Details
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Type:
New Feature
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Status: Ready for testing
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Priority:
Blocker
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Resolution: Unresolved
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Affects Version/s: None
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Component/s: Command Line Interface, jalview-j2s, JVL-Ajax
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Labels:None
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Sprint:2.11.3.0 Dev release
Description
Currently, PDB files cannot be associated with aligned sequences via the command line, which means Jalview cannot be used for batch generation of figures from alignments linked with structure data.
The main thing that needs to be fixed for this to happen:
* A new command line argument is needed so specific structure data files can be loaded onto the alignment being imported in to the application
This CLI arg need to also allow additional data to be passed - e.g. pae files, reliability score data.
Attachments
Issue Links
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JAL-2349 Contact prediction visualisation
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- In Progress
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JAL-2382 Import and display sequence-associated contact predictions in CASP-RR format
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- In Progress
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JAL-3858 Import and display alphafold alignment uncertainty matrices from JSON
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- In Progress
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- related with
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JAL-4160 New command line argument framework
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- Ready for testing
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JAL-4187 Powershell launcher script fails when given no arguments with the old ArgsParser
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- Ready for testing
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JAL-4185 Add argument to allow concurrent AlignFrame operations when being run from the command line with batch processing
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- In Progress
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JAL-4167 Create separate gradle test task for some tests
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- Ready for testing
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JAL-4121 Assume --headless when jalview is run with a command line argument that generates output
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- Being documented
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