-<html>\r
-<head><title>What's new ?</title></head>\r
-<body>\r
-<p><strong>What's new ?</strong> </p>\r
-<p>If you are reading this then you will already have seen some of the recent changes\r
- made to Jalview.<br>\r
- Jalview takes advantage of some of the more recent user interface developments\r
- in the Java programming language. For instance Jalview is now a multi windowed\r
- application, this keeps all your Jalview windows neatly together in one main\r
- application window. </p>\r
-<p>If you were familiar with the original Jalview, here is a list of important\r
- features you should know about the current development:</p>\r
-<ul>\r
- <li>Editing sequences is no longer the default when mouse clicking the alignment.\r
- Instead, mouse clicking on the alignment creates a "selection region"\r
- which may be full sequences or groups of residues.</li>\r
- <li>To insert or edit the gaps in one sequence in alignment, the "Shift"\r
- key must be held down when dragging the mouse.</li>\r
- <li>To insert or edit gaps for a group of sequences, the "Alt" key\r
- (or in X windows the "Control" key) must be held down.</li>\r
- <li>Selecting colour schemes in the colour menu either sets just the "background"\r
- colourscheme for the alignment, or - when the tickbox "Apply colour to\r
- all groups" is ticked, applies the scheme to the background and all groups\r
- defined on the alignment.</li>\r
- <li>Use the right mouse button (apple and click on the Mac) whilst the pointer\r
- is within the selection area to access the "define" region menu\r
- to define a new region, give it a name, and change its colourscheme and display\r
- properties.</li>\r
- <li>Conservation is automatically updated whenever the alignment is edited</li>\r
- <li>There is no "quick draw" option</li>\r
- <li>Edits can be undone, and redone!</li>\r
-</ul>\r
-<table border="1">\r
- <tr>\r
- <td><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
- <td><div align="center"><strong>2.06</strong><br>\r
- 28/9/05</div></td>\r
- <td><ul>\r
- <li>View annotations in wrapped mode</li>\r
- <li>More options for PCA viewer</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>GUI bugs resolved</li>\r
- <li>Runs with -nodisplay from command line</li>\r
- </ul></td>\r
- </tr>\r
- <tr>\r
- <td><div align="center"><strong>2.05b</strong><br>\r
- 15/9/05</div></td>\r
- <td><ul>\r
- <li>Choose EPS export as lineart or text</li>\r
- <li>Jar files are executable</li>\r
- <li>Can read in Uracil - maps to unknown residue</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Known OutOfMemory errors give warning message</li>\r
- <li>Overview window calculated more efficiently</li>\r
- <li>Several GUI bugs resolved</li>\r
- </ul></td>\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>Edit and annotate in "Wrapped" view</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Several GUI bugs resolved</li>\r
- </ul></td>\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>Hold down mouse wheel & scroll to change font size</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Improved JPred client reliability</li>\r
- <li>Improved loading of Jalview files</li>\r
- </ul></td>\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>Set Proxy server name and port in preferences</li>\r
- <li>Multiple URL links from sequence ids</li>\r
- <li>User Defined Colours can have a scheme name and added to Colour Menu</li>\r
- <li>Choose to ignore gaps in consensus calculation</li>\r
- <li>Unix users can set default web browser</li>\r
- <li>Runs without GUI for batch processing</li>\r
- <li>Dynamically generated Web Service Menus</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>InstallAnywhere download for Sparc Solaris</li>\r
- </ul></td>\r
- </tr>\r
- <tr>\r
- <td> <div align="center"><strong>2.02</strong><br>\r
- 18/7/05</div></td>\r
- <td> </td>\r
- <td><ul>\r
- <li>Copy & Paste order of sequences maintains alignment order.</li>\r
- </ul></td>\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>Use delete key for deleting selection.</li>\r
- <li>Use Mouse wheel to scroll sequences.</li>\r
- <li>Help file updated to describe how to add alignment annotations.</li>\r
- <li>Version and build date written to build properties file.</li>\r
- <li>InstallAnywhere installation will check for updates at launch of Jalview.</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Delete gaps bug fixed.</li>\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
- a search.<br>\r
- </li>\r
- </ul></td>\r
- </tr>\r
- <tr>\r
- <td> <div align="center"><strong>2.0</strong><br>\r
- 20/6/05</div></td>\r
- <td ><ul>\r
- <li> New codebase</li>\r
- </ul></td>\r
- <td > </td>\r
- </tr>\r
-</table>\r
-<p> </p>\r
-</body>\r
-</html>\r
+<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/>.
+-->
+<head>
+<title>What's new ?</title>
+</head>
+<body>
+<p><strong>What's new ?</strong></p>
+<p><strong>Highlights in Jalview Version 2.5</strong></p>
+<ul>
+ Linked viewing of nucleic acid sequences and structures<br/>
+ Automatic Scrolling option in View menu to display the
+ currently highlighted region of an alignment.<br/>
+ Order an alignment by sequence length, or using the average score or total feature count for each sequence.<br/>
+ Shading features by score or associated description<br/>
+ Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).<br/>
+ New hide/show options including Shift+Control+H to hide everything but the currently selected region.<br/>
+</ul>
+<em>Jalview Desktop:</em>
+<ul>
+ Fetch DB References capabilities and UI expanded to support
+ retrieval from DAS sequence sources<br/>
+ Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in application.<br/>
+ Group-associated consensus, sequence logos and conservation
+ plots<br/>
+ Symbol distributions for each column can be exported and
+ visualized as sequence logos<br/>
+ Jalview Java Console<br/>
+ New webservice for submitting sequences and IDs to <a
+ href="webServices/index.html#envision2">Envision2</a> Workflows<br/>
+ Improved VAMSAS synchronization and sharing of selections.<br/>
+</ul>
+<em>JalviewLite:</em>
+<ul>
+ Middle button resizes annotation row height<br/>
+ New Parameters - including default tree display settings.<br/>
+ Non-positional features displayed in ID tooltip<br/>
+</ul>
+<p><strong>Issues Resolved (a select list)</strong></p>
+<ul>
+ <ul>
+ Source field in GFF files parsed as feature source rather
+ than description<br/>
+ Non-positional features are now included in sequence feature
+ and gff files (controlled via non-positional feature visibility in
+ tooltip).<br/>
+ URL links generated for all feature links (bugfix)<br/>
+ Codons containing ambiguous nucleotides translated as 'X' in
+ peptide product<br/>
+ 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.<br/>
+ Jalview Annotation File generation/parsing consistent with
+ documentation (e.g. Stockholm annotation can be exported and
+ re-imported)<br/>
+ Find incrementally searches ID string matches as well as
+ subsequence matches, and correctly reports total number of both.<br/>
+ </ul>
+ <em>Desktop Issues</em>
+ <ul>
+ Better handling of exceptions during sequence retrieval<br/>
+ PDB files retrieved from URLs are cached properly<br/>
+ Sequence description lines properly shared via VAMSAS<br/>
+ Sequence fetcher fetches multiple records for all data
+ sources<br/>
+ Ensured that command line das feature retrieval completes
+ before alignment figures are generated.<br/>
+ Reduced time taken when opening file browser for first time.<br/>
+ User defined group colours properly recovered from Jalview projects.<br/>
+ </ul>
+</ul>
+
+<p> </p>
+<p>See the <a href="releases.html">Release History</a> page for
+details of all new features and resolved issues.</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff