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JAL-4175
Allow masking when visualising and analysing PAE matricesJAL-4170
links to external sites in jalview built-in help should open in the configured browserJAL-4155
ScalePanelTest fails when run after AlignViewportTest and PaintRefresherTest
Multi-Harmony service parsing error at JalviewJS launchJAL-4129
Migrate semantics for DBRefEntry version string to support versioned sources and cross-references
Interactive Matrix Viewer for PAE and other matrix objects
Jalview 2.11.2.5 not compatible with 3d-beacons api v2.0JAL-4113
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 2.11.2.6JAL-4087
Jalview GUI adapted for Touch and Gesture interactions
Seamless getdown updates between j8 based Jalview 2.11.x and j11 based Jalviews
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
Ensure Getdown can distinguish between macOS intel and macOS arm/Apple silicon
Use dedicated sequence data object when uniquifying the seuqences
Support extended PDB ids
broken tests in 2.12 branch - annotationreport and annotationcolourscheme
Jalview Develop Launcher fails if it used to launch a Jalview release channel
Should we use editorconfig to format code instead of CodeStyle?
Migrate Jalview JPred Client to use Slivka's JPred Services
Groovy console does not open when Jalview launched from shadowJar in Java 11 for recent versions of groovy
Make the alignment panel graphics layer HiDPI aware (i.e. use a higher resolution instead of automatically scaling lower resolution)
specify colour of helix and sheet symbols via GUI and Annotation File
Cannot export annotation rows for just selected/visible region via Stockholm
Provide undo/redo support when sequences are moved up or down the alignment via arrow keys
per-group annotations from AACon conservation calculations
Refactoring web services: callback-based communication between threads
UX for working with HMMs in Jalview
HMMER colourschemes are greyed out when HMMER suite is not configured
Jalview args CLI skips last format and outputs multiple files with input format
Jalview does not honour file format when exporting file as new format via command line
Combined row-wise and positional per-sequence annotation shading
Update SwingJS for missing classes needed in Jalview 2.12
Id width doesn't adjust for font size change
Update code and tests for short multi-line tooltips
Tidy up alignment panel tooltip code
allow for sequence mismatches between cross-referenced sequence records according to variant and splice-variant annotation
Preserve pfam and rfam metadata when exporting retrieved entries as Stockholm
All outside pings (e.g. telemetry and JABAWS/Slivka querying) will need to check existing Debian opt-in
Create Snap packaging for Jalview (complete package for various Linux distros, primarily Ubuntu)
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