---
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-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)
- <!-- 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
## New Known defects
- <!-- 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
git://source.jalview.org / jalview.git / blobdiff