merging Chimera spike to Jalview

Activity

CR-JAL-16 22

Keyboard shortcuts  
  • Summarize the review outcomes (optional)
     
    #permalink

    Details

    Warning: no files are visible, they have all been filtered.
    Participant Role Time Spent Comments Latest Comment
    Author 32m 8 Added a message on the viewer status bar e.g. "<n> attrib...
    Reviewer - 100% reviewed 2h 28m 14 (1 defect) thinking about this a bit more and looking at the code: l...
    Total   3h 1m 22 (1 defect)  
    #permalink

    Objectives

    • JAL-2295 step 1 new menu item to transfer Jalview attributes (no action yet)
    • JAL-2295 (unoptimised) write Jalview features as Chimera attributes
    • JAL-2295 small tidy of javadoc only
    • JAL-2295 handle no progress bar message properly
    • Merge branch 'develop' into features/JAL-2295setChimeraAttributes
    • JAL-2295 make RangeComparator a top level class for reuse
    • JAL-2295 extracted AtomSpecModel for reuse in Chimera commands
    • JAL-2295 method added to return a compact mapped range in the structure
    • JAL-2295 feature and colour commands refactored to use AtomSpecModel
    • JAL-2295 JAL-1596 method to pass a command script file to Chimera
    • JAL-2295 single constant for "RESNUM" feature name
    • JAL-2295 set attributes commands include feature value, sent via file
    • JAL-2295 additional tests, stronger sanitisation of attribute name
    • JAL-2295 correct test for Float.isNaN(score) !
    • JAL-2295 (optionally) return Chimera command reply
    • JAL-2295 sorted properties for readability
    • JAL-2295 test that verifies transfer of features to Chimera attributes
    • JAL-2295 set finishedInit to false before checking files loaded
    • JAL-1270 corrected command-line args
    • JAL-2295 improved integrity of 'isFinishedInit' flag
    • JAL-2295 JAL-2269 JAL-2319 mockable SIFTS file, fix to mapping details
    • JAL-2295 tests now 'network-free' with local PDB and SIFTS files
    • Merge branch 'develop' into features/JAL-2295setChimeraAttributes
    • JAL-2295 JAL-2296 skeleton 'attributes to features'; renamed methods with a view to pull-up
    • JAL-2296 report whether SequenceFeature actually added to sequence
    • JAL-2296 parse Chimera atomspec to AtomSpec
    • JAL-2295 don't copy 'Chimera' features back to Chimera
    • JAL-2296 new code and refactoring for 'copy Chimera attribute to features'
    • JAL-2295 don't exclude RESNUM from transfer to Chimera
    • JAL-2296 don't copy attribute with value False
    • Merge branch 'develop' into features/JAL-2295setChimeraAttributes
      Conflicts:
      src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
      src/jalview/gui/ChimeraViewFrame.java
    • Merge branch 'develop' into features/JAL-2295setChimeraAttributes
    • JAL-2296 unit test for reading Chimera attributes to Jalview features
    • Merge branch 'develop' into features/JAL-2295setChimeraAttributes
      Conflicts:
      src/jalview/structure/StructureSelectionManager.java
    • Merge branch 'develop' into features/JAL-2295setChimeraAttributes
      Conflicts:
      test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
    • JAL-1933 basic hack to get gap counts shown as an annotation row.
    • Merge branch 'develop' into features/JAL-2295setChimeraAttributes
    • JAL-1933 update the bounds for the Gap annotation row each time it is computed
    • Merge branch 'develop' into features/JAL-2295setChimeraAttributes
    • JAL-1933 switch from gap count to occupancy
    • JAL-1933 gap value as description; minor formatting
    • Merge branch 'develop' into features/JAL-2295setChimeraAttributes
      Conflicts:
      src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
    • JAL-1933 show occupancy count as a tooltip
    • Merge branch 'features/JAL-1933_occupancy' into features/JAL-2295setChimeraAttributes
    • Merge branch 'features/JAL-1933_occupancy' into features/JAL-2295setChimeraAttributes
    • JAL-1753 JAL-1596 JAL-1933 ensure AWT updates are on AWT thread
    • Merge branch 'develop' into features/JAL-2295setChimeraAttributes
    • Merge branch 'develop' into features/JAL-2295setChimeraAttributes
    • JAL-1933 update threshold on focus lost in text field
    • Merge branch 'features/JAL-2295setChimeraAttributes' into merges/develop_JAL2295setChimeraAttributes
      Conflicts:
      src/jalview/ext/rbvi/chimera/ChimeraCommands.java
      src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
      src/jalview/gui/ChimeraViewFrame.java
      test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java

