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 2.11.1.1</strong>
29 <p>Jalview 2.11.1.1 is the first patch release for Jalview version
30 2.11.1. In addition to fixes for some critical bugs, it also
31 contains a handful of new features suggested by the Jalview
34 <li>Shift+arrow keys navigate to next gap or residue in cursor
35 mode (enable with F2)</li>
36 <li>Support import of VCF 4.3 by updating HTSJDK from 2.12 to
38 <li>Improved recognition of GZipped files from local disk or
39 retrieved via the web</li>
40 <li>EMBL and EMBL CDS database records retrieved from the
41 European Nucleotide Archive's Data API as 'EMBL Flatfile' records</li>
42 <li>Improved <a href="logging.html">Java Console and
43 logging</a> to help track down problems
45 <li>Improved support for Hi-DPI (4K) screens when running on
46 Linux (Requires Java 11+)</li>
48 <p>Critical bug fixes include</p>
50 <li>Jalview runs correctly when launched with Turkish language
52 <li>Peptide-to-CDS tracking broken when multiple EMBL gene
53 products shown for a single contig (such as viral genomes)</li>
54 <li>Errors encountered when processing variants from VCF files
55 yield "Error processing VCF: Format specifier '%s'" on the console</li>
56 <li>Count of features not shown can be wrong when there are
57 both DNA and Protein features mapped to the position under
59 <li>Sequence ID for reference sequence is clipped when Right
60 align Sequence IDs enabled</li>
61 <li>Find doesn't report matches that span hidden gapped columns</li>
62 <li>Jalview ignores file format parameter specifying output
63 format when exporting an alignment via the command line</li>
66 For the full release notes, see <a href="releases.html#Jalview.2.11.1.1">the
67 Jalview 2.11.1.1 release notes</a>.
70 <strong>Known Issues</strong>
73 <li>We've had reports from a small number of windows 10 users
74 who see a warning dialog pop up when Jalview tries to save a new
75 version of an existing file. If you are affected by this bug and
76 this latest version of Jalview doesn't fix it, please let us know!</li>
77 <li>Co-located features exported and re-imported are ordered
78 differently when shown on alignment and in tooltips. (Also affects
80 <li>Drag and drop of alignment file onto alignment window when
81 in a HiDPI scaled mode in Linux only works for the top left
82 quadrant of the alignment window</li>