gracefully cope with non-standard nucleotide or amino acid symbols in pairwise alignment.

[jalview.git] / help / html / releases.html

diff --git a/help/html/releases.html b/help/html/releases.html
index a7f6cfd..19c6d53 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -17,9 +17,80 @@
                </td>
        </tr>
        <tr>
+       
                <td>
+               <div align="center"><strong>2.4.1</strong><br>
+               <em>Not Yet Released</em></div>
+               </td>
+               <td>
+               <ul>
+               <li>Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources</li> 
+               <li>Local DAS Sequence sources can be added via the command line or via the Add local source dialog box.</li>
+               <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>
+               <li>Order an alignment in order of average feature score or total feature count</li> 
+               </ul>
+               </td>
+               <td>
+               <ul>
+               <li>Better handling of exceptions during sequence retrieval</li>
+               <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>Codons containing ambiguous nucleotides translated as 'X' in peptide product</li>
+               <li>Sequence description lines properly shared via VAMSAS</li>
+               <li>Match case switch in find dialog box works for both sequence ID and sequence string and query strings do not have to be in upper case to match case-insensitively.</li>
+               <li>Sequence fetcher fetches multiple records for all data sources</li>
+               </ul>
+               </td>
+       
+       </tr>
+               <tr>
+       <td>
+       <div align="center"><strong>2.4.0.b2</strong><br>
+               28/10/2009</div>
+       </td>
+       <td>
+               <ul><li>Experimental support for google analytics usage tracking.</li>
+       <li>Jalview privacy settings (user preferences and docs).</li>
+       </ul>
+       </td>
+       <td>
+               <ul><li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
+               <li>Exception when feature created from selection beyond length of sequence.</li>
+               <li>Allow synthetic PDB files to be imported gracefully</li>
+               <li>Sequence associated annotation rows associate with all sequences with a given id</li>
+               <li>Find function matches case-insensitively for sequence ID string searches</li>               
+               <li>Non-standard characters do not cause pairwise alignment to fail with exception</li>         
+               </ul><em>Application Issues</em><ul>
+               <li>Sequences are now validated against EMBL database</li>
+               <li>Sequence fetcher fetches multiple records for all data sources</li>
+               </ul>
+               <em>InstallAnywhere Issues</em>
+               <ul>
+               <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with installAnywhere mechanism)</li>  
+               <li>Command line launching of JARs from InstallAnywhere version (java class versioning error fixed)</li>
+               </ul>
+       </td>
+       </tr>
+               <tr>
+           <td>
+               
                <div align="center"><strong>2.4</strong><br>
-               27/8//2008</div>
+               27/8/2008</div>
                </td>
                <td>
                        <em>User Interface</em>
@@ -168,7 +239,7 @@
                        <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>