added command line help documentation and preferences help to

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

diff --git a/help/html/releases.html b/help/html/releases.html
index e37c5b5..5cdf8a5 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -9,17 +9,107 @@
     <td ><div align="center"><em><strong>Issues Resolved</strong></em></div></td>\r
   </tr>\r
   <tr> \r
+    <td><div align="center"><strong>2.2.1</strong><br>\r
+        ?/ 2/07</div></td>\r
+    <td><ul>\r
+        <li>Non standard characters can be read and displayed\r
+        <li>Annotations/Features can be imported/exported to the applet via textbox\r
+        <li>Applet allows editing of sequence/annotation/group name &amp; description\r
+        <li>Preference setting to display sequence name in italics\r
+        <li>Annotation file format extended to allow Sequence_groups\r
+        to be defined\r
+        <li>Default opening of alignment overview panel can be specified in\r
+        preferences\r
+        <li>PDB residue numbering annotation added to associated sequences\r
+        </ul></td>\r
+    <td> <ul>\r
+        <li>Applet crash under certain Linux OS with Java 1.6 installed\r
+        <li>Annotation file export / import bugs fixed\r
+        <li>PNG / EPS image output bugs fixed</ul></td>\r
+  </tr>\r
+  <tr> \r
+    <td><div align="center"><strong>2.2</strong><br>\r
+        27/11/06</div></td>\r
+    <td><ul>\r
+        <li>Multiple views on alignment \r
+        <li>Sequence feature editing \r
+        <li>&quot;Reload&quot; alignment \r
+        <li>&quot;Save&quot; to current filename \r
+        <li>Background dependent text colour \r
+        <li>Right align sequence ids \r
+        <li>User-defined lower case residue colours \r
+        <li>Format Menu \r
+        <li>Select Menu \r
+        <li>Menu item accelerator keys \r
+        <li>Control-V pastes to current alignment \r
+        <li>Cancel button for DAS Feature Fetching \r
+        <li>PCA and PDB Viewers zoom via mouse roller \r
+        <li>User-defined sub-tree colours and sub-tree selection \r
+        <li>'New Window' button on the 'Output to Text box' </ul></td>\r
+    <td> <ul>\r
+        <li>New memory efficient Undo/Redo System \r
+        <li>Optimised symbol lookups and conservation/consensus calculations \r
+        <li>Region Conservation/Consensus recalculated after edits \r
+        <li>Fixed Remove Empty Columns Bug (empty columns at end of alignment) \r
+        <li>Slowed DAS Feature Fetching for increased robustness. \r
+        <li>Made angle brackets in ASCII feature descriptions display correctly \r
+        <li>Re-instated Zoom function for PCA \r
+        <li>Sequence descriptions conserved in web service analysis results \r
+        <li>Uniprot ID discoverer uses any word separated by &#8739; \r
+        <li>WsDbFetch query/result association resolved \r
+        <li>Tree leaf to sequence mapping improved \r
+        <li>Smooth fonts switch moved to FontChooser dialog box. </ul></td>\r
+  </tr>\r
+  <tr> \r
+    <td> <div align="center"><strong>2.1.1</strong><br>\r
+        12/9/06</div></td>\r
+    <td><ul>\r
+        <li>Copy consensus sequence to clipboard</li>\r
+      </ul></td>\r
+    <td><ul>\r
+        <li>Image output - rightmost residues are rendered if sequence id panel \r
+          has been resized</li>\r
+        <li>Image output - all offscreen group boundaries are rendered </li>\r
+        <li>Annotation files with sequence references - all elements in file are \r
+          relative to sequence position</li>\r
+        <li>Mac Applet users can use Alt key for group editing</li>\r
+      </ul></td>\r
+  </tr>\r
+  <tr> \r
+    <td><div align="center"><strong>2.1</strong><br>\r
+        22/8/06</div></td>\r
+    <td><ul>\r
+        <li>MAFFT Multiple Alignment in default Web Service list</li>\r
+        <li>DAS Feature fetching</li>\r
+        <li>Hide sequences and columns</li>\r
+        <li>Export Annotations and Features</li>\r
+        <li>GFF file reading / writing</li>\r
+        <li>Associate structures with sequences from local PDB files</li>\r
+        <li>Add sequences to exisiting alignment</li>\r
+        <li>Recently opened files / URL lists</li>\r
+        <li>Applet can launch the full application</li>\r
+        <li>Applet has transparency for features (Java 1.2 required)</li>\r
+        <li>Applet has user defined colours parameter</li>\r
+        <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>\r
+      </ul></td>\r
+    <td><ul>\r
+        <li>Redundancy Panel reinstalled in the Applet</li>\r
+        <li>Monospaced font - EPS / rescaling bug fixed</li>\r
+        <li>Annotation files with sequence references bug fixed</li>\r
+      </ul></td>\r
+  </tr>\r
+  <tr> \r
     <td><div align="center"><strong>2.08.1</strong><br>\r
         2/5/06</div></td>\r
     <td><ul>\r
         <li>Change case of selected region from Popup menu</li>\r
         <li>Choose to match case when searching</li>\r
-        <li>Middle mouse button and mouse movemnet can compress / expand the visible \r
+        <li>Middle mouse button and mouse movement can compress / expand the visible \r
           width and height of the alignment</li>\r
       </ul></td>\r
     <td><ul>\r
         <li>Annotation Panel displays complete JNet results</li>\r
-        </ul></td>\r
+      </ul></td>\r
   </tr>\r
   <tr> \r
     <td><div align="center"><strong>2.08b</strong><br>\r