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 <li><strong><a href="features/importvcf.html#attribs">Standard
37 attributes for filtering variants</a></strong> (e.g. position, QUAL field etc) a new feature suggested by
38 a user at the Jalview booth during ISMB 2019.</li>
41 See the <a href="releases.html#Jalview.2.11.1.0">2.11.1.0
42 release notes</a> for full details of bugs fixed and new known issues.
45 <strong>Jalview 2.11 - new installer and new capabilities</strong>
47 <p>Jalview 2.11 introduces support for loading VCF files, and new
48 filters and shading models for sequence features. Under the hood,
49 we've addressed many bugs, and also made some important changes in
50 the way the Jalview desktop is installed and launched.</p>
52 <li><strong>The Jalview Launcher and Update System</strong>.
53 Jalview's new installation model means you'll only need to
54 download and install Jalview once. After installation, Jalview
55 will automatically keep itself up to date. The launcher also sets
56 Jalview's memory automatically, so you'll never again have to
57 manually configure Java's memory settings.<br />We are grateful
58 to ej Technologies for providing a free open source project
60 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>,
62 href="https://en.wikipedia.org/wiki/Three_Rings_Design">Three
63 Rings Design</a> for Jalview's new over the air update system: <a
64 href="https://github.com/threerings/getdown">Getdown</a>.</li>
65 <li><strong>VCF Support</strong>. Proteins and genomic contigs with
66 chromosomal location annotation (such as protein coding genes
67 retrieved from Ensembl) can be annotated with variants <a
68 href="features/importvcf.html">imported from a local VCF file</a>.</li>
69 <li><strong>Feature filters and attribute colourschemes</strong>. A new
70 <a href="features/featureschemes.html">Feature Display
71 Settings</a> dialog allows filters and feature attribute based
72 colourschemes to be constructed, and a new <em>filters</em> column
73 added to the <a href="features/featuresettings.html">Feature
74 Settings</a> dialog. Jalview's sequence feature datamodel has also
75 been further optimised, and is now maintained as a separate
76 library <em>IntervalStoreJ</em> (available at https://github.com/bartongroup/IntervalStoreJ)</li>
77 <li><strong>Alternative tables for CDS translation</strong>. The <a
78 href="menus/alwcalculate.html">Translate as cDNA</a> option now
79 offers alternative amino acid coding schemes.</li>
80 <li><strong>PCA plots stored in Jalview Projects</strong>. The <a
81 href="calculations/pca.html">PCA viewer</a> user interface has
82 also been improved.</li>
83 <li><strong>Backup files</strong>. Jalview will automatically
84 create backups when overwriting existing files, and - unlike with
85 earlier versions - should Jalview crash during a save, the original
86 file will be unaffected. The <a
87 href="features/preferences.html#backups">Backups tab</a> in
88 Jalview's preferences dialog allows the number and format of
89 backup filenames to be configured.</li>
92 The full list of bugs fixed in this release can be found in the <a
93 href="releases.html#Jalview.2.11.0">2.11 Release Notes</a>.
96 <strong>Jalview and Java 11, and onwards</strong>
98 <p>The Jalview application comes bundled with its own independent
99 Java installation. Version 2.11.0 includes an AdoptOpenJDK Java 1.8
100 runtime which will be kept up to date. A Java 11 based installation
101 is available from the Jalview development pages.</p>
103 <em>Saying goodbye...</em><br>Long time Jalview users will notice
104 that this release no longer features the
105 <em>Vamsas</em> desktop menu, or a <em>Distributed
106 Annotation System (DAS)</em> tab on the feature settings dialog.
107 DAS is no longer supported by major bioinformatics databases, and we
108 decided that it was no longer feasible to maintain either JDAS or
109 the VAMSAS client library which rely on out-dated Java XML binding
113 <em>Next up...</em><br /> Keep an eye on the Jalview web site for
114 news about JalviewJS - the web based JavaScript implementation of
115 Jalview. Whilst Jalview 2.11 has been in development, we have also
116 been working with Prof. Bob Hanson (Jmol and JSmol) to enable
117 Jalview to run as both a Java application and a JavaScript app in a
118 web page. To find out more, open <em>http://www.jalview.org/jalview-js/</em>
119 in Chrome or Firefox.