--- /dev/null
+---
+channel: release
+version: 2.4
+date: 2008-08-27
+---
+
+## 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
git://source.jalview.org / jalview.git / blobdiff