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JAL-3199 'Sort Annotations by...' now a one-off action, not a 'state'

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JAL-3210 Barebones gradle/buildship/eclipse. See README

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    ./calculations/recoverInputdata.html
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    ./calculations/scorematrices.html
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Merge branch 'develop' into developtomchmmer JAL-3285 merged 2.11 develop into the features/mchmmer branch - need to fix code for migration from Castor to JAXB - need to check Stockholm file IO and tests Good luck !

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Can remove class Jalview$FeatureFetcher.

Can remove class Jalview$FeatureFetcher.

JAL-3224 JAL-3225 Fixed help image mangling, moved help to help/help and added this in to eclipse classpath generation

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JAL-1793 basic help text for VCF option

JAL-3111 additional release notes

JAL-3111 small simplification of table tags, valign top

JAL-3111 release notes first pass complete

JAL-2620 updated help page to mention alternative genetic code tables

JAL-3111 fix 2.11 html anchor in docs

JAL-3111 Jalview 2.11 what’s New and estimated release date

JAL-3111 tweak PCA documentation

JAL-3215 colours updated on help page

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    ./colourSchemes/hydrophobic.html
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JAL-2250 now done.

JAL-2250 now done.

JAL-2903 typos fixed

Were added 2012 commit 3d37b44 "jdas runtime dependencies". All classes in jars are org.springframework.*, no longer referenced in any source code in Jalview. I will remove from classpath and THIRD...

Were added 2012 commit 3d37b44 "jdas runtime dependencies".
All classes in jars are org.springframework.*, no longer referenced in any source code in Jalview.
I will remove from classpath and THIRDPARTYLIBS.

yeah. probably.

yeah. probably.

JAL-3035 more das bits removed

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I tried removing these (Spring jars) and Jalview seemed to function ok. Can they go?

I tried removing these (Spring jars) and Jalview seemed to function ok. Can they go?

JAL-2846 ahem - proper release note for this fix from KJVDH !

JAL-3178 known defect in release notes

JAL-3111 JAL-2846 release notes

JAL-3111 tweaked release notes and documented JAL-2864

JAL-2865 release notes

JAL-2541 JAL-2822 release notes

JAL-3111 bump release 2.11 release to January 2019

we don't have consistent colourscheme class docs. will add minimal.

we don't have consistent colourscheme class docs. will add minimal.

Took a closer look and the hiddenRepSequences is indeed redundant (assuming we only care about represented sequences held by the view, not some other aggregation). Have also raised JAL-3156 - since...

Took a closer look and the hiddenRepSequences is indeed redundant (assuming we only care about represented sequences held by the view, not some other aggregation). Have also raised JAL-3156 - since there's an inconsistency in how SequenceCollectionI.getSequences(..) is implemented - for groups, all the hidden represented sequences are returned, but for an alignment, none of them are. This is quite subtle, but will be more important when we implement automated selection of representative sequences.