-<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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<head>
+<title>What's new ?</title>
+</head>
+<body>
+ <p>
+ <strong>What's new ?</strong><br /> Jalview 2.8.0b1 is a bugfix
+ release for Jalview version 2.8. <br /> As usual you can find the
+ highlights below, and the comprehensive list is given in the <a
+ href="releases.html#Jalview2.8.0b1">Jalview 2.8.0b1 Release Notes</a>.
+ </p>
+ <p>
+ This bug fix release includes numerous minor enhancements made over
+ the last 12 months. Importantly, it is also the first release that
+ provides Jalview as a trusted application, signed with a certificate
+ donated to us by <a href="certum.eu">Certum</a>.
+ </p>
+ <strong>Enhancements and new features</strong>
+ <ul>
+ <li>Allow disorder predictions to be made on the current
+ selection (or visible selection) in the same way that JPred works</li>
+ <li>allow import of data from gzipped files</li>
+ <li>Improved per-sequence 'colour-by-annotation' performance</li>
+ <li>Support '' style escaping of quotes in Newick files</li>
+ <li>group options for JABAWS service by command line name</li>
+ <li>Select primary source when selecting authority in database
+ fetcher GUI</li>
+ <li>COMBINE statement uses current SEQUENCE_REF and GROUP_REF
+ scope to group annotation rows</li>
+ <li>add .mfa to FASTA file extensions recognised by Jalview</li>
+ <li>groovy scripting for headless jalview operation</li>
+ <li>Output in Stockholm format</li>
+ </ul>
+ <strong>Bug fixes</strong>
+ <ul>
+ <li>Uniprot and PDB database cross-reference fetching works
+ properly</li>
+ <li>'View all structures' in the desktop is more reliable</li>
+ <li>Web services parameter dialog box shows the options enabled
+ for different presets</li>
+ <li>Interactive creation of RNA secondary structure works more
+ smoothly</li>
+ <li>Keyboard mode 'P' command jumps to the right place</li>
+ <li>Improved support for parsing database cross-references via
+ Stockholm and Rfam database</li>
+ <li>Improved semantics in annotation files for grouping
+ annotation rows associated with particular sequences and groups</li>
+ <li>More robust DNA->Amino acid translation</li>
+ <li>Improved Headless-mode operation for DAS annotation
+ retrieval, groovy script execution and alignment figure generation</li>
+ <li>annotation label tooltip text needs to be wrapped</li>
+ </ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff