<body>\r
<p><strong>Release History</strong> </p>\r
<table border="1">\r
- <tr> \r
+ <tr>\r
<td width="60" nowrap><div align="center"><em><strong>Release</strong></em></div></td>\r
<td ><div align="center"><em><strong>New Features</strong></em></div></td>\r
<td ><div align="center"><em><strong>Issues Resolved</strong></em></div></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
+ <td><div align="center"><strong>2.3</strong><br>\r
+ 8/5/07</div></td>\r
+ <td><ul>\r
+ <li>Jmol 11.0.2 integration</li>\r
+ <li>PDB views stored in Jalview XML files</li>\r
+ <li>Slide sequences</li>\r
+ <li>Edit sequence in place</li>\r
+ <li>EMBL CDS features</li>\r
+ <li>DAS Feature mapping</li>\r
+ <li>Feature ordering</li>\r
+ <li>Alignment Properties</li>\r
+ <li>Annotation Scores</li>\r
+ <li>Sort by scores</li>\r
+ <li>Feature/annotation editing in applet</li>\r
+</ul></td><td>\r
+ <ul>\r
+ <li>Headless state operation in 2.2.1</li>\r
+ <li>Incorrect and unstable DNA pairwise alignment</li>\r
+ <li>Cut and paste of sequences with annotation</li>\r
+ <li>Feature group display state in XML</li>\r
+ <li>Feature ordering in XML</li>\r
+ <li>blc file iteration selection using filename # suffix</li>\r
+ <li>Stockholm alignment properties</li>\r
+ <li>Stockhom alignment secondary structure annotation</li>\r
+ <li>2.2.1 applet had no feature transparency</li>\r
+ <li>Number pad keys can be used in cursor mode</li>\r
+ <li>Structure Viewer mirror image resolved</li>\r
+ </ul>\r
+ </td>\r
+\r
+ </tr>\r
+ <tr>\r
<td><div align="center"><strong>2.2.1</strong><br>\r
- ?/ 2/07</div></td>\r
+ 12/2/07</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 & description\r
<li>Preference setting to display sequence name in italics\r
- <li>Annotation file format extended to allow Sequence_groups to be defined</ul></td>\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
+ <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>"Reload" alignment \r
- <li>"Save" 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>Multiple views on alignment\r
+ <li>Sequence feature editing\r
+ <li>"Reload" alignment\r
+ <li>"Save" 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 ∣ \r
- <li>WsDbFetch query/result association resolved \r
- <li>Tree leaf to sequence mapping improved \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 ∣\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
+ <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
+ <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
+ <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
+ <tr>\r
<td><div align="center"><strong>2.1</strong><br>\r
22/8/06</div></td>\r
<td><ul>\r
<li>Annotation files with sequence references bug fixed</li>\r
</ul></td>\r
</tr>\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 movement 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
</tr>\r
- <tr> \r
+ <tr>\r
<td><div align="center"><strong>2.08b</strong><br>\r
18/4/06</div></td>\r
<td> </td>\r
<li>Righthand label on wrapped alignments shows correct value</li>\r
</ul></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td><div align="center"><strong>2.08</strong><br>\r
10/4/06</div></td>\r
<td><ul>\r
</ul></td>\r
<td><ul>\r
<li>Drag & Drop fixed on Linux</li>\r
- <li>Jalview Archive file faster to load/save, sequence descriptions saved. \r
+ <li>Jalview Archive file faster to load/save, sequence descriptions saved.\r
</li>\r
</ul></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td><div align="center"><strong>2.07</strong><br>\r
12/12/05</div></td>\r
<td><ul>\r
<li>Sequence Feature retrieval and display enhanced</li>\r
<li>Choose to output sequence start-end after sequence name for file output</li>\r
<li>Sequence Fetcher WSDBFetch@EBI</li>\r
- <li>Applet can read feature files, PDB files and can be used for HTML \r
+ <li>Applet can read feature files, PDB files and can be used for HTML\r
form input</li>\r
</ul></td>\r
<td><ul>\r
<li>File IO bugs</li>\r
</ul></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td><div align="center"><strong>2.06</strong><br>\r
28/9/05</div></td>\r
<td><ul>\r
<li>Runs with -nodisplay from command line</li>\r
</ul></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td height="63"> <div align="center"><strong>2.05b</strong><br>\r
15/9/05</div></td>\r
<td><ul>\r
<li>Several GUI bugs resolved</li>\r
</ul></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td><div align="center"><strong>2.05</strong><br>\r
30/8/05</div></td>\r
<td><ul>\r
<li>Several GUI bugs resolved</li>\r
</ul></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td><div align="center"><strong>2.04</strong><br>\r
24/8/05</div></td>\r
<td><ul>\r
<li>Improved loading of Jalview files</li>\r
</ul></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td> <div align="center"><strong>2.03</strong><br>\r
18/8/05</div></td>\r
<td><ul>\r
<li>InstallAnywhere download for Sparc Solaris</li>\r
</ul></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td> <div align="center"><strong>2.02</strong><br>\r
18/7/05</div></td>\r
<td> </td>\r
<li>Copy & Paste order of sequences maintains alignment order.</li>\r
</ul></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td><div align="center"><strong>2.01</strong><br>\r
12/7/05</div></td>\r
<td><ul>\r
<li>FileChooser sorts columns.</li>\r
<li>Can remove groups one by one.</li>\r
<li>Filechooser icons installed.</li>\r
- <li>Finder ignores return character when searching. Return key will initiate \r
+ <li>Finder ignores return character when searching. Return key will initiate\r
a search.<br>\r
</li>\r
</ul></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td> <div align="center"><strong>2.0</strong><br>\r
20/6/05</div></td>\r
<td ><ul>\r
git://source.jalview.org / jalview.git / blobdiff