Details
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Type: Improvement
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Status: Resolved
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Priority: Major
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Resolution: Fixed
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Affects Version/s: None
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Fix Version/s: 2.8.0b1
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Component/s: file format issue
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Labels:None
Description
Newick tree files that contain nodes that include two consecutive single or double quotes in their names are currently not properly imported by Jalview.
For example:
'Syn_RCC307_5.3_3d''|CK_Syn_RCC307_2042'
raises an exception in the jalview.io.NewickFile parser.
The "''" in this case is generated by the NewickFile.print() method to escape node names that contain a ' - it's worth noting that this 'double-quote' escape convention (where a '' should be interpreted as a single ' in the name) is not necessarily standard procedure for NHX format, and it should be verified/qualified in the documentation.
Attachments
Issue Links
- blocks
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JAL-1313 jalview fail to load newick tree with quoted label
- Resolved