CR-JAL-109 JAL-2777: Exceptions and superposition failure when viewing PDB files with empty chain codes in Chimera

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JAL-2777: Exceptions and superposition failure when viewing PDB files with empty...

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Number of files included: 4

jalview 0
- Folder help/html 0
  - File releases.html 1 Remove
- Folder src/jalview 0
  - Folder ext/rbvi/chimera 0
    - File AtomSpecModel.java 0 Remove
  - Folder gui 0
    - File FeatureSettings.java 2 Remove
- Folder test/jalview/ext/rbvi/chimera 0
  - File AtomSpecModelTest.java 0 Remove

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Participant	Role	Time Spent	Comments	Latest Comment
Jim Procter	Author	7m	2	oops - this is the wrong issue number :q
Kira Mourão	Reviewer - 93% reviewed	7m	2	Not quite sure what the FeatureSettings changes were fixi...
Total		14m	4

Linked Issue:
JAL-2777

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PDB files produced by modelling tools often lack PDB chain codes (like the one attached). Importing these to view in Chimera yields the following exception:

Time for creating model: 68 ms
Exception in thread "Thread-132" java.lang.NullPointerException
at java.util.Collections.sort(Collections.java:175)
at jalview.ext.rbvi.chimera.AtomSpecModel.getAtomSpec(AtomSpecModel.java:130)
at jalview.ext.rbvi.chimera.ChimeraCommands.buildColourCommands(ChimeraCommands.java:121)
at jalview.ext.rbvi.chimera.ChimeraCommands.getColourBySequenceCommand(ChimeraCommands.java:75)
at jalview.ext.rbvi.chimera.JalviewChimeraBinding.getColourBySequenceCommands(JalviewChimeraBinding.java:701)
at jalview.structures.models.AAStructureBindingModel.colourBySequence(AAStructureBindingModel.java:814)
at jalview.gui.JalviewChimeraBindingModel.updateColours(JalviewChimeraBindingModel.java:90)
at jalview.gui.ChimeraViewFrame.run(ChimeraView...

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Key	Summary	State	Assignee

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General Comments

Kira Mourão

Not quite sure what the FeatureSettings changes were fixing - doesn't look li...

Not quite sure what the FeatureSettings changes were fixing - doesn't look like it was anything referred to in the bug report. Difficult to review/test without knowing that.

18 Oct 17

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CR-JAL-109

JAL-2777: Exceptions and superposition failure when viewing PDB files with empty...

CR-JAL-109 4

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Kira Mourão

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JAL-2777: Exceptions and superposition failure when viewing PDB files with empty...

CR-JAL-109 4

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Kira Mourão

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