Details
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Type:
Improvement
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Status: Open
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: 2.12.0
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Component/s: None
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Labels:None
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Epic Link:
Description
Update for 2.12:
This requires a rearrangement of the 'use original colours' option logic such that it allows conservation style shading, or even employ a complex graduated scheme, rather than simply re-using the existing shading but *only* when there is no annotation row specific shading provided. The annotation shading mechanism has been recruited for additional purposes (Hmmer posterior bleaching JAL-3623, PAE groupsJAL-4158) and will become more sophisticated in the future, so a UX review is now a priority.
Original story:
Currently, the AnnotationColourScheme logic supports three modes of per-Sequence or single row based alignment/group shading:
i. min/max linear gradient
ii. Reuse of existing 'Background Colour'
iii. Use of colours defined in alignment annotation row.
The Annotation Colouring dialog allows the user to switch between i and ii but iii is currently only available for alignment annotation programmatically created (e.g. via a T-COFFEE file import).
The ability to switch between all three modes, with out data loss, could be useful, but use cases are needed (e.g. toggling between a linear scheme vs the predefined colourscheme provided by T-COFFEE, etc).
This requires a rearrangement of the 'use original colours' option logic such that it allows conservation style shading, or even employ a complex graduated scheme, rather than simply re-using the existing shading but *only* when there is no annotation row specific shading provided. The annotation shading mechanism has been recruited for additional purposes (Hmmer posterior bleaching JAL-3623, PAE groups
Original story:
Currently, the AnnotationColourScheme logic supports three modes of per-Sequence or single row based alignment/group shading:
i. min/max linear gradient
ii. Reuse of existing 'Background Colour'
iii. Use of colours defined in alignment annotation row.
The Annotation Colouring dialog allows the user to switch between i and ii but iii is currently only available for alignment annotation programmatically created (e.g. via a T-COFFEE file import).
The ability to switch between all three modes, with out data loss, could be useful, but use cases are needed (e.g. toggling between a linear scheme vs the predefined colourscheme provided by T-COFFEE, etc).
Attachments
Issue Links
- related with
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JAL-4438 refactor ResidueShaderI to support new types of data-dependent shading
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- Open
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