CR-JAL-234 JAL-3390: Option to hide unmapped residues in structure viewer

open for 22 months

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JAL-3390: Option to hide unmapped residues in structure viewer

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Number of files included: 42

jalview 0
- Folder resources/lang 0
  - File Messages.properties 0 Remove
  - File Messages_es.properties 0 Remove
- Folder src 0
  - Folder ext/edu/ucsf/rbvi/strucviz2 0
    - File ChimeraManager.java 0 Remove
  - Folder jalview 0
    - Folder api 0
      - Folder structures 0
        
        File JalviewStructureDisplayI.java 0 Remove
      - File AlignmentViewPanel.java 0 Remove
    - Folder appletgui 0
      - File AlignmentPanel.java 0 Remove
      - File AppletJmol.java 0 Remove
      - File AppletJmolBinding.java 0 Remove
    - Folder datamodel 0
      - File ColumnSelection.java 0 Remove
    - Folder ext 0
      - Folder jmol 0
        
        File JalviewJmolBinding.java 0 Remove
        
        File JmolCommands.java 0 Remove
      - Folder pymol 0
        
        File PymolCommands.java 0 Remove
      - Folder rbvi/chimera 0
        
        File AtomSpecModel.java 0 Remove
        
        File ChimeraCommands.java 0 Remove
        
        File ChimeraXCommands.java 0 Remove
        
        File JalviewChimeraBinding.java 0 Remove
        
        File StructureCommands.java 0 Remove
    - Folder gui 0
      - File AlignFrame.java 0 Remove
      - File AlignmentPanel.java 0 Remove
      - File AppJmol.java 0 Remove
      - File AppJmolBinding.java 0 Remove
      - File ChimeraViewFrame.java 0 Remove
      - File JalviewChimeraBindingModel.java 0 Remove
      - File PymolViewer.java 0 Remove
      - File StructureViewerBase.java 0 Remove
      - File ViewSelectionMenu.java 0 Remove
    - Folder jbgui 0
      - File GStructureViewer.java 0 Remove
    - Folder structure 0
      - File StructureCommandsBase.java 0 Remove
      - File StructureCommandsI.java 0 Remove
      - File StructureSelectionManager.java 0 Remove
    - Folder structures/models 0
      - File AAStructureBindingModel.java 0 Remove
    - Folder util 0
      - File StructureCommands.java 0 Remove
- Folder test/jalview 0
  - Folder ext 0
    - Folder jmol 0
      - File JalviewJmolBindingTest.java 0 Remove
      - File JmolCommandsTest.java 0 Remove
    - Folder pymol 0
      - File PymolCommandsTest.java 0 Remove
    - Folder rbvi/chimera 0
      - File AtomSpecModelTest.java 0 Remove
      - File ChimeraCommandsTest.java 0 Remove
      - File ChimeraXCommandsTest.java 0 Remove
      - File JalviewChimeraBindingTest.java 0 Remove
  - Folder structures/models 0
    - File AAStructureBindingModelTest.java 0 Remove
- Folder utils/testnglibs 0
  - File testng-sources.jar 0 Remove
- File gradle.properties 0 Remove

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Participant	Role	Time Spent	Comments
Mungo Carstairs	Author
Jim Procter	Reviewer - 3% reviewed	2m
Total		2m	0

Linked Issue:
JAL-3390

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Objectives

Would like the option to hide regions of 3d structure with no mapping to the visible region of the alignment.
This would allow the structure viewer display to match an alignment which has been restricted to a domain of interest.

Would like the option to either hide hidden mapped regions in structure viewer, or show gray (as at present).

Branches in review

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Issues Raised From Comments

Key	Summary	State	Assignee

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General Comments

There are no general comments on this review.

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/src/jalview/.../chimera/AtomSpecModel.java Deleted

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/src/jalview/util/StructureCommands.java Deleted

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/test/.../jmol/JalviewJmolBindingTest.java Deleted

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/test/.../chimera/AtomSpecModelTest.java Deleted

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/test/.../chimera/JalviewChimeraBindingTest.java Deleted

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CR-JAL-234

JAL-3390: Option to hide unmapped residues in structure viewer

CR-JAL-234 0

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JAL-3390: Option to hide unmapped residues in structure viewer

CR-JAL-234 0

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