Jalview 2.11.0


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Version Date: 
04-07-2019

Jalview 2.11.0 introduces support for loading VCF files, and new filters and shading models for sequence features. Under the hood, we've addressed many bugs, and also made some important changes in the way the Jalview desktop is installed and launched.

New Features

  • Jalview Native Application and Installers built with install4j (licensed to the Jalview open source project) rather than InstallAnywhere
  • Jalview Launcher System to auto-configure memory settings, receive over the air updates and launch specific versions via (Three Rings' GetDown)
  • File type associations for formats supported by Jalview (including .jvp project files)
  • Jalview launch files (.jvl) to pass command line arguments and switch between different getdown channels
  • Backup files created when saving Jalview project or alignment files
  • Annotate nucleotide alignments from VCF data files
  • Version of HTSJDK shipped with Jalview updated to version 2.12.0
  • Alternative genetic code tables for 'Translate as cDNA'
  • Update of Ensembl Rest Client to API v10.0
  • Enhanced visualisation and analysis of Sequence Features
    • IntervalStoreJ (NCList implementation that allows updates) used for Sequence Feature collections
    • Sequence features can be filtered and shaded according to any associated attributes (e.g. variant attributes from VCF file, or key-value pairs imported from column 9 of GFF file)
    • Feature Attributes and shading schemes stored and restored from Jalview Projects
    • Use full Sequence Ontology (via BioJava) to recognise variant features
    • Show synonymous codon variants on peptide sequences (also coloured red by default)
    • Popup window to show full report for a selected sequence feature's details
    • More efficient sequence feature render algorithm (Z-sort/transparency and filter aware)
    • Improved tooltips in Feature Settings dialog
  • Symmetric score matrices for faster tree and PCA calculations
  • Principal Components Analysis Viewer
    • Principal Components Analysis results and Viewer state saved in Jalview Project
    • 'Change parameters' option removed from viewer's drop-down menus
    • Can use shift + arrow keys to rotate PCA image incrementally
    • PCA plot is depth cued
  • New 'Colour by Sequence ID' option
  • Speed and Efficiency
    • More efficient creation of selections and multiple groups when working with large alignments
    • Speedier import of annotation rows when parsing Stockholm files
  • User Interface
    • Finder panel remembers last position in each view
    • Alignment Overview now WYSIWIS (What you see is what is shown)
      Only visible regions of alignment are shown by default (can be changed in user preferences)
    • File Chooser stays open after responding Cancel to the Overwrite Dialog
    • Better popup menu behaviour when all sequences are hidden
    • Status bar shows bounds when dragging a selection region, and gap count when inserting or deleting gaps
    • Status bar updates over sequence and annotation labels
    • Annotation tooltips and popup menus are shown when in wrapped mode
    • Can select columns by dragging left/right in a graph or histogram annotation
    • Help button on Uniprot and PDB search panels
    • Cursor changes over draggable box in Overview panel
    • Consistent ordering of links in sequence id popup menu
    • Red line indicating tree-cut position not shown if no subgroups are created
    • Removed ability to configure length of search history by right-clicking search box
  • Jalview Groovy Scripting Console updated to Groovy v2.5
  • Java 11 Support (not yet on general release)
    • OSX GUI integrations for App menu's 'About' entry and trapping CMD-Q

Deprecations

  • DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop
  • Castor library for XML marshalling and unmarshalling has been replaced by JAXB for Jalview projects and XML based data retrieval clients
  • Disable VAMSAS menu in preparation for removal
  • Jalview Desktop no longer distributed via Java Web Start

Documentation

  • Added remarks about transparent rendering effects not supported in EPS figure export
  • Typos in documentation for Preferences dialog

Development and Release Processes

  • Build system migrated from Ant to Gradle
  • Enhanced checks for missing and duplicated keys in Message bundles
  • Eclipse project configuration managed with gradle-eclipse
  • Atlassian Bamboo continuous integration for unattended Test Suite execution
  • Memory test suite to detect leaks in common operations
  • More unit test coverage, and minor issues resolved
  • Developer documentation migrated to markdown (with HTML rendering)
  • HelpLinksChecker runs on Windows
  • New URLs for publishing development versions of Jalview

