CR-JAL-16 merging Chimera spike to Jalview

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merging Chimera spike to Jalview

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Number of files included: 47

jalview 0
- Folder resources/lang 0
  - File Messages.properties 2 Remove
  - File Messages_es.properties 0 Remove
- Folder src 0
  - Folder MCview 0
    - File PDBChain.java 0 Remove
  - Folder ext/edu/ucsf/rbvi/strucviz2 0
    - File ChimeraManager.java 0 Remove
  - Folder jalview 0
    - Folder analysis 0
      - File AAFrequency.java 1 Remove
      - File AlignmentUtils.java 0 Remove
    - Folder api 0
      - File AlignViewportI.java 0 Remove
    - Folder datamodel 0
      - File AlignmentAnnotation.java 0 Remove
      - File Sequence.java 0 Remove
      - File SequenceFeature.java 0 Remove
      - File SequenceI.java 0 Remove
    - Folder ext 0
      - Folder ensembl 0
        
        File EnsemblSeqProxy.java 0 Remove
      - Folder jmol 0
        
        File JalviewJmolBinding.java 1 Remove
        
        File JmolCommands.java 0 Remove
      - Folder rbvi/chimera 0
        
        File AtomSpecModel.java 0 Remove
        
        File ChimeraCommands.java 0 Remove
        
        File ChimeraListener.java 0 Remove
        
        File JalviewChimeraBinding.java 3 Remove
    - Folder gui 0
      - File AnnotationRowFilter.java 0 Remove
      - File AppJmol.java 0 Remove
      - File ChimeraViewFrame.java 6 Remove
      - File JalviewChimeraBindingModel.java 0 Remove
      - File StructureViewerBase.java 4 Remove
    - Folder io 0
      - File PDBFeatureSettings.java 1 Remove
    - Folder javascript 0
      - File MouseOverStructureListener.java 0 Remove
    - Folder jbgui 0
      - File GStructureViewer.java 0 Remove
    - Folder structure 0
      - File AtomSpec.java 0 Remove
      - File StructureMapping.java 0 Remove
      - File StructureSelectionManager.java 2 Remove
    - Folder structures/models 0
      - File AAStructureBindingModel.java 0 Remove
    - Folder util 0
      - File RangeComparator.java 0 Remove
    - Folder viewmodel 0
      - File AlignmentViewport.java 0 Remove
    - Folder workers 0
      - File ConsensusThread.java 0 Remove
    - Folder ws/sifts 0
      - File SiftsClient.java 0 Remove
- Folder test/jalview 0
  - Folder datamodel 0
    - File SequenceFeatureTest.java 0 Remove
  - Folder ext 0
    - Folder jmol 0
      - File JmolCommandsTest.java 0 Remove
      - File JmolViewerTest.java 0 Remove
    - Folder rbvi/chimera 0
      - File 4zho.pdb 0 Remove
      - File 4zho.xml.gz 0 Remove
      - File AtomSpecModelTest.java 0 Remove
      - File ChimeraCommandsTest.java 0 Remove
      - File JalviewChimeraView.java 2 Remove
      - File testProps.jvprops 0 Remove
  - Folder gui 0
    - File AnnotationChooserTest.java 0 Remove
  - Folder structure 0
    - File AtomSpecTest.java 0 Remove
    - File StructureMappingTest.java 0 Remove
  - Folder structures/models 0
    - File AAStructureBindingModelTest.java 0 Remove

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Details

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Participant	Role	Time Spent	Comments	Latest Comment
Mungo Carstairs	Author	32m	8	Added a message on the viewer status bar e.g. "<n> attrib...
Jim Procter	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)

Linked Issue:
JAL-2295

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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

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Issues Raised From Comments

Key	Summary	State	Assignee
JAL-2448
JAL-2449

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General Comments

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CR-JAL-16

merging Chimera spike to Jalview

CR-JAL-16 22

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merging Chimera spike to Jalview

CR-JAL-16 22

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