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


CR-JAL-109 4

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


    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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    Issues Raised From Comments

    Key Summary State Assignee

    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.

    /help/html/releases.html Changed 1
    /src/jalview/.../chimera/AtomSpecModel.java Changed
    Open in IDE #permalink
    /src/jalview/gui/FeatureSettings.java Changed 2
    /test/.../chimera/AtomSpecModelTest.java Changed
    Open in IDE #permalink

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