<html>
-<head><title>Release History</title></head>
-<body>
-<p><strong>Release History</strong> </p>
-<table border="1">
- <tr>
- <td width="60" nowrap><div align="center"><em><strong>Release</strong></em></div></td>
- <td ><div align="center"><em><strong>New Features</strong></em></div></td>
- <td ><div align="center"><em><strong>Issues Resolved</strong></em></div></td>
- </tr>
- <tr>
- <td><div align="center"><strong>2.2</strong><br>
- 27/11/06</div></td><td><ul>
- <li>Multiple views on alignment
-<li>Sequence feature editing
-<li>"Reload" alignment
-<li>"Save" to current filename
-<li>Background dependent text colour
-<li>Right align sequence ids
-<li>User-defined lower case residue colours
-<li>Format Menu
-<li>Select Menu
-<li>Menu item accelerator keys
-<li>Control-V pastes to current alignment
-<li>Cancel button for DAS Feature Fetching
-<li>PCA and PDB Viewers zoom via mouse roller
-<li>User-defined sub-tree colours and sub-tree selection
-<li>'New Window' button on the 'Output to Text box'
-</ul>
- </td>
- <td>
-<ul>
-<li>New memory efficient Undo/Redo System
-<li>Optimised symbol lookups and conservation/consensus calculations
-<li>Region Conservation/Consensus recalculated after edits
-<li>Fixed Remove Empty Columns Bug (empty columns at end of alignment)
-<li>Slowed DAS Feature Fetching for increased robustness.
-<li>Made angle brackets in ASCII feature descriptions display correctly
-<li>Re-instated Zoom function for PCA
-<li>Sequence descriptions conserved in web service analysis results
-<li>Uniprot ID discoverer uses any word separated by ∣
-<li>WsDbFetch query/result association resolved
-<li>Tree leaf to sequence mapping improved
-<li>Smooth fonts switch moved to FontChooser dialog box.
-</ul></td>
- </tr>
- <tr>
- <td>
-<div align="center"><strong>2.1.1</strong><br>
- 12/9/06</div></td>
- <td><ul>
- <li>Copy consensus sequence to clipboard</li>
- </ul></td>
- <td><ul>
- <li>Image output - rightmost residues are rendered if sequence id panel
- has been resized</li>
- <li>Image output - all offscreen group boundaries are rendered </li>
- <li>Annotation files with sequence references - all elements in file are
- relative to sequence position</li>
- <li>Mac Applet users can use Alt key for group editing</li>
- </ul></td>
- </tr>
- <tr>
- <td><div align="center"><strong>2.1</strong><br>
- 22/8/06</div></td>
- <td><ul>
- <li>MAFFT Multiple Alignment in default Web Service list</li>
- <li>DAS Feature fetching</li>
- <li>Hide sequences and columns</li>
- <li>Export Annotations and Features</li>
- <li>GFF file reading / writing</li>
- <li>Associate structures with sequences from local PDB files</li>
- <li>Add sequences to exisiting alignment</li>
- <li>Recently opened files / URL lists</li>
- <li>Applet can launch the full application</li>
- <li>Applet has transparency for features (Java 1.2 required)</li>
- <li>Applet has user defined colours parameter</li>
- <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
- </ul></td>
- <td><ul>
- <li>Redundancy Panel reinstalled in the Applet</li>
- <li>Monospaced font - EPS / rescaling bug fixed</li>
- <li>Annotation files with sequence references bug fixed</li>
- </ul></td>
- </tr>
- <tr>
- <td><div align="center"><strong>2.08.1</strong><br>
- 2/5/06</div></td>
- <td><ul>
- <li>Change case of selected region from Popup menu</li>
- <li>Choose to match case when searching</li>
- <li>Middle mouse button and mouse movement can compress / expand the visible
- width and height of the alignment</li>
- </ul></td>
- <td><ul>
- <li>Annotation Panel displays complete JNet results</li>
- </ul></td>
- </tr>
- <tr>
- <td><div align="center"><strong>2.08b</strong><br>
- 18/4/06</div></td>
- <td> </td>
- <td><ul>
- <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
- <li>Righthand label on wrapped alignments shows correct value</li>
- </ul></td>
- </tr>
- <tr>
- <td><div align="center"><strong>2.08</strong><br>
- 10/4/06</div></td>
- <td><ul>
- <li>Editing can be locked to the selection area</li>
- <li>Keyboard editing</li>
- <li>Create sequence features from searches</li>
- <li>Precalculated annotations can be loaded onto alignments</li>
- <li>Features file allows grouping of features</li>
- <li>Annotation Colouring scheme added</li>
- <li>Smooth fonts off by default - Faster rendering</li>
- <li>Choose to toggle Autocalculate Consensus On/Off</li>
- </ul></td>
- <td><ul>
- <li>Drag & Drop fixed on Linux</li>
- <li>Jalview Archive file faster to load/save, sequence descriptions saved.