    Branches in review

    #permalink

    Issues Raised From Comments

    Key Summary State Assignee
    JAL-2448
    JAL-2449
    #permalink

    General Comments

    There are no general comments on this review.
    /resources/lang/Messages.properties Changed 2
    /resources/lang/Messages_es.properties Changed
    /src/MCview/PDBChain.java Changed
    /src/ext/.../strucviz2/ChimeraManager.java Changed
    Open in IDE #permalink
    /src/jalview/analysis/AAFrequency.java Changed 1
    /src/jalview/analysis/AlignmentUtils.java Changed
    /src/jalview/api/AlignViewportI.java Changed
    /src/.../datamodel/AlignmentAnnotation.java Changed
    Open in IDE #permalink
    /src/jalview/datamodel/Sequence.java Changed
    /src/.../datamodel/SequenceFeature.java Changed
    Open in IDE #permalink
    /src/jalview/datamodel/SequenceI.java Changed
    /src/jalview/.../ensembl/EnsemblSeqProxy.java Changed
    /src/jalview/.../jmol/JalviewJmolBinding.java Changed 1
    /src/jalview/ext/jmol/JmolCommands.java Changed
    /src/jalview/.../chimera/AtomSpecModel.java Added
    Open in IDE #permalink
    /src/jalview/.../chimera/ChimeraCommands.java Changed
    /src/jalview/.../chimera/ChimeraListener.java Changed
    /src/.../chimera/JalviewChimeraBinding.java Changed 3
    /src/jalview/gui/AnnotationRowFilter.java Changed
    Open in IDE #permalink
    /src/jalview/gui/AppJmol.java Changed
    /src/jalview/gui/ChimeraViewFrame.java Changed 6
    /src/.../gui/JalviewChimeraBindingModel.java Changed
    /src/jalview/gui/StructureViewerBase.java Changed 4
    /src/jalview/io/PDBFeatureSettings.java Changed 1
    Open in IDE #permalink
    /src/.../javascript/MouseOverStructureListener.java Changed
    /src/jalview/jbgui/GStructureViewer.java Changed
    /src/jalview/structure/AtomSpec.java Changed
    Open in IDE #permalink
    /src/.../structure/StructureMapping.java Changed
    /src/.../structure/StructureSelectionManager.java Changed 2
    /src/.../models/AAStructureBindingModel.java Changed
    /src/jalview/util/RangeComparator.java Added
    Open in IDE #permalink
    /src/.../viewmodel/AlignmentViewport.java Changed
    /src/jalview/workers/ConsensusThread.java Changed
    /src/jalview/ws/sifts/SiftsClient.java Changed
    /test/.../datamodel/SequenceFeatureTest.java Changed
    Open in IDE #permalink
    /test/jalview/.../jmol/JmolCommandsTest.java Changed
    /test/jalview/ext/jmol/JmolViewerTest.java Changed
    /test/jalview/ext/rbvi/chimera/4zho.pdb Added
    Open in IDE #permalink
    /test/jalview/ext/rbvi/chimera/4zho.xml.gz Added
    Open in IDE #permalink
    /test/.../chimera/AtomSpecModelTest.java Added
    Open in IDE #permalink
    /test/.../chimera/ChimeraCommandsTest.java Changed
    /test/.../chimera/JalviewChimeraView.java Changed 2
    /test/jalview/.../chimera/testProps.jvprops Changed
    Open in IDE #permalink
    /test/.../gui/AnnotationChooserTest.java Changed
    Open in IDE #permalink
    /test/jalview/structure/AtomSpecTest.java Added
    Open in IDE #permalink
    /test/.../structure/StructureMappingTest.java Added
    Open in IDE #permalink
    /test/.../models/AAStructureBindingModelTest.java Changed

    Review updated: Reload | Ignore | Collapse

    You cannot reload the review while writing a comment.

    Log time against