Jalview 2.11.4.0

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The 2.11.4 series is the fourth in the minor-release trilogy planned for Jalview’s 2.11 series.

This release adds new capabilities for visualisation and clustering of protein secondary structure annotations, along with enhanced control of the display and analysis of secondary structure from different sources of 3D structure and prediction.

The Calculations dialog has also been revised to accommodate a new implementation of the spatial clustering method PASiMap (Su et al. 2022 Comp. Struc. Biotech.) which was added to Jalview by Thomas Morell and Jennifer Fleming.

Jalview 2.11.4 also has new installers and command line scripts that bring several minor improvements, and also makes it easier for IT admins to manage Jalview installations on computers used by many different people. New installations of Jalview will by default store updates in user’s home directories, Automatic updates can also be disabled, and updates instead carried out using a new jalview_update command line tool.

Experimental features

This release includes experimental support (enabled in the Tools menu) for handling drag’n’drop of alignment, tree, annotations and feature file(s) onto the Jalview Desktop. They can also be dragged onto the Jalview icon.

New Features
  • Pairwise alignment can be performed with different substitution matrices
  • PCA, Pairwise alignment, trees and PaSiMap window titles include the matrix and additional parameters used
  • “Select format by extension” option in Jalview’s “Save As” dialog’s file type dropdown menu

Experimental Features (enable via Desktop’s tools menu)

  • PCA and PaSiMap panels allow Right-click and drag to select several sequences at once
  • Jalview sensibly handles opening or a drag’n’drop of several .features, .annotations and .newick files onto an alignment

development and deployment

  • Add a command-line wrapper script to macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
  • Redirect stdout and stderr to file when launched from getdown
  • OSX DMGs have custom icons and mount point includes architecture and version details
  • Add error message when launched directly from Jalview Installer DMG volume
  • Allow jalview auto-updates to download to and work from separate user-space directory
  • Gradle build with install4j launchers
  • Implement in Jalview (and getdown for JVL) the use of specific scheme names for different channels (e.g. jalviewd://)
  • integrate OSX codesigning scripts in jalview’s repository
  • new documentation describing how jalview project XML schema is maintained (in doc/jalview-projects.md)
  • updated Jalview’s Ensembl’s client for v15.8 of the REST API - change in BRAF query returned by ensembl Genes for chicken for GRCg7b (now ENSGALG00010013466, was ENSGALG00000012865)
  • “Getdown DEVELOP Channel” linkCheck fails if there’s a link to whatsNew#experimental or releaseHistory from other help pages

Issues Resolved

  • jalview does not fetch from a URL containing a redirect
  • HTTP errors are often interpreted to the user as a file format error - and FileNotFound errors are not propagated from Web or Local file import
  • launcher.log from jalview runtime missing newlines and also lacks stdout/stderr reported in Jalview Console
  • Possible “Zip Slip Vulnerability” in getdown
  • jalview.bin.CommandsTest.headlessOrGuiImageOutputTest produces different images for –gui and –headless when using certain .jalview_properties
  • Release installer DMG does not display the background image
  • Getdown splash screen should disappear as soon as the Jalview Desktop is created/visible
  • Race condition in Jalview quit handler that can cause a hang on very slow interactive systems
  • Adjusting the saved as file format via the Alignment window Save As… dialog box doesn’t actually change the format used to save the alignment
  • Annotation labels from protein disorder services include html tags from description

development and deployment

  • Removed gradle build’s dependency on gradle-imagemagick plugin to allow building on windows (still need imagemagick installed on path for splashscreen commit watermark)
  • Fixed inconsistencies in test suite on different platforms
  • The rendering of the text “Window” for the Window menu item is different to the other menus when testing in Linux

New Known Issues

  • PaSiMap not available in JalviewJS
  • Jalview ignores ncrna genes when importing from genbank format files
  • Sequence letter aspect ratio not set correctly when aspect ratio is very narrow after middle-mouse drag
  • cannot store/restore group associated secondary structure consensus annotations
  • spurious output image .extensions cause jalview CLI execution to fail with Null Pointer Exception (since 2.11.3.0)