Version 2.4

Thank you to everyone who wrote letters of support last year for our application to the BBSRC, we should hear the outcome in the next couple of months.

We are now applying to the Wellcome Trust to renew funding to support Jalview's use in biomedical sequence analysis, including interpretation of genomic variation and long read RNA data (e.g. Nanopore) at the protein coding level. If you would like Jalview to continue to develop and be supported then please take a few minutes to write us a support letter saying how you use Jalview in your research/teaching.

Write as a PDF including your institution's heading and send to: by Friday 22nd March 2019.

Thank you!

Version Date: 

New Features

User Interface

  • Linked highlighting of codon and amino acid from translation and protein products
  • Linked highlighting of structure associated with residue mapping to codon position
  • Sequence Fetcher provides example accession numbers and 'clear' button
  • MemoryMonitor added as an option under Desktop's Tools menu
  • Extract score function to parse whitespace separated numeric data in description line
  • Column labels in alignment annotation can be centred.
  • Tooltip for sequence associated annotation give name of sequence

Web Services and URL fetching

  • JPred3 web service
  • Prototype sequence search client (no public services available yet)
  • Fetch either seed alignment or full alignment from PFAM
  • URL Links created for matching database cross references as well as sequence ID
  • URL Links can be created using regular-expressions

Sequence Database Connectivity

  • Retrieval of cross-referenced sequences from other databases
  • Generalised database reference retrieval and validation to all fetchable databases
  • Fetch sequences from DAS sources supporting the sequence command

Import and Export

  • export annotation rows as CSV for spreadsheet import
  • Jalview projects record alignment dataset associations, EMBL products, and cDNA sequence mappings
  • Sequence Group colour can be specified in Annotation File
  • Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme
  • VAMSAS Client capabilities (Experimental)

  • treenode binding for VAMSAS tree exchange
  • local editing and update of sequences in VAMSAS alignments (experimental)
  • Create new or select existing session to join
  • load and save of vamsas documents

Application command line

  • -tree parameter to open trees (introduced for passing from applet)
  • -fetchfrom command line argument to specify nicknames of DAS servers to query for alignment features
  • -dasserver command line argument to add new servers that are also automatically queried for features
  • -groovy command line argument executes a given groovy script after all input data has been loaded and parsed

Applet-Application data exchange

  • Trees passed as applet parameters can be passed to application (when using "View in full application")

Applet Parameters

  • feature group display control parameter
  • debug parameter
  • showbutton parameter

Applet API methods

  • newView public method
  • Window (current view) specific get/set public methods
  • Feature display control methods
  • get list of currently selected sequences

New Jalview distribution features

  • InstallAnywhere Installer upgraded to IA 2008 VP1
  • RELEASE file gives build properties for the latest Jalview release.
  • Java 1.1 Applet build made easier and donotobfuscate property controls execution of obfuscator
  • Build target for generating source distribution
  • Debug flag for javacc
  • .jalview_properties file is documented (slightly) in jalview.bin.Cache
  • Continuous Build Integration for stable and development version of Application, Applet and source distribution

Issues Resolved

  • selected region output includes visible annotations (for certain formats)
  • edit label/displaychar contains existing label/char for editing
  • update PDBEntries when DBRefEntries change (vamsas)
  • shorter peptide product names from EMBL records
  • Newick string generator makes compact representations
  • bootstrap values parsed correctly for tree files with comments
  • pathological filechooser bug avoided by not allowing filenames containing a ':'
  • Fixed exception when parsing GFF files containing global sequence features
  • Alignment datasets are finalized only when number of references from alignment sequences goes to zero
  • Close of tree branch colour box without colour selection causes cascading exceptions
  • occasional negative imgwidth exceptions
  • better reporting of non-fatal warnings to user when file parsing fails.
  • Save works when Jalview project is default format
  • Save as dialog opened if current alignment format is not a valid output format
  • Uniprot canonical names introduced for both das and vamsas
  • Histidine should be midblue (not pink!) in Zappo
  • error messages passed up and output when data read fails
  • edit undo recovers previous dataset sequence when sequence is edited
  • allow PDB files without pdb ID HEADER lines (like those generated by MODELLER) to be read in properly
  • allow reading of JPred concise files as a normal filetype
  • Stockholm annotation parsing and alignment properties import fixed for PFAM records
  • Structure view windows have correct name in Desktop window list
  • annotation consisting of sequence associated scores can be read and written correctly to annotation file
  • Aligned cDNA translation to aligned peptide works correctly
  • Fixed display of hidden sequence markers and non-italic font for representatives in Applet
  • Applet Menus are always embedded in applet window on Macs.
  • Newly shown features appear at top of stack (in Applet)
  • Annotations added via parameter not drawn properly due to null pointer exceptions
  • Secondary structure lines are drawn starting from first column of alignment
  • Uniprot XML import updated for new schema release in July 2008
  • Sequence feature to sequence ID match for Features file is case-insensitive
  • Sequence features read from Features file appended to all sequences with matching IDs
  • PDB structure coloured correctly for associated views containing a sub-sequence
  • PDB files can be retrieved by applet from Jar files
  • feature and annotation file applet parameters referring to different directories are retrieved correctly
  • Fixed application hang whilst waiting for splash-screen version check to complete
  • Applet properly URLencodes input parameter values when passing them to the launchApp service
  • display name and local features preserved in results retrieved from web service
  • Visual delay indication for sequence retrieval and sequence fetcher initialisation
  • updated Application to use DAS 1.53e version of dasobert DAS client
  • Re-instated Full AMSA support and .amsa file association