Jalview 2.4

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WARNING! Downloading this JVL file might automatically switch your Jalview installation to version 2.4 (without auto-updates).

To revert back to the Jalview RELEASE channel, please visit the Using the Jalview Launch file page.

Download the Jalview Launch file (.jvl) for version 2.4?


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
  • Fixed parsing of JNet Concise annotation sans sequences