</td>
</tr>
<tr>
+
<td>
- <div align="center"><strong>2.4</strong><br>
- Feb/2008</div>
+ <div align="center"><strong>2.4.1</strong><br>
+ <em>Not Yet Released</em></div>
</td>
<td>
<ul>
- <li>New VAMSAS capabilities in Jalview
+ <li>Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
+ </li>
+ <li>URL links generated from description line for regular-expression based URL links (applet and application)
+ </li>
+ <li>Non-positional features displayed in sequence ID tooltip on applet
+ </li>
+ <li>Non-positional feature URL links are shown in link menu (applet and application)
+ </li>
+ <li>Automatic Scrolling option in View menu to display the currently highlighted region of an alignment.
+ </li>
+ <li>Improved VAMSAS synchronization (jalview archive used to preserve views, structures, and tree display settings)
+ </li>
+ <li>Sharing of selected regions between views and with other VAMSAS applications (Experimental feature!)
+ </li>
+ <li>New hidden columns and rows and representatives capabilities in annotations file (in progress - not yet fully implemented)</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>URL links generated for all feature links (bugfix)</li>
+ <li>Dasobert generated non-positional feature URL link text excludes the start_end suffix (application)</li>
+ <li>Added URL embedding instructions to features file documentation.</li>
+ <li>Sequences are now validated against EMBL database (broken in Version 2.4.0)</li>
+ <li>Codons containing ambiguous nucleotides translated as 'X' in peptide product</li>
+ <li>Sequence description lines properly shared via VAMSAS</li>
+ </ul>
+ </td>
+
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.4</strong><br>
+ 27/8//2008</div>
+ </td>
+ <td>
+ <em>User Interface</em>
<ul>
- <li>treenode binding for VAMSAS tree exchange</li>
- <li>local editing and update of sequences in VAMSAS alignments
- (experimental)</li>
- <li>Create new or select existing session to join</li>
- <li>load and save of vamsas documents</li>
- </ul>
- </li>
- <li>Retrieval of cross-referenced sequences from other databases
- </li>
- <li>export annotation rows as CSV for spreadsheet import</li>
- <li>Jalview projects record alignment dataset associations, EMBL
- products, and cDNA sequence mappings</li>
<li>Linked highlighting of codon and amino acid from translation
and protein products</li>
+ <li>Linked highlighting of structure associated with residue mapping to codon position</li>
+ <li>Sequence Fetcher provides example accession numbers and 'clear' button</li>
+ <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
+ <li>Extract score function to parse whitespace separated numeric data in description line</li>
+ <li>Column labels in alignment annotation can be centred.</li>
+ <li>Tooltip for sequence associated annotation give name of sequence</li>
+ </ul>
+ <em>Web Services and URL fetching</em>
+ <ul>
<li>JPred3 web service</li>
+ <li>Prototype sequence search client (no public services available yet)</li>
+ <li>Fetch either seed alignment or full alignment from PFAM</li>
+ <li>URL Links created for matching database cross references as well as sequence ID</li>
+ <li>URL Links can be created using regular-expressions</li>
+ </ul>
+ <em>Sequence Database Connectivity</em>
+ <ul>
+ <li>Retrieval of cross-referenced sequences from other databases
+ </li>
<li>Generalised database reference retrieval and validation to
all fetchable databases</li>
<li>Fetch sequences from DAS sources supporting the sequence command</li>
- <li>Sequence Fetcher GUI provides example accession numbers and 'clear' button</li>
- <li>Application command line
+ </ul>
+ <em>Import and Export</em>
+ <li>export annotation rows as CSV for spreadsheet import</li>
+ <li>Jalview projects record alignment dataset associations, EMBL
+ products, and cDNA sequence mappings</li>
+ <li>Sequence Group colour can be specified in Annotation File</li>
+ <li>Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme</li>
+ </ul>
+ <em>VAMSAS Client capabilities (Experimental)</em>
+ <ul>
+ <li>treenode binding for VAMSAS tree exchange</li>
+ <li>local editing and update of sequences in VAMSAS alignments
+ (experimental)</li>
+ <li>Create new or select existing session to join</li>