Issues Resolved

  • Timeouts when retrieving data from Ensembl
  • 'View [Structure] Mappings' and structure superposition in Jmol fail on Windows
  • Blank error dialog is displayed when discovering structures for sequences with lots of PDB structures
  • Text misaligned in EPS or SVG image export with monospaced font
  • Warning of 'Duplicate entry' when saving Jalview project involving multiple views
  • Overview for complementary view in a linked CDS/Protein alignment is not updated when Hide Columns by Annotation dialog hides columns
  • Selection highlighting in the complement of a CDS/Protein alignment stops working after making a selection in one view, then making another selection in the other view
  • Annotations tooltip changes beyond visible columns
  • Table Columns could be re-ordered in Feature Settings and Jalview Preferences panels
  • Jalview hangs when closing windows, or redrawing the overview with large alignments
  • Tree and PCA calculation fails for selected region if columns were selected by dragging right-to-left and the mouse moved to the left of the first column
  • Couldn't hide selected columns adjacent to a hidden column marker via scale popup menu
  • Error message for trying to load in invalid URLs doesn't tell users the invalid URL
  • Tooltips displayed for features filtered by score from view
  • Sequence Variants retrieved from Ensembl during show cross references or Fetch Database References are shown in red in original view
  • stop_gained variants not shown correctly on peptide sequence (computed variant shown as p.Res.null)
  • 'Graduated colour' option not offered for manually created features (where feature score is Float.NaN)
  • Blank extra columns drawn or printed when columns are hidden
  • Regular expression error for '(' in Select Columns by Annotation description
  • Scroll doesn't stop on mouse up after dragging out of Scale or Annotation Panel
  • Column selection incorrect after scrolling out of scale panel
  • Left/right drag in annotation can scroll alignment down
  • Error if mouse moved before clicking Reveal in scale panel
  • Column display is out by one after Page Down, Page Up in wrapped mode
  • Finder doesn't skip hidden regions
  • Finder searches in minimised alignments
  • 'Apply Colour to All Groups' not always selected on opening an alignment
  • 'Colour by Annotation' not marked selected in Colour menu
  • Per-group Clustal colour scheme changes when different groups in the alignment are selected
  • Internationalised colour scheme names not shown correctly in menu
  • Colour by Annotation can go black at min/max threshold limit
  • Value input for graduated feature colour threshold gets 'unrounded'
  • PCA image export doesn't respect background colour
  • PCA points don't dim when rotated about y axis
  • PCA Print dialog continues after Cancel
  • Cancel in Tree Font dialog resets alignment, not Tree font
  • Associate Tree with All Views not restored from project file
  • Scrolling of split frame is sluggish if Overview shown in complementary view
  • Codon consensus incorrectly scaled when shown without normalisation
  • Sequence Details report should open positioned at top of report
  • Help page can be opened twice
  • Fuzzy text in web service status menu on OSX Mojave

Editing

  • Start and End should be updated when sequence data at beginning or end of alignment added/removed via 'Edit' sequence
  • Delete/Cut selection doesn't relocate sequence features correctly when start of sequence is removed (Known defect since 2.10)
  • Inserting gap sequence via the Edit Sequence dialog corrupts dataset sequence
  • Structure colours not updated when associated tree repartitions the alignment view (Regression in 2.10.5)

Datamodel

  • Sequence.findIndex returns wrong value when sequence's End is greater than its length

Bugs fixed for Java 11 Support (not yet on general release)

  • Menus work properly in split-screen

New Known Defects

  • Select columns containing feature by double clicking ignores bounds of an existing selected region
  • Codon consensus logo incorrectly scaled in gapped regions of protein alignment.
  • Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
  • Alignment panel height can be too small after 'New View'
  • Display is incorrect after removing gapped columns within hidden columns
  • Rightmost selection is lost when mouse re-enters window after dragging left to select columns to left of visible region
  • Features coloured according to their description string and thresholded by score in earlier versions of Jalview are not shown as thresholded features in 2.11. To workaround please create a Score filter instead.
  • Cancel on Feature Settings dialog doesn't reset group visibility
  • F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
  • Closing tree windows with CMD/CTRL-W for alignments with multiple views can close views unexpectedly

Java 11 Specific defects

  • Jalview Properties file is not sorted alphabetically when saved