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JAL-4439
Multiple pseudo windowsJAL-4422
improve space and time efficiency for comparison and redundancy calculations
Release installer DMG does not display the background image
Enabling just "Add Secondary Structure" Structure preference when importing structure via CLI results in temperature factor being shown in alignment
Recognise and map multimeric models from swissmodel via 3d-beacons
Friendlier names for automatically created groupsJAL-4399
Consensus annotations and Tree visualisations for sequence annotation
Allow local_eclipse.properties to be read by buildship
Dynamic value colouring of annotations, e.g. linegraph, can be misleading
Annotation not redrawn correctly when scrolling left-right via trackpad in wrap mode
The jalview:// (or jalviewx://) scheme does not work when a port is specified
Quitting the JalviewJS desktop makes the browser hangJAL-4359
patch JalviewJS to correctly handle relative and absolute paths from page rather than j2s directory
CMD+W closes the tree viewer rather than Jmol when viewing example 2.7 project
When the Groovy console is opened Jalview does not prompt to save before quitting
properly handle 3d-beacons sources other than alphafold providing PLDDT confidence scores & shading from model quality score type response
tree vertical scale not correct when shown in tree viewer (but fine when exported)
sequence ID tooltip in JalviewJS has double line spacing
java.util.Random.NextLong not implemented
PAEs not being shown in JalviewJS
sub-labels for annotation rowsJAL-4138
user preferences and structure chooser controls for automatically showing PAE annotation row along side pLDDT when loading structure from alphafold, and control secondary structure and temp factor display
Configure how temperature factor column should be interpreted when loading a 3D structure for a sequence
update swingJS for JalviewJS 2.11.2,2.11.3, and 2.11.4
Disable startup preferences and other irrelevant widgets for JalviewJS
Mouseover on genomic loci propagated to 2D and 3D structures of transcripts and products
Import model reliability scores encoded as temperature factor annotation with their correct name and semantics
propagate mouseover, region highlights and selection events on reference to transcripts and products
IntervalStore should preserve order of addition of co-located features
Automatically hide alignment calculation rows when only one sequence is present
Make it easier to modify colour for a group or all groups via the Colours menu
no binding between derived annotation rows and original structure data file parsed via Jmol
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