-<html>\r
-<head><title>What's new ?</title></head>\r
-<body>\r
-<p><strong>What's new ?</strong> </p>\r
-<p>Jalview Version 2.08</p>\r
-<p> <a href="editing/index.html">Editing</a> can be locked to the selection area. \r
- Any edits made within the locked area do not affect the rest of the alignment.</p>\r
-<p> Keyboard editing - press F2 to toggle <a href="features/cursorMode.html">cursor mode</a> On / Off. For a full list \r
- of keyboard controls, look <a href="keys.html">here</a>.</p>\r
-<p> <a href="features/search.html">Create sequence features from searches</a>. \r
- Previously, the regions of sequences highlighted as the result of\r
- searches were added as new regions in the alignment. Now, the sequence region\r
- selected by a search can be used to define named sequences features\r
- attached to the sequence, rather than the alignment.\r
- </p>\r
-<p>Sequence feature display and rendering has also been enhanced, with\r
- the addition of sequence feature groups (which can be used to show\r
- or hide a set of feature types <em>en masse</em>) and user defined\r
- feature colours as well as transparency controls, using the <a\r
- href="features/seqfeatures.html">Sequence Feature Settings</a>\r
- window. The <a href="features/featuresFormat.html">Features file</a>\r
- has also been extended to accomodate these enhancements.</p>\r
-<p>Alignment annotation and colouring is also considerably\r
- enhanced. Precalculated symbolic and quantitative annotations (text labels,\r
- secondary structure symbols and multiple scalar graphs) can now be\r
- loaded onto alignments via the <a\r
- href="features/annotationsFormat.html">Annotation\r
- File</a>. Additionally, the <a\r
- href="colourSchemes/annotationColouring.html">Annotation\r
- Colouring</a> dialog box allows an alignment to be coloured based on\r
- any of the graphed quantities with which it is annotated.</p>\r
-<p>Rendering speed has been improved by disabling anti-aliasing via\r
- the <strong>Smooth Fonts</strong>\r
- option in the <strong>View \r
- menu</strong> (its default set in <strong>Preferences</strong>). In addition, response\r
- times when editing alignments can be reduced by turning off the automatic\r
- calculation of amino acid property Consensus (which has been\r
- reintroduced to the <strong>Calculate</strong> menu as <strong>Autocalculate Consensus</strong>).<br>\r
-</p>\r
-<p><strong>Issues Resolved</strong></p>\r
-<ul>\r
-<li>Drag & Drop now works on common Linux desktops (at least KDE\r
-and Gnome)</li>\r
-<li>Jalview XML Archive Input/Output is now faster (using an\r
-internal Jalview schema), and sequence description strings are now\r
-preserved in the archive.</li>\r
-<li>Jalview can now correctly read and write <a\r
-href="http://salilab.org/modeller/modeller.html">MODELLER</a> style\r
-PIR description lines for proteins with a PDB reference.\r
-</li>\r
-</ul>\r
-<p>See the <a href="releases.html">Release History</a> page for details of all\r
- new features and resolved issues. </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