---
version: 2.11.3.0
-date: 2023-07-19
+date: 2023-10-25
channel: "release"
---
## New Features
- <!-- JAL-4064 --> Native M1 build for macOS using Adoptium JRE 11 macos-aarch64
-- <!-- JAL-4054 --> Installers built with install4j10
-- <!-- JAL-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
-- <!-- JAL-3416 --> FlatLAF default look and feel on Linux, OSX and everywhere else ?
-
+- <!-- JAL-3416 --> Jalview now uses a standard 'look and feel' (FlatLaf) on Linux, OSX and everywhere else
- <!-- JAL-4019 --> Ambiguous Base Colourscheme
- <!-- JAL-4061 --> Find can search sequence features' type and description
- <!-- JAL-4062 --> Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences
-- <!-- JAL-1556 --> Quickly enable select and/or colour by for displayed annotation row via its popup menu
+- <!-- JAL-1556 --> Quickly enable select and/or colour by for displayed annotation row via annotation panel popup menu
- <!-- JAL-4094 --> Shift+Click+Drag to adjust height of all annotation tracks of same type
- <!-- JAL-4190 --> Pressing escape in tree panel clears any current selection
-
- <!-- JAL-4089 --> Use selected columns for superposition
- <!-- JAL-4086 --> Highlight aligned positions on all associated structures when mousing over a column
-
- <!-- 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-4307 --> Show or hide ligands in a Jmol structure view via View Ligands submenu
### Improved support for working with 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-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-4123 --> GUI and command line allows configuration of how temperature factor in imported 3D structure data should be interpreted
- <!-- JAL-3914 --> Import model reliability scores encoded as temperature factor annotation with their correct name and semantics
- <!-- JAL-4124 --> Store/Restore PAE data and visualisation settings from Jalview Project
- <!-- JAL-4083 --> Multiple residue sidechain highlighting in structure viewers from PAE mouseovers
-
### Jalview on the command line
-
-- <!-- JAL-4160,JAL-629 --> New command line argument framework allowing flexible batch processing, figure generation, and import of structures, pae matrices and other sequence associated data
+- <!-- JAL-4160,JAL-629,JAL-4262,JAL-4265, --> New command line argument framework allowing flexible batch processing, import of structures, pae matrices and other sequence associated data, and alignment and structure figure generation.
+- <!-- JAL-3830 --> Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
- <!-- 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
### 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-4253 --> Lower line of the sequence group border does not align with vertical and background residue box
+- <!-- 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-4213 --> "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range
- <!-- JAL-4119 --> EMBL-EBI SIFTS file downloads now use split directories
-
-- <!-- 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-4187 Powershell launcher script fails when given no arguments with the old ArgsParser
-
-known issue ? <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated
-
-
-- <!-- JAL-3830 --> Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
- <!-- JAL-3820 --> In Linux desktops' task-managers, the grouped Jalview windows get a generic name
-
-## Still in progress (delete on release)
-
-- <!-- JAL-2382 --> Import and display sequence-associated contact predictions in CASP-RR format
-- <!-- JAL-2349 --> Contact prediction visualisation
-- <!-- JAL-2348 --> modularise annotation renderer
+- <!-- JAL-4206 --> Improved file chooser's 'recent files' view and added filter for 'All known alignment files'
+- <!-- 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-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
### 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-4243 --> Jalview bio.tools description maintained under jalview's git repo and bundled with source release
- <!-- JAL-4182 --> reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active
- <!-- JAL-4177 --> Can press 'Add' or 'New View' multiple times when manually adding and viewing a 3D structure via structure chooser
- <!-- 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-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-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-2910 --> HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2))
## 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-4302 --> Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled.
- <!-- 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-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
+
git://source.jalview.org / jalview.git / blobdiff