Jalview 2.10.4

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New Features

  • New Structure Chooser control for disabling automatic superposition of multiple structures and open structures in existing views
  • Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them.
  • Jalview uses HTTPS for Uniprot, Xfam and Ensembl services
  • Improved performance for large alignments and lots of hidden columns
  • Improved performance when rendering lots of features (particularly when transparency is disabled)
  • Experimental features in 2.10.2 for exchange of Jalview features and Chimera attributes made generally available

Issues Resolved

  • Structure and Overview aren’t updated when Colour By Annotation threshold slider is adjusted
  • Slow redraw when Overview panel shown overlapping alignment panel
  • Overview doesn’t show end of unpadded sequence as gaps
  • Cross-reference handling improved: CDS not handled correctly if transcript has no UTR
  • Secondary structure and temperature factor annotation not added to sequence when local PDB file associated with it by drag’n’drop or structure chooser
  • Answering ‘No’ to PDB Autoassociate dialog doesn’t import PDB files dropped on an alignment
  • Linked scrolling via protein horizontal scroll bar doesn’t work for some CDS/Protein views
  • Trackpad scrolling is broken on OSX on Java 1.8u153 onwards and Java 1.9u4+.
  • Tooltip shouldn’t be displayed for empty columns in annotation row
  • Preferences panel’s ID Width control is not honored in batch mode
  • Linked sequence highlighting doesn’t work for structures added to existing Jmol view
  • ‘View Mappings’ includes duplicate entries after importing project with multiple views
  • Viewing or annotating Uniprot protein sequences via SIFTS from associated PDB entries with negative residue numbers or missing residues fails
  • Exception when shading sequence with negative Temperature Factor values from annotated PDB files (e.g. as generated by CONSURF)
  • Uniprot ‘sequence variant’ features tooltip doesn’t include a text description of mutation
  • Invert displayed features very slow when structure and/or overview windows are also shown
  • Selecting columns from highlighted regions very slow for alignments with large numbers of sequences
  • Copy Consensus fails for group consensus with ‘StringIndexOutOfBounds’
  • VAqua(4) provided as fallback Look and Feel for OSX platforms running Java 10
  • Adding a structure to existing structure view appears to do nothing because the view is hidden behind the alignment view

Applet

  • Copy consensus sequence option in applet should copy the group consensus when popup is opened on it

Batch Mode

  • Fixed ID width preference is not respected

New Known Defects

  • Exceptions occasionally raised when editing a large alignment and overview is displayed
  • ‘Overview updating’ progress bar is shown repeatedly after a series of edits even when the overview is no longer reflecting updates
  • ‘SIFTS Mapping Error’ when viewing structures for protein subsequence (if ‘Trim Retrieved Sequences’ enabled) or Ensembl isoforms (Workaround in 2.10.4 is to fail back to N&W mapping)
  • Export Annotations from File Menu with CSV option gives blank output