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JAL-4613
Selection can go beyond right-most rendered position in wrapped alignment in 2.12 merge
Secondary structure consensus not displayed despite preference enabled
rightmost column in Wrapped alignment not being renderedJAL-4609
implement save session for Jmol as blocking callback off gui thread
tidy up asynchronous callbacks associated with gui windows that have been closed
Export images of alignments missing part of sequence
Hide the 'All' secondary structure consensus annotation when just one type is available
Manual import of JPred annotation data does not trigger display of secondary structure consensus
Allow enabling/disabling of autocalculated rows for alignment independently of the 'New View' preferencesJAL-4598
The macOS (Intel) Disk Image download link appears to be broken
sync jalview's biotools record with bio.tools
Secondary structure consensus appears to overlap with other annotation
Fileformat Exception reported for retrieval of a nonexistant PFAM accession rather than recognising when entry 'Does not exist'
avoid race conditions when workers have not updated after annotations are addedJAL-4587
Shade group associated annotation label with colour assigned to group (e.g. from tree partition)
exon features become visible when adjusting feature settings for CDS alignment
Web service URL configuration dialog doesn't work in JalviewJS
Secondary Structure Provider Colours for 2.11.5.1 - JalviewJS
Use GA4 / Plausible for jalview's online help documentation
structures with no biopolymer chains generate (non-fatal) exceptions when mapping them to a sequence
Allow 'jvl' files to be processed via the jalview commandline tool
Handle relative paths in JVL files
New views for a CDS/Protein alignment have a 'cDNA PID' annotation row
review and revise the binary node / SequenceNode / Column model for trees
more clearly document the way the overview works
trackpad scrolling on annotation panel when structure view is open causes massive slow down
Enable column selection on line graph annotations
Update jalview webservices documentation page
Input sequences returned as alignment result if job fails on server
sensible precision for tree distance labels
Jalview reports that input data didn't have enough sequences if slivka rejects an MSA job
Location of structure viewer not faithfully saved and restored in project
FAQ for the 'delete userland getdown directory' to rescue a stubbornly broken Jalview install
Migrate to Java 11 for Jalview production versionJAL-4488
routine service and program integration tests
Temporarily configure 3d structure viewer via CLI for a jalview session
allow pairwise alignment gap parameters to be adjusted
Progress bars for PCA, trees and pairwise alignments, and cancel buttons.
Automatically manage 'experimental' feature documentation in release notes
highlight positions in structures associated with many aligned transcripts
Add support for PaSiMap analysis in JalviewJS
Jmol view doesn't show all selected structures in 3d structure chooser mapped to sequences
refactor ResidueShaderI to support new types of data-dependent shading
Jalview could recognise .features, .annotations and .newick files belonging to an alignment file when all dragged-and-dropped onto it
Consensus annotations and Tree visualisations for sequence annotation
Dynamic value colouring of annotations, e.g. linegraph, can be misleading
Annotation not redrawn correctly when scrolling left-right via trackpad in wrap mode
Convert loadFileWaitTillLoaded to a promise
Quitting the JalviewJS desktop makes the browser hang
update getdown/jre updater for apple silicon
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