Details
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Type: Bug
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Status: Closed
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Priority: Major
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Resolution: Fixed
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Affects Version/s: 2.11.3.2
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Fix Version/s: 2.11.3.3
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Component/s: Command Line Interface
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Labels:None
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Urgency:Urgent
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Sprint:2.11.3.3 release
Description
When attempting to output structure images of multiple structures opened for one or more sequences in a single alignment, each structure has its image written over all of the output structure image filenames.
e.g.
jalview --open alignment.fa \
--structure struc1.pdb --seqid 101 --structureimage struc1.png \
--srtucture struc2.pdb --seqid 101 --structureimage struc2.png \
--all --overwrite
will result in the image of struc1.pdb first being written to BOTH struc1.png and struc2.png, and THEN
the image of struc2.pdb will be written to BOTH struc1.png and struc2.png.
--structureimage should be limited after a --structure argument up to the next --structureimage, or next --open.
This can probably be done relatively easily by adding a Type.STRUCTURE (like the Type.IMAGE, although --structureimage will be both, with Opt.PRIMARY applying to both -- might be worth adding an Opt.STRUCTUREPRIMARY, Opt.IMAGEPRIMARY though this becomes slightly less generic).
e.g.
jalview --open alignment.fa \
--structure struc1.pdb --seqid 101 --structureimage struc1.png \
--srtucture struc2.pdb --seqid 101 --structureimage struc2.png \
--all --overwrite
will result in the image of struc1.pdb first being written to BOTH struc1.png and struc2.png, and THEN
the image of struc2.pdb will be written to BOTH struc1.png and struc2.png.
--structureimage should be limited after a --structure argument up to the next --structureimage, or next --open.
This can probably be done relatively easily by adding a Type.STRUCTURE (like the Type.IMAGE, although --structureimage will be both, with Opt.PRIMARY applying to both -- might be worth adding an Opt.STRUCTUREPRIMARY, Opt.IMAGEPRIMARY though this becomes slightly less generic).
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