Ready for test and merged in:
* JAL-384 custom colour schemes
* JAL-1476 message for failed superposition
* JAL-2243 update Feature Settings when features added
* JAL-2295 exchange features/attributes Jalview/Chimera
* JAL-2361 (for retest) colour menu options
* JAL-2362 structure colour command
* JAL-2373 group colour menu behaviour
* JAL-2379 PCA footprint
* JAL-2383 above PID threshold not restored from project etc
* JAL-2384 change colour preserve threshold
* JAL-2385 update threshold slider on change of group
*
* JAL-2386 Change Colour Apply to All Groups behaviour
* JAL-2398 BLOSUM62 C->R score
* JAL-2401 Lower Case Colour button
* JAL-2405 new group colour options
* JAL-2430 structure colour of hidden columns
* JAL-2442 transparency in applet
* JAL-2443 a sub-task of 2436/2438
Ready for test but not yet merged in:
* JAL-1608 Create Group text / disabling / applet
* JAL-2431 New View cDNA consensus
* JAL-2435 change font in split frame
* JAL-2399 cancel group text colour change
* JAL-2400 Text Colour widget (on bug/2399)
* JAL-2346 Colour by Annotation widget behaviour
Work in progress and might or might not make 2.10.2:
* JAL-2393, 210, 374, 790, 791, 838, 1632, 2397, 2416, 2423, 2428
* features/JAL-2393 branch
* parameterisation of Tree / PCA calculation, custom substitution
matrices
Work in progress and not expected to make 2.10.2:
* features/JAL-2446
* structured features storage including NCList
Mungo
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