Details
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Type: Improvement
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Status: Closed
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Priority: Minor
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Resolution: Fixed
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Affects Version/s: 2.10.1
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Fix Version/s: 2.10.2
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Component/s: None
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Labels:None
Description
- nucleotide colour schemes are enabled in the Colour menu if alignment is nucleotide, else disabled (except for 'Nucleotide'!!)
- this logic is missing in the pop-up menu for a selection group
- peptide colour schemes are always enabled (although not applicable to nucleotide data)
Three possible improvements:
1) enable/disable nucleotide colour schemes also in the pop-up menu
2) enable/disable peptide colour schemes in AlignFrame and pop-up menus
3) drive this by a property of the SequenceCollectionI rather than hard-code lists of colour schemes
1) and 2) are straightforward. Adding methods isNucleotide(), isPeptide() to ColourSchemeI would help.
3) needs some thought:
- SequenceGroup doesn't have a method isNucleotide(), preventing adding this to SequenceCollectionI
- could perhaps abstract a bit further e.g.
ColourSchemeI.isApplicableTo(SequenceCollectionI)
- with current implementation limited to the nucleotide / peptide check
Attachments
Issue Links
- blocks
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JAL-2405 Protein specific colours enabled in selected group colour menu for nucleotide alignment
- Closed
- duplicates
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JAL-1451 do not apply default colourscheme if not compatible with sequence type
- Open
- related with
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JAL-840 Clustal colouring rules differ from documentation
- Resolved
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JAL-2489 BioJSON export fails on develop
- Closed
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JAL-2371 Separate colour threshold/fading from colour schemes
- Closed
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JAL-2394 Simplify colourschemeI interface to avoid requiring boilerplate is/newInstance/update mathods
- Open
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JAL-2717 Colour scheme names not showing correctly in menu
- Closed