Details
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Type:
Bug
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Status: Being documented
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Priority:
Blocker
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Resolution: Unresolved
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Affects Version/s: 2.11.4.0, 2.11.4.1
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Component/s: Command Line Interface, Structures
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Labels:
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Sprint:2.11.5.0 alpha
Description
This command (or variants of it) should open the example alignment with features and a structure view bound to a sequence.
java -jar build/libs/jalview-all-TEST-j11.jar --open https://www.jalview.org/examples/plantfdx.fa --features https://www.jalview.org/examples/plantfdx.features --structure https://www.jalview.org/examples/1gaq.txt --seqid FER1_MAIZE
In all released versions of Jalview, the structure is not loaded, with an error suggesting the URL has not been processed correctly:
WARN - The following errors and warnings occurred whilst processing files:
- Structure file '/Users/jprocter/uod-development/git/jalview-2025/https:/www.jalview.org/examples/1gaq.txt' not found.
java -jar build/libs/jalview-all-TEST-j11.jar --open https://www.jalview.org/examples/plantfdx.fa --features https://www.jalview.org/examples/plantfdx.features --structure https://www.jalview.org/examples/1gaq.txt --seqid FER1_MAIZE
In all released versions of Jalview, the structure is not loaded, with an error suggesting the URL has not been processed correctly:
WARN - The following errors and warnings occurred whilst processing files:
- Structure file '/Users/jprocter/uod-development/git/jalview-2025/https:/www.jalview.org/examples/1gaq.txt' not found.
Attachments
Issue Links
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