What's new ?

Highlights in Jalview Version 2.4

DNA and protein product highlighting
URL links generated with regular expressions
URL links for sequence database cross references
New sequence fetcher dialog and DAS Sequence Fetching
JPred Service upgraded to Jpred3
Memory monitor
PFAM full alignment retrieval
Generalised sequence database reference validation
DNA Protein Product sequence db traversal (Experimental)
VAMSAS Interoperation Client (Experimental)
export annotation rows as CSV for spreadsheet import
New application command line args and optional Groovy suport
New Applet API methods and parameters

Issues Resolved (a select list)

Aligned cDNA translation to aligned peptide works correctly
selected region output includes visible annotations (for certain formats)
edit label/displaychar contains existing label/char for editing
Newick tree support improved for clustalW trees and preserving NHX style comments
Pathological filechooser bug avoided by not allowing filenames containing a ':'
Fixed exception when parsing GFF files containing global sequence features
Reference counting for alignment datasets
better reporting of non-fatal warnings and error messages to user when file parsing fails.
Save works when Jalview project is default format
Histidine should be midblue (not pink!) in Zappo
Undo recovers dataset sequence metadata when sequence regions are cut
PDB files without pdb ID HEADER lines (like those generated by MODELLER) are read in properly
Stockholm annotation parsing fixed and improved (PFAM records)
Re-instated Full AMSA support and .amsa file association (MyHits)
annotation consisting of sequence associated scores can be read and written correctly to annotation file
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)
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
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

See the Release History page for details of all new features and resolved issues.