--- channel: release version: 2.10.3 date: 2017-11-17 --- ## 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)