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JAL-4286
Allow command line / programmatic export of images from external structure viewers
Focus on specific regions of RNA structure when viewing in VARNAJAL-4267
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 CLIJAL-4263
Test and squash memory leaks when working with lots of files via Jalview's NG-CLI
allow adjustment of gap opening and extension for built in nw alignment
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 filesJAL-4241
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
Include link for 'View in VARNA' for RNA secondary structure annotation tracks
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
links to external sites in jalview built-in help should open in the configured browser
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
Temperature and Secondary structure reference annotation not displayed when PDB + PAE loaded via structure chooser local file option
Multi-Harmony service parsing error at JalviewJS launch
user preference for automatically showing PAE annotation row along side pLDDT when loading structure from alphafold
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
Jalview 2.11.2.5 not compatible with 3d-beacons api v2.0
Recipe for embedding a Jalview MSA in a JavaFX app
Allow gradle build to create suffixed DEVELOP-... builds with channel appbase
Output stderr and stdout when running tests via gradle
allow default jalview loglevel to be configured via a system property
updated test dependencies (testng-7.7.0,classgraph-4.8.152,mockito-core-4.10.0,jquery-3.6.1)
update 2.12 alpha branch from 2.11.2.6
Application ownership
ncRNA and genes without product attributes are not imported from Genbank and EMBL format files
easier select-by-annotation and shade-by-annotation optionsJAL-4087
Jalview GUI adapted for Touch and Gesture interactions
Saving a project to a windows shared drive and loading it again doesn't restore Jmol views
Update installer and instructions to support installation in multi-user context
Seamless getdown updates between j8 based Jalview 2.11.x and j11 based Jalviews
Add a facility in Jalview application for user to put jalview launch script in their PATH
Mouseover on genomic loci propagated to 2D and 3D structures of transcripts and products
Use timers to maintain interactivity when retrieving structure data prior to viewing
Add EBI phmmer web service
Support for multi-character chain IDs
Select/Fetch all button for database query results
Preferences dialog blocks the UI if the web service host is slow to response.
'Find' dialog doc not listed in contents, and referred to as 'Search Dialog' in the window menus docs
remove defunct RNAView from Jalview
Improve getdown launcher so it continues to launch Jalview when it can't update, Shift + launch to recover 'installer version of jalview', and other improvements
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