-<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>2.0</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
- <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>2.02</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>2.03</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
-</table>\r
-<p> </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