<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<head>
<title>Exporting alignments as artwork</title>
</head>
<body>
-<p><strong>Export<a name="export"></a></strong></p>
-<p>The alignment view can be printed using
-<strong>File→Print</strong>, or exported in a number of ways via the
-<strong>File→Export</strong> menu:
-<ul>
-<li>HTML<br><em>for viewing in a web browser</em>
-</li>
-<li>PNG - a Portable Networks Graphics image<br><em>For low quality
-diagrams and powerpoint presentations</em>
-</li>
-<li>EPS - an Encapsulated Postscript Document<br><em>For high quality
-diagrams and publications.</em>
-</li></ul>
-
-<p><em>Tips for working with EPS Files</em></p><ul><li>The EPS file generated by jalview contains vector
- graphics which are directly editable in graphics applications such as
- Adobe Illustrator.</li>
-<li>When importing an EPS into to a Microsoft office document, a snapshot image of the
- file will be displayed which often looks blurred. Right-click the
- image and choose "Edit image." to convert it to word
- drawing objects which give a truer WYSIWIG representation.
- </li>
- <li>
- Mac OSX users will find that eps files are automatically converted into
- PDF files.
- </li>
-</p>
+ <p>
+ <strong>Exporting alignments as graphics and lineart<a
+ name="export"
+ ></a></strong>
+ </p>
+ <p>
+ The alignment view can be printed using <strong>File→Print</strong>,
+ or exported in a number of ways via the <strong>File→Export</strong>
+ menu:
+ <ul>
+ <li>HTML<br> <em>for viewing in a web browser</em>
+ </li>
+ <li>PNG - a Portable Networks Graphics image<br> <em>For
+ low quality diagrams and powerpoint presentations</em>
+ </li>
+ <li>EPS - an Encapsulated Postscript Document<br> <em>For
+ high quality diagrams and publications.</em>
+ <li>SVG - a Scalable Vector Graphics document<br> <em>For
+ high quality diagrams in publications and on the web.</em>
+ </li>
+ <li>BioJS MSA - A JavaScript based multiple sequence alignment
+ viewer. <br> <em>For interactive alignment data
+ visualisation in a web browser.<br />Get more info about the
+ BioJS MSA viewer at a
+ href="http://msa.biojs.net/">http://msa.biojs.net/</a>
+ </em>
+ </li>
+
+ </ul>
+ <a name="htmlexport" />
+ <p>
+ <strong>Exporting alignments as Web Pages</strong>
+ <p>
+ In Jalview 2.9, new HTML exporting options were introduced. The
+ standard HTML export option displays alignments as SVG documents
+ embedded as scollable panes. Exported pages can optionally also
+ include <a href="../features/bioJsonFormat.html">BioJSON</a> data,
+ which allows Jalview to extract the original data used to create the
+ page. Jalview can also generate HTML pages which embed BioJSON data
+ and the BioJS MSA viewer, a pure javascript alignment viewer that
+ provides a range of interactive analysis capabiltiies.
+ </p>
+ <p>
+ <p>
+ <strong>Tips for working with EPS Files</strong>
+ </p>
+ <li>The EPS file generated by Jalview contains vector graphics
+ which are directly editable in graphics applications such as Adobe
+ Illustrator.</li>
+ <li>EPS files can be produced as "Text" or
+ "Lineart". Use "Text" if you want the final
+ document to be MUCH smaller in diskspace and be able to search, edit
+ and select text. Use "Lineart" if you want an exact image
+ of the alignment as displayed in Jalview. This is useful if a 3rd
+ Party EPS viewer does not have the same Font which the EPS file was
+ created with.</li>
+ <li>When importing an EPS file into a Microsoft office document,
+ a snapshot image of the file will be displayed which often looks
+ blurred. Right-click the image and choose "Edit image." to
+ convert it to word drawing objects which give a truer WYSIWIG
+ representation.</li>
+ <li>Mac OSX users will find that eps files are automatically
+ converted into PDF files.</li>
+ </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff