3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>What's new ?</title>
27 <strong>Jalview 2.11 - new installer and new capabilities</strong>
29 <p>Jalview 2.11 introduces support for loading VCF files, and new
30 filters and shading models for sequence features. Under the hood,
31 we've addressed many bugs, and also made some important changes in
32 the way the Jalview desktop is installed and launched.</p>
34 <li><strong>The Jalview Launcher and Update System</strong>.
35 Jalview's new installation model means you'll only need to
36 download and install Jalview once. After installation, Jalview
37 will automatically keep itself up to date. The launcher also sets
38 Jalview's memory automatically, so you'll never again have to
39 manually configure Java's memory settings.<br />We are grateful
40 to ej Technologies for providing a free open source project
42 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>,
44 href="https://en.wikipedia.org/wiki/Three_Rings_Design">Three
45 Rings Design</a> for Jalview's new over the air update system: <a
46 href="https://github.com/threerings/getdown">Getdown</a>.</li>
47 <li><strong>VCF Support</strong>. Proteins and genomic contigs with
48 chromosomal location annotation (such as protein coding genes
49 retrieved from Ensembl) can be annotated with variants <a
50 href="features/importvcf.html">imported from a local VCF file</a>.</li>
51 <li><strong>Feature filters and attribute colourschemes</strong>. A new
52 <a href="features/featureschemes.html">Feature Display
53 Settings</a> dialog allows filters and feature attribute based
54 colourschemes to be constructed, and a new <em>filters</em> column
55 added to the <a href="features/featuresettings.html">Feature
56 Settings</a> dialog. Jalview's sequence feature datamodel has also
57 been further optimised, and is now maintained as a separate
58 library <em>IntervalStoreJ</em> (available at https://github.com/bartongroup/IntervalStoreJ)</li>
59 <li><strong>Alternative tables for CDS translation</strong>. The <a
60 href="menus/alwcalculate.html">Translate as cDNA</a> option now
61 offers alternative amino acid coding schemes.</li>
62 <li><strong>PCA plots stored in Jalview Projects</strong>. The <a
63 href="calculations/pca.html">PCA viewer</a> user interface has
64 also been improved.</li>
65 <li><strong>Backup files</strong>. Jalview will automatically
66 create backups when overwriting existing files, and - unlike with
67 earlier versions - should Jalview crash during a save, the original
68 file will be unaffected. The <a
69 href="features/preferences.html#backups">Backups tab</a> in
70 Jalview's preferences dialog allows the number and format of
71 backup filenames to be configured.</li>
74 The full list of bugs fixed in this release can be found in the <a
75 href="releases.html#Jalview.2.11.0">2.11 Release Notes</a>.
78 <strong>Jalview and Java 11, and onwards</strong>
80 <p>The Jalview application comes bundled with its own independent
81 Java installation. Version 2.11.0 includes an AdoptOpenJDK Java 1.8
82 runtime which will be kept up to date. A Java 11 based installation
83 is available from the Jalview development pages.</p>
85 <em>Saying goodbye...</em><br>Long time Jalview users will notice
86 that this release no longer features the
87 <em>Vamsas</em> desktop menu, or a <em>Distributed
88 Annotation System (DAS)</em> tab on the feature settings dialog.
89 DAS is no longer supported by major bioinformatics databases, and we
90 decided that it was no longer feasible to maintain either JDAS or
91 the VAMSAS client library which rely on out-dated Java XML binding
95 <em>Next up...</em><br /> Keep an eye on the Jalview web site for
96 news about JalviewJS - the web based JavaScript implementation of
97 Jalview. Whilst Jalview 2.11 has been in development, we have also
98 been working with Prof. Bob Hanson (Jmol and JSmol) to enable
99 Jalview to run as both a Java application and a JavaScript app in a
100 web page. To find out more, open <em>http://www.jalview.org/jalview-js/</em>
101 in Chrome or Firefox.