest.java
    • -0
    • +158
    /test/jalview/datamodel/features/NCListTest.java
Merge branch 'bug/JAL-2421overviewboxflicker' into develop

JAL-2388 Comment typo

JAL-2388 ViewportRanges unit test

    • -0
    • +100
    /test/jalview/viewmodel/ViewportRangesTest.java
JAL-2437 Synchronization corrections and unit tests

JAL-2388 Renamed column and row subtraction functions

Merge branch 'merges/develop_JAL2295setChimeraAttributes' into develop

JAL-1933 refactor parameter for code clarity

    • -8
    • +8
    /src/jalview/analysis/AAFrequency.java
JAL-2388 Applied ViewportRanges to code

    • -28
    • +36
    /src/jalview/appletgui/AlignFrame.java
    • -1
    • +1
    /src/jalview/appletgui/AlignViewport.java
    • -8
    • +13
    /src/jalview/appletgui/IdCanvas.java
    • -5
    • +9
    /src/jalview/appletgui/ScalePanel.java
    • -12
    • +19
    /src/jalview/appletgui/SeqCanvas.java
    • -17
    • +26
    /src/jalview/appletgui/SeqPanel.java
    • -12
    • +16
    /src/jalview/gui/AlignFrame.java
    • -27
    • +34
    /src/jalview/gui/AlignmentPanel.java
  1. … 12 more files in changeset.
JAL-2388 Renamed viewport position props to viewport ranges

    • -6
    • +3
    /src/jalview/appletgui/AlignViewport.java
    • -3
    • +3
    /src/jalview/appletgui/OverviewPanel.java
    • -0
    • +186
    /src/jalview/viewmodel/ViewportRanges.java
    • -51
    • +51
    /test/jalview/viewmodel/OverviewDimensionsTest.java
JAL-2388 Unit test update

JAL-2388 Applet update for overview panel

    • -4
    • +4
    /src/jalview/appletgui/OverviewPanel.java
JAL-2439 Out-by-one in setting endRes/endSeq

JAL-2388 Unit tests and tidies

    • -0
    • +2
    /src/jalview/appletgui/AlignViewport.java
    • -21
    • +14
    /src/jalview/appletgui/OverviewPanel.java
    • -26
    • +17
    /src/jalview/gui/OverviewPanel.java
    • -70
    • +66
    /test/jalview/viewmodel/OverviewDimensionsTest.java
Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow

JAL-2388 Working overview panel

JAL-2439 Fixes to out-by-one sequence indexing in gui classes

JAL-2388 New hidden cols/seqs functions to support overview panel

JAL-2437 Fixed reordering of sequences when hiding and revealing

    • -12
    • +12
    /src/jalview/datamodel/Alignment.java
    • -2
    • +15
    /src/jalview/datamodel/AlignmentI.java
JAL-2388 Moving some alignment panel logic into overview (in progress)

    • -35
    • +14
    /test/jalview/viewmodel/OverviewDimensionsTest.java
JAL-2388 Minor fix for annotation graph, removed unit test dep on gui

    • -2
    • +2
    /src/jalview/appletgui/OverviewPanel.java
    • -229
    • +103
    /test/jalview/viewmodel/OverviewDimensionsTest.java
JAL-2430 colour columns hidden in alignment gray on structure

    • -3
    • +4
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -5
    • +19
    /src/jalview/ext/jmol/JmolCommands.java
    • -10
    • +24
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
    • -1
    • +2
    /test/jalview/ext/jmol/JmolCommandsTest.java
JAL-2295 avoid quotes breaking attribute value parsing

JAL-2388 Fixed inherited&new out-by-one errors; further unit tests

    • -32
    • +33
    /test/jalview/viewmodel/OverviewDimensionsTest.java
JAL-2295 status messages for Chimera attributes set and for failed superposition

    • -1
    • +1
    /resources/lang/Messages_es.properties
    • -50
    • +41
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -11
    • +16
    /src/jalview/gui/ChimeraViewFrame.java
    • -10
    • +51
    /src/jalview/gui/StructureViewerBase.java
    • -3
    • +2
    /src/jalview/jbgui/GStructureViewer.java
JAL-2388 Additional unit tests

    • -110
    • +87
    /test/jalview/viewmodel/OverviewDimensionsTest.java
JAL-2388 Missed commit

Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow