jalview 2.5.1 release notes
authorjprocter <Jim Procter>
Fri, 11 Jun 2010 14:39:04 +0000 (14:39 +0000)
committerjprocter <Jim Procter>
Fri, 11 Jun 2010 14:39:04 +0000 (14:39 +0000)
help/html/releases.html
help/html/whatsNew.html

index 4c2d98c..3599194 100755 (executable)
                </td>
        </tr>
        <tr>
+               <td>
+               <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
+               <em>14/6/2010</em></div>
+               </td>
+               <td></td>
+               <td>
+               <ul>
+                       <li>Alignment prettyprinter doesn't cope with long sequence IDs
+                       </li>
+                       <li>clustalx colourscheme colours Ds preferentially when both
+                       D+E are present in over 50% of the column</li>
+                       <li>nucleic acid structures retrieved from PDB do not import
+                       correctly</li>
+                       <li>More columns get selected than were clicked on when a number
+                       of columns are hidden</li>
+                       <li>annotation label popup menu not providing correct
+                       add/hide/show options when rows are hidden or none are present</li>
+               </ul>
+               <em>Applet</em>
+               <ul>
+                       <li>annotation panel disappears when annotation is
+                       hidden/removed</li>
+               </ul>
+               <em>Application</em>
+               <ul>
+                       <li>Alignment view not redrawn properly when new alignment
+                       opened where annotation panel is visible but no annotations are
+                       present on alignment</li>
+                       <li>pasted region containing hidden columns is incorrectly
+                       displayed in new alignment window</li>
+                       <li>Jalview slow to complete operations when stdout is flooded
+                       (fix is to close the Jalview console)</li>
+                       <li>CSV output of consensus only includes the percentage of all
+                       symbols if sequence logo display is enabled</li>
+                       <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
+                       selected Rregions menu item.</li>
+                       <li>inconsistent group submenu and Format submenu entry 'Un' or
+                       'Non'conserved</li>
+                       <li>Sequence feature settings are being shared by multiple
+                       distinct alignments</li>
+                       <li>group annotation not recreated when tree partition is
+                       changed</li>
+                       <li>double click on group annotation to select sequences does
+                       not propagate to associated trees</li>
+                       <li>Mac OSX specific issues:
+                       <ul>
+                               <li>exception raised when mouse clicked on desktop window
+                               background</li>
+                               <li>Desktop menu placed on menu bar and application name set
+                               correctly</li>
+                               <li>sequence feature settings not wide enough for the save
+                               feature colourscheme button</li>
+                       </ul>
+                       </li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
 
                <td>
                <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
index 4723a9a..e6ab695 100755 (executable)
@@ -21,6 +21,9 @@
 </head>
 <body>
 <p><strong>What's new ?</strong></p>
+<p>Jalview 2.5.1 is a bug fix release for the 2.5 version of
+Jalview. See the <a href="releases.html#Jalview2.5.1">release
+history</a> for the bugs that this release resolves.</p>
 <p><strong>Highlights in Jalview Version 2.5</strong></p>
 <ul>
                        Linked viewing of nucleic acid sequences and structures<br/>