Merge branch 'develop' into features/JAL-2446NCList

JAL-2384 JAL-2371 update ResidueShader on change of colour by
conservation / pid

JAL-2361 simplify constructors, select unsaved but applied user defined
colour scheme in menu

JAL-2361 apply any saved changes to current colour scheme

JAL-2446 various get and find methods added with test coverage

JAL-2446 method isNonPositional() added

Merge branch 'develop' into features/JAL-2446NCList

JAL-2314 made non-test method non-public

Merge branch 'develop' into bug/JAL-2314

Merge branch 'develop' into bug/JAL-2461

JAL-2446 pseudo-random generator unit test, and fixes arising

Merge branch 'develop' into features/JAL-2446NCList

JAL-2405 additional checks for circular reference in context or dataset

JAL-2472 PrivilegedAccessor added

Merge branch 'develop' into bug/JAL-2431splitFrameNewView

JAL-2430 code tidy, unit test for Jmol hidden column colours

Merge branch 'develop' into bug/JAL-1608createGroups

JAL-1608 leave Create Group, Remove Group menu items enabled

JAL-2401 code and help tidy for review comments

JAL-2401 don't apply lower case colour to upper case

Merge branch 'develop' into bug/JAL-2399textColour

JAL-2346 JAL-1933 test updated to include Occupancy

JAL-2346 always run setup!

JAL-2346 more test coverage for AnnotationColourGradient

Merge branch 'develop' into bug/JAL-2346annotationChoice

Conflicts:
src/jalview/gui/AnnotationRowFilter.java

Merge branch 'develop' into bug/JAL-1608createGroups

JAL-2360 fix applet build by separating castor XML dependency from jalview.schemes.ColourSchemes to jalview.schemes.ColourSchemeLoader

Merge remote-tracking branch 'origin/develop' into bug/JAL-2314

JAL-2314 Tidy up

JAL-2314 Fixes to DisorderAnnotExportImport test

JAL-2464 fix cancel tree print behaviour

Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

JAL-2388 unit test initialisation fix for running full suite

JAL-2314 Tweaks to stop thread sync issues

JAL-2464 fix cancel tree print behaviour

JAL-2314 Tidies

JAL-2314 Re-annotated unit tests using Jws2Discoverer

JAL-2446 optimised new method to find feature colour for overview

Merge branch 'develop' into features/JAL-2446NCList

Conflicts:
src/jalview/gui/SeqCanvas.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java

JAL-2461 Removed DAS error stack trace, updated message

JAL-2388 Reinstated original overview checks for annotation display

Merge remote-tracking branch
'origin/bug/JAL-2436featureRendererThreading' into develop

Conflicts:
src/jalview/appletgui/OverviewPanel.java
src/jalview/gui/OverviewPanel.java

Merge remote-tracking branch 'origin/develop' into
bug/JAL-2436featureRendererThreading

Conflicts:
src/jalview/appletgui/OverviewPanel.java
src/jalview/gui/OverviewPanel.java

JAL-2311 suppress autocalc'd annotation to isolate the 'real' failure

JAL-2307 Fixed SiftsClient unit test

JAL-2306 assert no DAS sources

Merge branch 'develop' into features/JAL-2446NCList

Conflicts:
src/jalview/datamodel/Sequence.java
src/jalview/gui/OverviewPanel.java

JAL-2438 removed (non-functional) lastSeq, lastSequenceFeatures

JAL-2243 update discovered features on opening structure in Chimera

JAL-2438 check for null FeatureRenderer

Merge branch 'features/JAL-2388OverviewWindow' into develop

JAL-2446 FeatureStore with NCList - work in progress

Merge branch 'bug/JAL-2421overviewboxflicker' into develop

JAL-2388 Comment typo

JAL-2388 ViewportRanges unit test

JAL-2437 Synchronization corrections and unit tests

JAL-2388 Renamed column and row subtraction functions

Merge branch 'merges/develop_JAL2295setChimeraAttributes' into develop

JAL-1933 refactor parameter for code clarity

JAL-2388 Applied ViewportRanges to code

JAL-2388 Renamed viewport position props to viewport ranges

JAL-2388 Unit test update

JAL-2388 Applet update for overview panel

JAL-2439 Out-by-one in setting endRes/endSeq

JAL-2431 show cDNA consensus after New View in split frame

JAL-2388 Unit tests and tidies

JAL-2443 push getResidueBoxColour inside getResidueColour

JAL-2438 corrected getFeatureRenderer()

JAL-2442 applet feature transparency also on overview or structure

JAL-2438 handle null FeatureRenderer in FeatureColourFinder

JAL-2438 refactored checks for 'no features displayed'

JAL-2438 clarify code and javadoc, reinstate updateFeatures() check

Merge branch 'develop' into bug/JAL-2436featureRendererThreading

Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow

JAL-2388 Working overview panel

JAL-2439 Fixes to out-by-one sequence indexing in gui classes

JAL-2388 New hidden cols/seqs functions to support overview panel

JAL-2438 unit test, fixes, Javadoc updates

JAL-2438 unit tests for FeatureColourFinder (transparency tbc!)

JAL-2438 Javadoc updates

JAL-2438 comment/Javadoc tidies

JAL-2438 corrected handling of default colour

JAL-2438 FeatureColourFinder refactored from FeatureRenderer, fr not
cloned for structure viewers

JAL-2437 Fixed reordering of sequences when hiding and revealing

JAL-2388 Moving some alignment panel logic into overview (in progress)

JAL-2426 Checks on conservation thread in case we are shutting down

JAL-2426 Removal of NPE in conservation thread when closing Jalview

JAL-2388 Minor fix for annotation graph, removed unit test dep on gui

JAL-2430 colour columns hidden in alignment gray on structure

JAL-2295 avoid quotes breaking attribute value parsing

JAL-2388 Fixed inherited&new out-by-one errors; further unit tests

JAL-2295 status messages for Chimera attributes set and for failed
superposition

JAL-2388 Additional unit tests

JAL-2388 Missed commit

Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow

JAL-2429 Messed something up, merged conflicts

JAL-2429 findColumnPosition returns 0 for cols in region starting at 0

JAL-2429 Additional fix to ColumnSelection when hidden cols start at 0

JAL-2388 Dependency tidy

JAL-2388 Remove OverviewDimensions dependency on gui classes