Jalview 2.11.3.0

Version Date: 15 November 2023

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The 2.11.3 Jalview release features a new and more powerful command line interface, support for in-depth exploration of predicted alignment error (PAE) matrices from AlphaFold in the context of multiple alignments, AlphaFold’s standard Blue-Orange-Red confidence colourscheme, and a substantial number of minor improvements and bug fixes.

Interactive exploration of AlphaFold Predicted Alignment Error Matrices

Predicted alignment error (PAE) matrices are JSON files produced by AlphaFold and other 3D structure prediction tools, which reflect how well any two positions in a predicted structure are positioned correctly relative to each other. Jalview automatically imports PAE matrices when retrieving protein structures from the EBI-AlphaFold database. A PAE matrix file can also be provided when manually importing 3D structure data.

Once imported, PAE matrices are shown in annotation tracks as a heat map shaded pale to dark green, where darker shades indicate higher confidence in relative positioning. Right-clicking a PAE Matrix’s annotation label provides the option to cluster the columns of the matrix, producing a tree where regions of well arranged structure are grouped together, allowing columns containing those regions to be selected and manipulated further.

Jalview’s Next Generation Command Line Interface

Jalview 2’s original command line interface (CLI) allowed alignments to be imported, annotated and overlaid with sequence features, coloured, associated with trees, and exported either as figures (EPS, PNG, SVG, HTML SVG or an interactive BioJS page) or with one of Jalview’s supported alignment export file formats. The new command line interface provides all this, as well as a range of additional functionality previously only available via the GUI:

3D structures can be associated with sequences in alignments and shown in Jmol or external viewers
Secondary structure, Model Reliability and Temperature factor can be shown and used to colour alignments
PAE Matrices can be imported and shown as annotation
3D structure data shown in Jmol can be exported as PNG
Scale factors and dimensions can be specified, allowing high resolution image exports

In addition to these new functionality, next generation CLI operations can be applied to a range of files and directories through the use of wild-cards. This allows faster and more efficient processing of large numbers of alignments. It also facilitates modularisation of operations through the use of ‘command-line argument files’.

All new CLI parameters are preceded by ‘–’, as opposed to an optional single ‘-’ which was used in Jalview’s old CLI. Old style arguments can still be used, so existing scripts will still work as before, but old-style operations cannot be mixed with new operations in the same CLI call. Use of old command line operations will also raise a warning, and we plan to completely remove support in Jalview’s next major release (2.12).

As usual, please let us know via Jalview’s Discussion forum of any issues you encounter using the new CLI, and of course any requests for improvement or new functionality !

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)