Jalview 2.10.3

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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)