CR-JAL-16 22
- Details
- Objectives
- General Comments 0
- Unresolved
- Resolved
- Number of files included: 47
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jalview
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Folder
resources/lang
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- File Messages.properties 2 Remove
- File Messages_es.properties 0 Remove
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Folder
src
0
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Folder
MCview
0
- File PDBChain.java 0 Remove
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Folder
ext/edu/ucsf/rbvi/strucviz2
0
- File ChimeraManager.java 0 Remove
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Folder
jalview
0
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Folder
analysis
0
- File AAFrequency.java 1 Remove
- File AlignmentUtils.java 0 Remove
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api
0
- File AlignViewportI.java 0 Remove
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datamodel
0
- File AlignmentAnnotation.java 0 Remove
- File Sequence.java 0 Remove
- File SequenceFeature.java 0 Remove
- File SequenceI.java 0 Remove
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Folder
ext
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ensembl
0
- File EnsemblSeqProxy.java 0 Remove
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jmol
0
- File JalviewJmolBinding.java 1 Remove
- File JmolCommands.java 0 Remove
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Folder
rbvi/chimera
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- File AtomSpecModel.java 0 Remove
- File ChimeraCommands.java 0 Remove
- File ChimeraListener.java 0 Remove
- File JalviewChimeraBinding.java 3 Remove
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Folder
ensembl
0
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Folder
gui
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- 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
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Folder
io
0
- File PDBFeatureSettings.java 1 Remove
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Folder
javascript
0
- File MouseOverStructureListener.java 0 Remove
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Folder
jbgui
0
- File GStructureViewer.java 0 Remove
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Folder
structure
0
- File AtomSpec.java 0 Remove
- File StructureMapping.java 0 Remove
- File StructureSelectionManager.java 2 Remove
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Folder
structures/models
0
- File AAStructureBindingModel.java 0 Remove
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Folder
util
0
- File RangeComparator.java 0 Remove
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Folder
viewmodel
0
- File AlignmentViewport.java 0 Remove
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Folder
workers
0
- File ConsensusThread.java 0 Remove
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Folder
ws/sifts
0
- File SiftsClient.java 0 Remove
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analysis
0
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Folder
MCview
0
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test/jalview
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datamodel
0
- File SequenceFeatureTest.java 0 Remove
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Folder
ext
0
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Folder
jmol
0
- File JmolCommandsTest.java 0 Remove
- File JmolViewerTest.java 0 Remove
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Folder
rbvi/chimera
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- 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
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Folder
jmol
0
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Folder
gui
0
- File AnnotationChooserTest.java 0 Remove
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Folder
structure
0
- File AtomSpecTest.java 0 Remove
- File StructureMappingTest.java 0 Remove
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Folder
structures/models
0
- File AAStructureBindingModelTest.java 0 Remove
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Folder
datamodel
0
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Folder
resources/lang
0
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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) |
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Linked Issue:
JAL-2295
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#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
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/resources/lang/Messages.properties
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2
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/resources/lang/Messages_es.properties
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/src/MCview/PDBChain.java
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/src/ext/.../strucviz2/ChimeraManager.java
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/src/jalview/analysis/AAFrequency.java
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1
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/src/jalview/analysis/AlignmentUtils.java
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/src/jalview/api/AlignViewportI.java
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/src/.../datamodel/AlignmentAnnotation.java
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/src/jalview/datamodel/Sequence.java
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/src/.../datamodel/SequenceFeature.java
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/src/jalview/datamodel/SequenceI.java
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/src/jalview/.../ensembl/EnsemblSeqProxy.java
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0
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/src/jalview/.../jmol/JalviewJmolBinding.java
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1
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/src/jalview/ext/jmol/JmolCommands.java
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/src/jalview/.../chimera/AtomSpecModel.java
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/src/jalview/.../chimera/ChimeraCommands.java
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/src/jalview/.../chimera/ChimeraListener.java
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/src/.../chimera/JalviewChimeraBinding.java
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3
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/src/jalview/gui/AnnotationRowFilter.java
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/src/jalview/gui/AppJmol.java
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/src/jalview/gui/ChimeraViewFrame.java
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6
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/src/.../gui/JalviewChimeraBindingModel.java
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/src/jalview/gui/StructureViewerBase.java
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/src/jalview/io/PDBFeatureSettings.java
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/src/.../javascript/MouseOverStructureListener.java
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/src/jalview/jbgui/GStructureViewer.java
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/src/jalview/structure/AtomSpec.java
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/src/.../structure/StructureMapping.java
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/src/.../structure/StructureSelectionManager.java
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/src/.../models/AAStructureBindingModel.java
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/src/jalview/util/RangeComparator.java
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/src/.../viewmodel/AlignmentViewport.java
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/src/jalview/workers/ConsensusThread.java
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/src/jalview/ws/sifts/SiftsClient.java
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/test/.../datamodel/SequenceFeatureTest.java
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/test/jalview/.../jmol/JmolCommandsTest.java
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/test/jalview/ext/jmol/JmolViewerTest.java
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/test/jalview/ext/rbvi/chimera/4zho.pdb
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/test/jalview/ext/rbvi/chimera/4zho.xml.gz
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/test/.../chimera/AtomSpecModelTest.java
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/test/.../chimera/ChimeraCommandsTest.java
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/test/.../chimera/JalviewChimeraView.java
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/test/jalview/.../chimera/testProps.jvprops
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/test/.../gui/AnnotationChooserTest.java
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/test/jalview/structure/AtomSpecTest.java
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/test/.../structure/StructureMappingTest.java
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/test/.../models/AAStructureBindingModelTest.java
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