Version Date:
10-05-2018
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)
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)
- Invert displayed features very slow when structure and/or overview windows are also shown
- Uniprot 'sequence variant' features tooltip doesn't include a text description of mutation
- 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)