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 2.11.1</strong>
30 Jalview 2.11.1.0 is the first minor release for the 2.11 series.
31 We've moved to a <em>four</em> number scheme to help you (and us!)
32 keep track of patch and bug fix releases (which we used to denote
36 See the <a href="releases.html#Jalview.2.11.1.0">2.11.1.0
37 release notes</a> for full details of bugs fixed and new known issues.
40 <strong>Jalview 2.11 - new installer and new capabilities</strong>
42 <p>Jalview 2.11 introduces support for loading VCF files, and new
43 filters and shading models for sequence features. Under the hood,
44 we've addressed many bugs, and also made some important changes in
45 the way the Jalview desktop is installed and launched.</p>
47 <li><strong>The Jalview Launcher and Update System</strong>.
48 Jalview's new installation model means you'll only need to
49 download and install Jalview once. After installation, Jalview
50 will automatically keep itself up to date. The launcher also sets
51 Jalview's memory automatically, so you'll never again have to
52 manually configure Java's memory settings.<br />We are grateful
53 to ej Technologies for providing a free open source project
55 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>,
57 href="https://en.wikipedia.org/wiki/Three_Rings_Design">Three
58 Rings Design</a> for Jalview's new over the air update system: <a
59 href="https://github.com/threerings/getdown">Getdown</a>.</li>
60 <li><strong>VCF Support</strong>. Proteins and genomic contigs with
61 chromosomal location annotation (such as protein coding genes
62 retrieved from Ensembl) can be annotated with variants <a
63 href="features/importvcf.html">imported from a local VCF file</a>.</li>
64 <li><strong>Feature filters and attribute colourschemes</strong>. A new
65 <a href="features/featureschemes.html">Feature Display
66 Settings</a> dialog allows filters and feature attribute based
67 colourschemes to be constructed, and a new <em>filters</em> column
68 added to the <a href="features/featuresettings.html">Feature
69 Settings</a> dialog. Jalview's sequence feature datamodel has also
70 been further optimised, and is now maintained as a separate
71 library <em>IntervalStoreJ</em> (available at https://github.com/bartongroup/IntervalStoreJ)</li>
72 <li><strong>Alternative tables for CDS translation</strong>. The <a
73 href="menus/alwcalculate.html">Translate as cDNA</a> option now
74 offers alternative amino acid coding schemes.</li>
75 <li><strong>PCA plots stored in Jalview Projects</strong>. The <a
76 href="calculations/pca.html">PCA viewer</a> user interface has
77 also been improved.</li>
78 <li><strong>Backup files</strong>. Jalview will automatically
79 create backups when overwriting existing files, and - unlike with
80 earlier versions - should Jalview crash during a save, the original
81 file will be unaffected. The <a
82 href="features/preferences.html#backups">Backups tab</a> in
83 Jalview's preferences dialog allows the number and format of
84 backup filenames to be configured.</li>
87 The full list of bugs fixed in this release can be found in the <a
88 href="releases.html#Jalview.2.11.0">2.11 Release Notes</a>.
91 <strong>Jalview and Java 11, and onwards</strong>
93 <p>The Jalview application comes bundled with its own independent
94 Java installation. Version 2.11.0 includes an AdoptOpenJDK Java 1.8
95 runtime which will be kept up to date. A Java 11 based installation
96 is available from the Jalview development pages.</p>
98 <em>Saying goodbye...</em><br>Long time Jalview users will notice
99 that this release no longer features the
100 <em>Vamsas</em> desktop menu, or a <em>Distributed
101 Annotation System (DAS)</em> tab on the feature settings dialog.
102 DAS is no longer supported by major bioinformatics databases, and we
103 decided that it was no longer feasible to maintain either JDAS or
104 the VAMSAS client library which rely on out-dated Java XML binding
108 <em>Next up...</em><br /> Keep an eye on the Jalview web site for
109 news about JalviewJS - the web based JavaScript implementation of
110 Jalview. Whilst Jalview 2.11 has been in development, we have also
111 been working with Prof. Bob Hanson (Jmol and JSmol) to enable
112 Jalview to run as both a Java application and a JavaScript app in a
113 web page. To find out more, open <em>http://www.jalview.org/jalview-js/</em>
114 in Chrome or Firefox.