--- version: 2.11.3.0 date: 2023-11-15 channel: "release" --- ## New Features - Native M1 build for macOS using Adoptium JRE 11 macos-aarch64 - Jalview now uses a standard 'look and feel' (FlatLaf) on Linux, OSX and everywhere else - Ambiguous Base Colourscheme - Find can search sequence features' type and description - Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences - Quickly enable select and/or colour by for displayed annotation row via annotation panel popup menu - Shift+Click+Drag to adjust height of all annotation tracks of same type - Pressing escape in tree panel clears any current selection - Use selected columns for superposition - Highlight aligned positions on all associated structures when mousing over a column - sequence descriptions are updated from database reference sources if not already defined - Visible adjuster marks to grab and adjust annotation panel height and id width - Adjustable ID margin when alignment is wrapped - Command line options and configurable bitmap export (via preferences file) for height, width and scale factor - Show or hide ligands in a Jmol structure view via View Ligands submenu - Jmol's display is antialiased by default (smoother, less pixellated) ### Improved support for working with structures and computationally determined models - Alphafold red/orange/yellow/green colourscheme for structures - Interactive picking of low pAE score regions - Predicted Alignment Error annotation tracks for structures from AlphaFold DB - Selections with visual feedback via contact matrix annotation - Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/ - Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows - GUI and command line allows configuration of how temperature factor in imported 3D structure data should be interpreted - Import model reliability scores encoded as temperature factor annotation with their correct name and semantics - Import and display alphafold alignment uncertainty matrices from JSON - Column-wise alignment groups and selections and interactive tree viewer for PAE matrices - Store/Restore PAE data and visualisation settings from Jalview Project - Store and restore adjustable ID margin and annotation panel height in Jalview projects - Multiple residue sidechain highlighting in structure viewers from PAE mouseovers - 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. - PDB or mmCIF files with chains with negative RESNUMs for their whole sequence extent cannot be linked to alignments ### Jalview on the command line - 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. - Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers) - Assume --headless when jalview is run with a command line argument that generates output - Automatically adjust Left margin on import to avoid cropping of annotation labels & sequence IDs - Specify alignment title on import via --title argument - 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 - Secondary structure annotation glyphs are rendered anti-aliasing when enabled - Helix and Sheet glyphs vertically centred with respect to grey coil secondary structure annotation track - feature should be displayed when its rendering and filtering settings are adjusted - Updated JFreeSVG (https://www.jfree.org/jfreesvg) from 2.1 to 3.4.3 - Name of alignment and view included in overview window's title - "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range - EMBL-EBI SIFTS file downloads now use split directories - In Linux desktops' task-managers, the grouped Jalview windows get a generic name - Improved file chooser's 'recent files' view and added filter for 'All known alignment files' - Relative files added to recent files list via import from command line are selected when Jalview opened from same location - Reduce number of database crossreferences shown in tooltip - Drag and drop feature colours file on an alignment to quickly apply feature settings - Improved startup info in console output: which properties file was being used and slight revisions to the formatting of platform information. - Upgrade bundled groovy to v4.0.15 and regularised interface for groovy scripts run from CLI, interactively and headlessly. - Overview display and hidden region visibility stored in Jalview projects - Updated faq and documentation urls in splashscreen and help documentation ### Development and Deployment - Installers built with install4j10 - Create separate gradle test task for some tests - Prevent gradle test on macOS continuously grabbing focus - Allow gradle build to create suffixed DEVELOP-... builds with channel appbase - Update .jvl generation in build.gradle for jalview branch builds - Jalview bio.tools description maintained under jalview's git repo and bundled with source release - Output stderr and stdout when running tests via gradle - New gradle task providing runtime acceptance test for JalviewJS based on Chromium for Tests (still work in progress) ## Issues Resolved - Jmol view not always centred on structures when multiple structures are viewed - Unsaved Alignment windows close without prompting to save, individually or at application quit. - Can quit Jalview while 'save project' is in progress - 'Use original colours' option of colour by annotation not honoured when restoring view from project - PDB structures slow to view when Jalview Java Console is open (2.11.2.7 patch) - Multiple overview windows can be opened for a particular alignment view when multiple views are present - Overview windows opened automatically (due to preferences settings) lack title - Show Crossrefs fails to retrieve CDS from ENA or Ensembl for sequences retrieved from Uniprot due to version numbers in cross-reference accession - Uniprot parser fails to import sequences with features that have 'unknown' start or end - Stockholm export does not include sequence descriptions - Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows - reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active - Can press 'Add' or 'New View' multiple times when manually adding and viewing a 3D structure via structure chooser - 3D beacons sources providing models scored with PLDDT and pTM not sorted against alphaFoldDB models - Jalview project does not preserve font aspect ratio when Viewport is zoomed with mouse - Lower line of the sequence group border does not align with vertical and background residue box - Resizing overview quickly with solid-drags enabled causes exception - Sequences copied to clipboard from within Jalview cannot be pasted via the desktop's popup menu to a new alignment window - Overview window is saved in project file, and state of 'show hidden regions' is preserved. - JvCacheableInputBoxTest flaky on build server - SLF4J produces an error to STDERR at Jalview startup due to missing class - macOS Dock and KDE taskbar names Jalview icon "java" when running jalview via the getdown app launcher - HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2)) - Groovy console does not open when Jalview launched from jalview's Java 11 executable jar (available via conda) for recent versions of groovy - Don't offer View model page for sources that do not have model pages - Java Console opening at startup with the exampleFile_v2_7.jvp opening (nearly always) causes Jalview to hang - 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) - RNAML import missing terminal residue - RNA secondary structure annotation final-ending-solo-brace arrow points the wrong way - Jalview source distribution unnecessarily includes dist directory with built jalview jar and dependencies - Jmol sessions involving large molecules may not be fully saved in Jalview project files (known defect in 2.11.2.x) ### New Known Issues - 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. - Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled. - PAE partition not shown in the same place when tree is closed and reopened - Cannot cancel structure view open action once it has been started via the structure chooser dialog - Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately - 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0) - Overview shown and then closed when importing legacy jalview projects without overview store/restore information - Missing last letter when copying consensus sequence from alignment if first column is hidden - Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export - Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x) - Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation - scripts adding new fileformats or colourschemes do not work when run via command line - Headless alignment export with structure annotations doesn't include secondary structure and temperature factor - Copy sequences from one alignment and Pasting as new window in another alignment doesn't propagate title from original alignment's window - Annotation colouring dialog box doesn't remember 'use original colours' settings when opened via the Colour menu - When the Groovy console is open Jalview does not prompt to save before quitting - Jalview works with but is not fully compatible with latest Ensembl REST API (15.6)