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JAL-4526
Update jalview webservices documentation pageJAL-4524
Input sequences returned as alignment result if job fails on server
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 projectJAL-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.
highlight positions in structures associated with many aligned transcripts
Add support for PaSiMap analysis in JalviewJS
refactor ResidueShaderI to support new types of data-dependent shading
Consensus annotations and Tree visualisations for sequence annotationJAL-4361
Convert loadFileWaitTillLoaded to a promise
update getdown/jre updater for apple silicon
Reduce load on structure viewer when moving mouse over ruler
Sonoma 14.1.1 permissions issue
Some files in a linux desktop installation are not deleted when uninstalling
CMD+W closes the tree viewer rather than Jmol when viewing example 2.7 projectJAL-4326
gui controls for configuring bitmap export preferences
Option to align after retrieval of sequences before display
scripts adding new fileformats or colourschemes do not work when run via command line
Optimise Console <> GUI threads to ensure minimal work on GUI thread and minimal blocking of operations on gui thread producing output
Redesign sequence ID tooltip to improve user experience
unify behaviour of groovy scripts when called via CLI, run from Groovy console and calculate 'run script' menu
New alignment windows from aligment webservices inherit feature settings and layout from input
Fix failing AlignPanelTest.testCalculateIdWidth_withMaxWidth()
Automatically discover and import alphaFold or best PDBe model when retrieving proteins from Uniprot
Allow command line / programmatic export of images from external structure viewers
Focus on specific regions of RNA structure when viewing in VARNA
Allow injection of custom structure viewer script when viewing 3D data from Jalview
Allow specific format to be specified when importing a file via GUI and CLI
Test and squash memory leaks when working with lots of files via Jalview's NG-CLI
New documentation: extending.md linked from building.md
Return null from getRootDatasetSequence if there is no dataset sequence
Support import of foldseek's m8 alignment files
Annotation analysis results not aligned to selection.
RNA specific services are enabled for protein sequences.
make it easier to pick preferred experimental modalities for structure data
off by one in displayed VARNA secondary structure
Cannot cancel structure view open action once it has been started...JAL-4175
Allow masking when visualising and analysing PAE matrices
Read (and write) Relaxed PHYLIP formatted data
ScalePanelTest fails when run after AlignViewportTest and PaintRefresherTest
example JVP files no longer have distinct locations for expanded windows
Multi-Harmony service parsing error at JalviewJS launch
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
Migrate semantics for DBRefEntry version string to support versioned sources and cross-references
'Reload' for a jalview project results in all windows being duplicated
Interactive Matrix Viewer for PAE and other matrix objects
Recipe for embedding a Jalview MSA in a JavaFX app
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