---
version: 2.11.3.0
-date: 2023-11-03
+date: 2023-11-15
channel: "release"
---
- <!-- JAL-4281 --> Store and restore adjustable ID margin and annotation panel height in Jalview projects
- <!-- JAL-4083 --> Multiple residue sidechain highlighting in structure viewers from PAE mouseovers
- <!-- JAL-4147 --> Per-structure and chain shown when annotation shown sorted by label enabling secondary structure and temperature factor scores from different chains and structures for the same sequence to be visually compared.
+- <!-- JAL-4216 --> PDB or mmCIF files with chains with negative RESNUMs for their whole sequence extent cannot be linked to alignments
### Jalview on the command line
- <!-- JAL-4121 --> Assume --headless when jalview is run with a command line argument that generates output
- <!-- JAL-244 --> Automatically adjust Left margin on import to avoid cropping of annotation labels & sequence IDs
- <!-- JAL-901 --> Specify alignment title on import via --title argument
-- <!-- JAL-4195,JAL-4194,JAL-4193 --> sensible responses from the CLI when things go wrong during image export
-- Add a command line option to set Jalview properties for this session only
-- Add a command line option to suppress opening the startup file for this session
+- <!-- JAL-4195 --> Sensible responses from the CLI when things go wrong during image export
+- <!-- JAL-4194 --> Add a command line option to set Jalview properties for this session only
+- <!-- JAL-4193 --> Add a command line option to suppress opening the startup file for this session
### Other improvements
- <!-- JAL-4250 --> Secondary structure annotation glyphs are rendered anti-aliasing when enabled
-- <!-- JAL-325 --> Helix and Sheet glyphs vertically centered with respect to grey coil secondary structure annotation track
+- <!-- JAL-325,JAL-4250 --> Helix and Sheet glyphs vertically centred with respect to grey coil secondary structure annotation track
- <!-- JAL-4317 --> feature should be displayed when its rendering and filtering settings are adjusted
- <!-- JAL-4250 --> Updated JFreeSVG (https://www.jfree.org/jfreesvg) from 2.1 to 3.4.3
- <!-- JAL-3119 --> Name of alignment and view included in overview window's title
- <!-- JAL-4206 --> Relative files added to recent files list via import from command line are selected when Jalview opened from same location
- <!-- JAL-4308 --> Reduce number of database crossreferences shown in tooltip
- <!-- 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-3676 --> Improved startup info in console output: which properties file was being used and slight revisions to the formatting of platform information.
- <!-- 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
+- <!-- JAL-4169 --> Updated faq and documentation urls in splashscreen and help documentation
### Development and Deployment
- <!-- JAL-4054 --> Installers built with install4j10
- <!-- 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-3776 --> Cancelling interactive calculation leaves empty progress bar.
- <!-- JAL-3772 --> Unsaved Alignment windows close without prompting to save, individually or at application quit.
- <!-- JAL-1988 --> Can quit Jalview while 'save project' is in progress
- <!-- JAL-4126 --> 'Use original colours' option of colour by annotation not honoured when restoring view from project
- <!-- JAL-3784 --> Multiple overview windows can be opened for a particular alignment view when multiple views are present
- <!-- JAL-3785 --> Overview windows opened automatically (due to preferences settings) lack title
- <!-- JAL-2353 --> Show Crossrefs fails to retrieve CDS from ENA or Ensembl for sequences retrieved from Uniprot due to version numbers in cross-reference accession
+- <!-- JAL-4334 --> Uniprot parser fails to import sequences with features that have 'unknown' start or end
- <!-- JAL-4184 --> Stockholm export does not include sequence descriptions
- <!-- JAL-4075 --> Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows
- <!-- JAL-4182 --> reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active
- <!-- JAL-2528, JAL-1713 --> Overview window is saved in project file, and state of 'show hidden regions' is preserved.
- <!-- JAL-4153 --> JvCacheableInputBoxTest flaky on build server
- <!-- JAL-4255 --> SLF4J produces an error to STDERR at Jalview startup due to missing class
-- <!-- JAL-4189 --> macOS Dock and KDE taskbar names Jalview icon "java" when running
+- <!-- JAL-4189 --> macOS Dock and KDE taskbar names Jalview icon "java" when running jalview via the getdown app launcher
- <!-- JAL-2910 --> HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2))
- <!-- JAL-3783 --> Groovy console does not open when Jalview launched from jalview's Java 11 executable jar (available via conda) for recent versions of groovy
- <!-- JAL-4310 --> Don't offer View model page for sources that do not have model pages
- <!-- 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
+### New Known Issues
- <!-- 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-4302 --> Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled.
+- <!-- JAL-4338 --> PAE partition not shown in the same place when tree is closed and reopened
- <!-- 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-4127 --> 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0)
- <!-- 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-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-4157 --> Annotation colouring dialog box doesn't remember 'use original colours' settings when opened via the Colour menu
+- <!-- JAL-4327 --> When the Groovy console is open Jalview does not prompt to save before quitting
+- <!-- JAL-4328 --> Jalview works with but is not fully compatible with latest Ensembl REST API (15.6)
git://source.jalview.org / jalview.git / blobdiff