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
32 The alignment view can be printed using <strong>File→Print</strong>,
33 or exported in a number of ways via the <strong>File→Export</strong>
36 <li>HTML<br> <em>for viewing in a web browser</em>
38 <li>PNG - a Portable Networks Graphics image<br> <em>For
39 low quality diagrams and powerpoint presentations</em>
41 <li>EPS - an Encapsulated Postscript Document<br> <em>For
42 high quality diagrams and publications.</em>
43 <li>SVG - a Scalable Vector Graphics document<br> <em>For
44 high quality diagrams in publications and on the web.</em>
46 <li>BioJS MSA - A JavaScript based multiple sequence alignment
47 viewer. <br> <em>For interactive alignment data
48 visualisation in a web browser.<br />Get more info about the
49 BioJS MSA viewer at <a href="http://msa.biojs.net/">http://msa.biojs.net/</a>
54 <a name="htmlexport" />
56 <strong>Exporting alignments as Web Pages</strong>
58 In Jalview 2.9, new HTML exporting options were introduced. The
59 standard HTML export option displays alignments as SVG documents
60 embedded as scrollable panes. Exported pages can optionally also
61 include <a href="../features/bioJsonFormat.html">BioJSON</a> data,
62 which allows Jalview to extract the original data used to create the
63 page. Jalview can also generate HTML pages which embed BioJSON data
64 and the BioJS MSA viewer, a pure javascript alignment viewer that
65 provides a range of interactive analysis capabilities.
69 <strong>Tips for working with EPS Files</strong>
71 <li>The EPS file generated by Jalview contains vector graphics
72 which are directly editable in graphics applications such as Adobe
74 <li>EPS files can be produced as "Text" or
75 "Lineart". Use "Text" if you want the final
76 document to be MUCH smaller in diskspace and be able to search, edit
77 and select text. Use "Lineart" if you want an exact image
78 of the alignment as displayed in Jalview. This is useful if a 3rd
79 Party EPS viewer does not have the same Font which the EPS file was
81 <li>When importing an EPS file into a Microsoft office document,
82 a snapshot image of the file will be displayed which often looks
83 blurred. Right-click the image and choose "Edit image." to
84 convert it to word drawing objects which give a truer WYSIWIG
86 <li>Mac OSX users will find that eps files are automatically
87 converted into PDF files.</li>