---
version: 2.11.3.0
-date: 2023-10-25
+date: 2023-11-03
channel: "release"
---
- <!-- JAL-4221 --> sequence descriptions are updated from database reference sources if not already defined
- <!-- JAL-4273 --> Visible adjuster marks to grab and adjust annotation panel height and id width
- <!-- JAL-4260 --> Adjustable ID margin when alignment is wrapped
-- <!-- JAL-4274 --> Command line options and configurable bitmap export preferences for height, width and scale factor
+- <!-- JAL-4274 --> Command line options and configurable bitmap export (via preferences file) for height, width and scale factor
- <!-- JAL-4307 --> Show or hide ligands in a Jmol structure view via View Ligands submenu
+- <!-- JAL-4252 --> Jmol's display is antialiased by default (smoother, less pixellated)
### Improved support for working with structures and computationally determined models
- <!-- JAL-3895 --> Alphafold red/orange/yellow/green colourscheme for structures
- <!-- JAL-4095 --> Interactive picking of low pAE score regions
-- <!-- JAL-4027 --> contact matrix datatype in Jalview
+- <!-- JAL-4027, JAL-3858, JAL-2292 --> Predicted Alignment Error annotation tracks for structures from AlphaFold DB
- <!-- JAL-4033 --> Selections with visual feedback via contact matrix annotation
- <!-- JAL-3855 --> Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/
- <!-- JAL-4091 --> Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows
- <!-- JAL-4315 --> Drag and drop feature colours file on an alignment to quickly apply feature settings
- <!-- JAL-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
- <!-- JAL-4304,JAL-4305 --> Upgrade bundled groovy to v4.0.15 and regularised interface for groovy scripts run from CLI, interactively and headlessly.
+- <!-- JAL-1713,JAL-2528 --> Overview display and hidden region visibility stored in Jalview projects
### Development and Deployment
- <!-- JAL-4054 --> Installers built with install4j10
- <!-- JAL-4167 --> Create separate gradle test task for some tests
- <!-- JAL-4212 --> Prevent gradle test on macOS continuously grabbing focus
- <!-- JAL-4111 --> Allow gradle build to create suffixed DEVELOP-... builds with channel appbase
+- <!-- JAL-4288 --> Update .jvl generation in build.gradle for jalview branch builds
- <!-- JAL-4243 --> Jalview bio.tools description maintained under jalview's git repo and bundled with source release
+- <!-- JAL-4110 --> Output stderr and stdout when running tests via gradle
+- <!-- JAL-3599 --> New gradle task providing runtime acceptance test for JalviewJS based on Chromium for Tests (still work in progress)
## Issues Resolved
- <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed
- <!-- JAL-4177 --> Can press 'Add' or 'New View' multiple times when manually adding and viewing a 3D structure via structure chooser
- <!-- JAL-4311 --> 3D beacons sources providing models scored with PLDDT and pTM not sorted against alphaFoldDB models
- <!-- JAL-4133 --> Jalview project does not preserve font aspect ratio when Viewport is zoomed with mouse
-- <!-- JAL-4253 --> Lower line of the sequence group border does not align with vertical and background residue box
+- <!-- JAL-4253,JAL-4293 --> Lower line of the sequence group border does not align with vertical and background residue box
- <!-- JAL-4128 --> Resizing overview quickly with solid-drags enabled causes exception
- <!-- JAL-4150 --> Sequences copied to clipboard from within Jalview cannot be pasted via the desktop's popup menu to a new alignment window
- <!-- JAL-2528, JAL-1713 --> Overview window is saved in project file, and state of 'show hidden regions' is preserved.
- <!-- JAL-4298 --> Java Console opening at startup with the exampleFile_v2_7.jvp opening (nearly always) causes Jalview to hang
- <!-- JAL-4282 --> automatic positioning of ID width for imported project can fail for certain font size configured in User preferences (affects most versions of Jalview prior to 2.11.3.0)
- <!-- JAL-4223 --> RNAML import missing terminal residue
+- <!-- JAL-3088 --> RNA secondary structure annotation final-ending-solo-brace arrow points the wrong way
+- <!-- JAL-4218 --> Jalview source distribution unnecessarily includes dist directory with built jalview jar and dependencies
+- <!-- JAL-3921 --> Jmol sessions involving large molecules may not be fully saved in Jalview project files (known defect in 2.11.2.x)
## New Known defects
- <!-- JAL-4303 --> EBI-AlphaFold PLDDT colours cannot be overlaid on alignment via 'Colour by annotation' unless the alignment's colourscheme has been set to 'None' via the Colours menu.
- <!-- JAL-4178 --> Cannot cancel structure view open action once it has been started via the structure chooser dialog
- <!-- JAL-4142 --> Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately
- <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated
+- <!-- JAL-4325 --> Overview shown and then closed when importing legacy jalview projects without overview store/restore information
- <!-- JAL-4165 --> Missing last letter when copying consensus sequence from alignment if first column is hidden
- <!-- JAL-4261 --> Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export
- <!-- JAL-3024 --> Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x)
- <!-- JAL-4291 --> Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation
- <!-- JAL-4323 --> scripts adding new fileformats or colourschemes do not work when run via command line
-
+- <!-- JAL-4290 --> Headless alignment export with structure annotations doesn't include secondary structure and temperature factor
+- <!-- JAL-4151 --> Copy sequences from one alignment and Pasting as new window in another alignment doesn't propagate title from original alignment's window
+- <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0)
git://source.jalview.org / jalview.git / blobdiff