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>Exporting alignments as artwork</title>
27 <strong>Exporting alignments as graphics and lineart<a
28 name="export"></a></strong>
31 The alignment view can be printed using <strong>File→Print</strong>,
32 or exported in a number of ways via the <strong>File→Export</strong>
37 <em>for viewing in a web browser</em>
39 <li>PNG - a Portable Networks Graphics image<br>
40 <em>For low quality diagrams and powerpoint presentations</em>
42 <li>EPS - an Encapsulated Postscript Document<br>
43 <em>For high quality diagrams and publications.</em>
44 <li>SVG - a Scalable Vector Graphics document<br>
45 <em>For high quality diagrams in publications and on the web.</em>
47 <li>BioJS MSA - A JavaScript based multiple sequence alignment
48 viewer. <br> <em>For interactive alignment data
49 visualisation in a web browser.<br />Get more info about the
51 href="http://msa.biojs.net/">http://msa.biojs.net/</a>
56 <a name="htmlexport" />
58 <strong>Exporting alignments as Web Pages</strong>
61 In Jalview 2.9, new HTML exporting options were introduced. The
62 standard HTML export option displays alignments as SVG documents
63 embedded as scollable panes. Exported pages can optionally also
64 include <a href="../features/bioJsonFormat.html">BioJSON</a> data,
65 which allows Jalview to extract the original data used to create the
66 page. Jalview can also generate HTML pages which embed BioJSON data
67 and the BioJS MSA viewer, a pure javascript alignment viewer that
68 provides a range of interactive analysis capabiltiies.
73 <em>Import of BioJSON data from HTML pages</em>
75 <p>When importing embedded data in an HTML document, Jalview
76 searches for a hidden input or div element named "seqData":
78 <code><div name="seqData" id="seqData" style="display: none;">#valid BioJSON data#</div></code>
82 <code><input type="hidden" id="seqData" name="seqData" value='#valid BioJSON data#'/></code>
84 Jalview can also import JSON data directly if it conforms to the BioJSON specification.
86 <p><em>Tips for working with EPS Files</em></p>
87 <li>The EPS file generated by Jalview contains vector graphics which are directly
88 editable in graphics applications such as Adobe Illustrator.</li>
89 <li>EPS files can be produced as "Text" or "Lineart". Use
90 "Text" if you want the final document to be MUCH smaller in diskspace
91 and be able to search, edit and select text. Use "Lineart" if you
92 want an exact image of the alignment as displayed in Jalview. This is useful
93 if a 3rd Party EPS viewer does not have the same Font which the EPS file was
95 <li>When importing an EPS file into a Microsoft office document, a snapshot image of the
96 file will be displayed which often looks blurred. Right-click the
97 image and choose "Edit image." to convert it to word
98 drawing objects which give a truer WYSIWIG representation.
101 Mac OSX users will find that eps files are automatically converted into