+ <li>load and save of vamsas documents</li>
+ </ul>
+ <em>Application command line</em>
<ul>
<li>-tree parameter to open trees (introduced for passing from
applet)</li>
<li>-groovy command line argument executes a given groovy
script after all input data has been loaded and parsed</li>
</ul>
- </li>
- <li>Trees passed as applet parameters can be passed to
+ <em>Applet-Application data exchange</em>
+ <ul>
+ <li>Trees passed as applet parameters can be passed to
application (when using "View in full application")</li>
- <li>MemoryMonitor added as an option under Desktop's Tools menu
- </li>
- <li>allow reading of JPred concise files as a normal filetype</li>
- <li>sort sequences by named annotation scores</li>
- <li>Re-instated Full AMSA support and .amsa file association</li>
- <li>Stockholm annotation parsing and alignment properties import
- </li>
- <li>Applet Parameters
+ </ul>
+ <em>Applet Parameters</em>
<ul>
<li>feature group display control parameter</li>
<li>debug parameter</li>
+ <li>showbutton parameter</li>
</ul>
- </li>
- <li>Applet API methods
+ <em>Applet API methods</em>
<ul>
<li>newView public method</li>
<li>Window (current view) specific get/set public methods</li>
<li>Feature display control methods</li>
+ <li>get list of currently selected sequences</li>
</ul>
- </li>
- </ul>
- <em>New Jalview distribution features</em>
+ <em>New Jalview distribution features</em>
<ul>
+ <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
<li>RELEASE file gives build properties for the latest Jalview
release.</li>
<li>Java 1.1 Applet build made easier and donotobfuscate
<li>Debug flag for javacc</li>
<li>.jalview_properties file is documented (slightly) in
jalview.bin.Cache</li>
- <li>Group colour can be given as an RGB triplet which is used to colour all non-gap characters</li>
- <!-- <li>DAS Sequence Retrieval (in progress)</li> -->
+ <li>Continuous Build Integration for stable and development version of Application, Applet and source distribution</li>
</ul>
+
</td>
<td>
<ul>
<li>better reporting of non-fatal warnings to user when file
parsing fails.</li>
<li>Save works when Jalview project is default format</li>
+ <li>Save as dialog opened if current alignment format is not a valid output format</li>
<li>Uniprot canonical names introduced for both das and vamsas</li>
<li>Histidine should be midblue (not pink!) in Zappo</li>
<li>error messages passed up and output when data read fails</li>
is edited</li>
<li>allow PDB files without pdb ID HEADER lines (like those
generated by MODELLER) to be read in properly</li>
+ <li>allow reading of JPred concise files as a normal filetype</li>
+ <li>Stockholm annotation parsing and alignment properties import fixed for PFAM records
+ </li>
+ <li>Structure view windows have correct name in Desktop window list</li>
<li>annotation consisting of sequence associated scores can be
read and written correctly to annotation file</li>
<li>Aligned cDNA translation to aligned peptide works correctly
<li>Secondary structure lines are drawn starting from first
column of alignment</li>
<li>Uniprot XML import updated for new schema release in July 2008</li>
+ <li>Sequence feature to sequence ID match for Features file is case-insensitive</li>
+ <li>Sequence features read from Features file appended to all sequences with matching IDs</li>
+ <li>PDB structure coloured correctly for associated views containing a sub-sequence</li>
+ <li>PDB files can be retrieved by applet from Jar files</li>
+ <li>feature and annotation file applet parameters referring to different directories are retrieved correctly</li>
<!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
-
+ <li>Fixed application hang whilst waiting for splash-screen version check to complete</li>
+ <li>Applet properly URLencodes input parameter values when passing them to the launchApp service</li>
+ <li>display name and local features preserved in results retrieved from web service</li>
+ <li>Visual delay indication for sequence retrieval and sequence fetcher initialisation</li>
+ <li>updated Application to use DAS 1.53e version of dasobert DAS client</li>
+ <li>Re-instated Full AMSA support and .amsa file association</li>
+ <li>Fixed parsing of JNet Concise annotation <em>sans</em> sequences</li>
</ul>
</td>
</tr>