-<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 <a href="editing/selectionAreas.html">locked to the\r
- selection area</a> so that any edits made within the locked area do\r
- not unexpectedly shift other parts 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 features <em>en masse</em>) and user defined\r
- feature colours as well as transparency controls, using the <a\r
- href="features/featuresettings.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="io/modellerpir.html">MODELLER style\r
-PIR</a> files.\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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 in Jalview 2.10.0b1 ?</strong>
+ </p>
+ <p>
+ Jalview 2.10.0b1 is a patch release for 2.10, the next major release
+ in the Jalview 2 series. Full details are in the <a
+ href="releases.html#Jalview.2.10.0b1">Jalview 2.10b1 Release
+ Notes</a>, but the highlights are below.
+ </p>
+ <ul>
+ <li>Drag and drop reinstated for the Jalview desktop on
+ Windows, Linux and older OSX systems.</li>
+ <li>Problems loading local PDB files have been fixed</li>
+ <li>Conservation shading can be disabled for PID and consensus
+ based colour scheme</li>
+ </ul>
+ <p><em>Major highlights of the 2.10.0 Release</em></p>
+ <ul>
+ <li><strong>Ensembl sequence fetcher</strong><br />Annotated
+ Genes, transcripts and proteins can be retrieved via Jalview's new
+ <a href="features/ensemblsequencefetcher.html">Ensembl REST
+ client</a>. Support for import of Ensembl data allows:
+ <ul>
+ <li><strong>Aligned locus view</strong><br />Transcripts
+ retrieved for a gene identifier via the Ensembl or
+ EnsemblGenomes sequence databases are automatically aligned to
+ their reference genome, and introns hidden from the view.</li>
+ <li><strong>Sequence variant data</strong><br />Jalview
+ propagates variant annotation on genomic regions onto
+ transcripts and protein products, complete with associated
+ metadata such as clinical significance.</li>
+ </ul></li>
+ <li><strong>Ensembl and ENA 'show cross-references'
+ support</strong><br />The Calculations menu's <strong>'Show
+ cross-references'</strong> now offers Ensembl as well as EMBLCDS and
+ Uniprot when CDS/Protein mapping data is available for download or
+ display. This allows variant annotation to be added directly to an
+ alignment of UniProt sequences.</li>
+ <li><strong>Working with structures</strong>
+ <ul>
+ <li><strong>More accurate structure mappings</strong><br />
+ Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
+ to <a href="features/siftsmapping.html">match structures
+ to UniProt sequences</a>, even for structures containing
+ multiple copies of a sequence.</li>
+ <li><strong>Import structures as mmCIF</strong><br />Jalview
+ now downloads data from the EMBL-EBI's PDBe site as <a
+ href="features/mmcif.html">mmCIF</a>. This allows very large
+ structures to be imported, such as the HIV virus capsid
+ assembly.</li>
+ <li><strong>Chimera users will need to upgrade to
+ 1.11.1</strong><br />If you use Chimera to view structures
+ downloaded by Jalview 2.10, you will need to make sure you are
+ running the latest version of <a href="features/chimera.html">Chimera</a>.</li>
+ </ul></li>
+ <li><strong>UniProt Free Text Search</strong><br />The new
+ search dialog for UniProt allows you to browse and retrieve
+ sequences with free-text search, or structured queries.</li>
+ <li><strong>Reference sequence alignment view</strong><br />
+ Jalview 2.9 introduced support for reference sequences. In 2.10,
+ when a reference sequence is defined for the alignment, the
+ alignment column ruler is now numbered according to the reference
+ sequence. The reference sequence for alignment views can also be
+ saved and restored from Jalview projects.</li>
+ </ul>
+
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff