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