Version Date:
17-11-2017
More efficienct data structures for handing sequence features and improved rendering performance when working with large alignments.
New Features
- Faster and more efficient management and rendering of sequence features
- More reliable Ensembl fetching with HTTP 429 rate limit request hander
- Structure views don't get updated unless their colours have changed
- All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)
- 'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
- Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references
- Start/End limits are shown in Pairwise Alignment report
- Sequence fetcher's Free text 'autosearch' feature can be disabled
- Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs
- Short names for sequences retrieved from Uniprot
Scripting
- Groovy interpreter updated to 2.4.12
- Example groovy script for generating a matrix of percent identity scores for current alignment.
Testing and Deployment
- Test to catch memory leaks in Jalview UI
Issues Resolved
General
- Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view
- Race condition when parsing sequence ID strings in parallel
- Overview windows are also closed when alignment window is closed
- Export of features doesn't always respect group visibility
- Jumping from column 1 to column 100,000 takes a long time in Cursor mode
Desktop
- Structures with whitespace chainCode cannot be viewed in Chimera
- Protein annotation panel too high in CDS/Protein view
- Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
- Slow EnsemblGenome ID lookup
- Revised Ensembl REST API CDNA query
- Hidden column marker in last column not rendered when switching back from Wrapped to normal view
- Annotation display corrupted when scrolling right in unwapped alignment view
- Existing features on subsequence incorrectly relocated when full sequence retrieved from database
- Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)
- Amend Features dialog doesn't allow features of same type and group to be selected for amending
- Jalview becomes sluggish in wide alignments when hidden columns are present
- Jalview freezes when loading and displaying several structures
- Black outlines left after resizing or moving a window
- Unable to minimise windows within the Jalview desktop on OSX
- Mouse wheel doesn't scroll vertically when in wrapped alignment mode
- Scale mark not shown when close to right hand end of alignment
- Pairwise alignment of selected regions of each selected sequence do not have correct start/end positions
- Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog
- Show cross-references not enabled after restoring project until a new view is created
- Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2)
- Overview redraws whole window when box position is adjusted
- Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10)
- Double residue highlights in cursor mode if new selection moves alignment window
- Alignment vanishes when using arrow key in cursor mode to pass hidden column marker
- Ensembl Genomes example ID changed to one that produces correctly annotated transcripts and products
- Toggling a feature group after first time doesn't update associated structure view
Applet
- Concurrent modification exception when closing alignment panel
BioJSON
- BioJSON export does not preserve non-positional features
New Known Issues
- Delete/Cut selection doesn't relocate sequence features correctly (for many previous versions of Jalview)
- Cursor mode unexpectedly scrolls when using cursor in wrapped panel other than top
- Select columns containing feature ignores graduated colour threshold
- Edit sequence operation doesn't always preserve numbering and sequence features
Known Java 9 Issues
- Groovy Console very slow to open and is not responsive when entering characters (Webstart, Java 9.01, OSX 10.10)