---
version: 2.11.3.0
-date: 2023-03-07
+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-4064 --> Native M1 build for macOS using Adoptium JRE 11 macos-aarch64
+- <!-- 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 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-3858 --> Import and display alphafold alignment uncertainty matrices from JSON
+- <!-- JAL-4134,JAL-4158 --> Column-wise alignment groups and selections and interactive tree viewer for PAE matrices
+- <!-- 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,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-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-3820 --> In Linux desktops' task-managers, the grouped Jalview windows get a generic name
+- <!-- 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
## Issues Resolved
-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-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-4116 --> PDB structures slow to view when Jalview Java Console is open (2.11.2.7 patch)
+- <!-- 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-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-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