- </li>
- </ul></td>
- </tr>
- <tr>
- <td><div align="center"><strong>2.07</strong><br>
- 12/12/05</div></td>
- <td><ul>
- <li>PDB Structure Viewer enhanced</li>
- <li>Sequence Feature retrieval and display enhanced</li>
- <li>Choose to output sequence start-end after sequence name for file output</li>
- <li>Sequence Fetcher WSDBFetch@EBI</li>
- <li>Applet can read feature files, PDB files and can be used for HTML
- form input</li>
- </ul></td>
- <td><ul>
- <li>HTML output writes groups and features</li>
- <li>Group editing is Control and mouse click</li>
- <li>File IO bugs</li>
- </ul></td>
- </tr>
- <tr>
- <td><div align="center"><strong>2.06</strong><br>
- 28/9/05</div></td>
- <td><ul>
- <li>View annotations in wrapped mode</li>
- <li>More options for PCA viewer</li>
- </ul></td>
- <td><ul>
- <li>GUI bugs resolved</li>
- <li>Runs with -nodisplay from command line</li>
- </ul></td>
- </tr>
- <tr>
- <td height="63"> <div align="center"><strong>2.05b</strong><br>
- 15/9/05</div></td>
- <td><ul>
- <li>Choose EPS export as lineart or text</li>
- <li>Jar files are executable</li>
- <li>Can read in Uracil - maps to unknown residue</li>
- </ul></td>
- <td><ul>
- <li>Known OutOfMemory errors give warning message</li>
- <li>Overview window calculated more efficiently</li>
- <li>Several GUI bugs resolved</li>
- </ul></td>
- </tr>
- <tr>
- <td><div align="center"><strong>2.05</strong><br>
- 30/8/05</div></td>
- <td><ul>
- <li>Edit and annotate in "Wrapped" view</li>
- </ul></td>
- <td><ul>
- <li>Several GUI bugs resolved</li>
- </ul></td>
- </tr>
- <tr>
- <td><div align="center"><strong>2.04</strong><br>
- 24/8/05</div></td>
- <td><ul>
- <li>Hold down mouse wheel & scroll to change font size</li>
- </ul></td>
- <td><ul>
- <li>Improved JPred client reliability</li>
- <li>Improved loading of Jalview files</li>
- </ul></td>
- </tr>
- <tr>
- <td> <div align="center"><strong>2.03</strong><br>
- 18/8/05</div></td>
- <td><ul>
- <li>Set Proxy server name and port in preferences</li>
- <li>Multiple URL links from sequence ids</li>
- <li>User Defined Colours can have a scheme name and added to Colour Menu</li>
- <li>Choose to ignore gaps in consensus calculation</li>
- <li>Unix users can set default web browser</li>
- <li>Runs without GUI for batch processing</li>
- <li>Dynamically generated Web Service Menus</li>
- </ul></td>
- <td><ul>
- <li>InstallAnywhere download for Sparc Solaris</li>
- </ul></td>
- </tr>
- <tr>
- <td> <div align="center"><strong>2.02</strong><br>
- 18/7/05</div></td>
- <td> </td>
- <td><ul>
- <li>Copy & Paste order of sequences maintains alignment order.</li>
- </ul></td>
- </tr>
- <tr>
- <td><div align="center"><strong>2.01</strong><br>
- 12/7/05</div></td>
- <td><ul>
- <li>Use delete key for deleting selection.</li>
- <li>Use Mouse wheel to scroll sequences.</li>
- <li>Help file updated to describe how to add alignment annotations.</li>
- <li>Version and build date written to build properties file.</li>
- <li>InstallAnywhere installation will check for updates at launch of Jalview.</li>
- </ul></td>
- <td><ul>
- <li>Delete gaps bug fixed.</li>
- <li>FileChooser sorts columns.</li>
- <li>Can remove groups one by one.</li>
- <li>Filechooser icons installed.</li>
- <li>Finder ignores return character when searching. Return key will initiate
- a search.<br>
- </li>
- </ul></td>
- </tr>
- <tr>
- <td> <div align="center"><strong>2.0</strong><br>
- 20/6/05</div></td>
- <td ><ul>
- <li> New codebase</li>
- </ul></td>
- <td > </td>
- </tr>
-</table>
-<p> </p>
-</body>
-</html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
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