Jalview 2.10.1

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New Features

General

  • Improved memory usage: sparse arrays used for all consensus calculations
  • Jmol updated to version 14.6.4 (released 3rd Oct 2016)
  • Updated Jalview’s Certum code signing certificate for 2016-2017

Application

  • Sequence ID tool tip presents abridged set of database cross-references, sorted alphabetically
  • New replacement token for creating URLs just from database cross references. Users with custom links will receive a warning dialog asking them to update their preferences.
  • Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session
  • Jalview’s Chimera control window closes if the Chimera it is connected to is shut down
  • New keystroke (B) and Select highlighted columns menu item to mark columns containing highlighted regions (e.g. from structure selections or results of a Find operation)
  • Command line option for batch-generation of HTML pages rendering alignment data with the BioJS MSAviewer

Issues Resolved

General

  • Columns with more than one modal residue are not coloured or thresholded according to percent identity (first observed in Jalview 2.8.2)
  • Threonine incorrectly reported as not hydrophobic
  • Updates to documentation pages (above PID threshold, amino acid properties)
  • Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report
  • Identical features with non-numeric scores could be added multiple times to a sequence
  • Disulphide bond features shown as two highlighted residues rather than a range in linked structure views, and treated correctly when selecting and computing trees from features
  • Custom URL links for database cross-references are matched to database name regardless of case

Application

  • Custom URL links for specific database names without regular expressions also offer links from Sequence ID
  • Removing a single configured link in the URL links pane in Connections preferences doesn’t actually update Jalview configuration
  • CTRL-Click on a selected region to open the alignment area popup menu doesn’t work on El-Capitan
  • Jalview doesn’t offer to associate mmCIF files with similarly named sequences if dropped onto the alignment
  • Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file
  • Certain structures do not get mapped to the structure view when displayed with Chimera
  • No chains shown in the Chimera view panel’s View->Show Chains submenu
  • Export as HTML with embedded SVG doesn’t work for wrapped alignment views
  • Rename UI components for running JPred predictions from ‘JNet’ to ‘JPred’
  • Export as PNG or SVG is corrupted when annotation panel vertical scroll is not at first annotation row
  • Attempting to view structure for Hen lysozyme results in a PDB Client error dialog box
  • Structure View’s mapping report switched ranges for PDB and sequence for SIFTS