JAL-2438: Make findFeatureColour thread-safe and smarter
Activity
CR-JAL-18 11
- Details
- Objectives
- General Comments 0
- Unresolved
- Resolved
- Number of files included: 30
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jalview
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src
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MCview
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- File AppletPDBCanvas.java 0 Remove
- File PDBCanvas.java 0 Remove
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jalview
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api
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- File FeatureRenderer.java 0 Remove
- File SequenceRenderer.java 0 Remove
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appletgui
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- File AppletJmolBinding.java 0 Remove
- File ExtJmol.java 0 Remove
- File OverviewPanel.java 0 Remove
- File SeqCanvas.java 0 Remove
- File SequenceRenderer.java 0 Remove
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ext
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jmol
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- File JalviewJmolBinding.java 3 Remove
- File JmolCommands.java 0 Remove
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rbvi/chimera
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- File ChimeraCommands.java 0 Remove
- File JalviewChimeraBinding.java 2 Remove
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varna
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- File VarnaCommands.java 0 Remove
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jmol
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gui
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- File AppJmolBinding.java 0 Remove
- File FeatureRenderer.java 0 Remove
- File JalviewChimeraBindingModel.java 3 Remove
- File OverviewPanel.java 0 Remove
- File SeqCanvas.java 0 Remove
- File SequenceRenderer.java 0 Remove
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io
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- File JSONFile.java 0 Remove
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javascript
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- File MouseOverStructureListener.java 0 Remove
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renderer/seqfeatures
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- File FeatureColourFinder.java 0 Remove
- File FeatureRenderer.java 3 Remove
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structures/models
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- File AAStructureBindingModel.java 0 Remove
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viewmodel/seqfeatures
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- File FeatureRendererModel.java 0 Remove
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api
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MCview
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test/jalview
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ext
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jmol
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- File JmolCommandsTest.java 0 Remove
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rbvi/chimera
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- File ChimeraCommandsTest.java 0 Remove
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jmol
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renderer/seqfeatures
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- File FeatureColourFinderTest.java 0 Remove
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structures/models
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- File AAStructureBindingModelTest.java 0 Remove
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ext
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src
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Participant | Role | Time Spent | Comments | Latest Comment |
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Author | 20m | 5 | I agree. I had swerved these fields as not sure what they... | |
Reviewer - Complete | 57m | 4 | I realise this code is unchanged, but I think it actually... | |
Total | 1h 17m | 11 |
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Linked Issue:
JAL-2438
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Objectives
FeatureRenderer.findFeatureColour is called when determining feature colours for structures or the overview window. Because it is not currently thread-safe, 'clones' of FeatureRenderer are used for this. This is fragile (see JAL-2436 for a bug resulting).
Proposed to explore how to make the method thread-safe so that no clones are needed, only a 'read-only' view of the FeatureRenderer.
Performance is critical here so must be preserved - and improved where possible.
Branches in review
Repository | Branch to review | Branched from |
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/src/MCview/AppletPDBCanvas.java
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/src/MCview/PDBCanvas.java
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/src/jalview/api/FeatureRenderer.java
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/src/jalview/api/SequenceRenderer.java
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/src/.../appletgui/AppletJmolBinding.java
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/src/jalview/appletgui/ExtJmol.java
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/src/jalview/appletgui/OverviewPanel.java
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/src/jalview/appletgui/SeqCanvas.java
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/src/.../appletgui/SequenceRenderer.java
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/src/jalview/.../jmol/JalviewJmolBinding.java
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3
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/src/jalview/ext/jmol/JmolCommands.java
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/src/jalview/.../chimera/ChimeraCommands.java
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/src/.../chimera/JalviewChimeraBinding.java
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/src/jalview/ext/varna/VarnaCommands.java
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/src/jalview/gui/AppJmolBinding.java
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/src/jalview/gui/FeatureRenderer.java
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/src/.../gui/JalviewChimeraBindingModel.java
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/src/jalview/gui/OverviewPanel.java
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/src/jalview/gui/SeqCanvas.java
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/src/jalview/gui/SequenceRenderer.java
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/src/jalview/io/JSONFile.java
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/src/.../javascript/MouseOverStructureListener.java
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/src/.../seqfeatures/FeatureColourFinder.java
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/src/.../seqfeatures/FeatureRenderer.java
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/src/.../models/AAStructureBindingModel.java
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/src/.../seqfeatures/FeatureRendererModel.java
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/test/jalview/.../jmol/JmolCommandsTest.java
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/test/.../chimera/ChimeraCommandsTest.java
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/test/.../seqfeatures/FeatureColourFinderTest.java
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/test/.../models/AAStructureBindingModelTest.java
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