<title>Exporting alignments as artwork</title>
</head>
<body>
-<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 - A JavaScript based multiple sequence alignment visualiser. <br><em>For viewing in a web browser. Get more info about BioJS at <a href="http://msa.biojs.net/">http://msa.biojs.net/</a></em>
-</li>
+ <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>
-
-<p>From Jalview 2.9, the HTML exporting system was re-implemented to use SVG rendering. Also, optional embedding of <a href="../features/bioJsonFormat.html">BioJSON</a> data to the generated HTML file was introduced.
-This is achieved using a hidden input or div element which MUST be named "seqData" as seen in the examples below:
-<pre><code> <div name="seqData" id="seqData" style="display: none;">#valid BioJSON data#</div>
- OR
- <input type="hidden" id="seqData" name="seqData" value='#valid BioJSON data#'/></pre></code>
-HTML file embedded with BioJSON can be imported back to Jalview at a later date. During the import operation, Jalview uses an API called JSoup to traverse through the HTML file and extract the embedded BioJSON data from the target div or input element named <b>'seqData'</b>. The extracted data is then parsed as a BioJSON format.
-
-
-
-<p><em>Tips for working with EPS Files</em></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>
+ </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 scrollable 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 capabilities.
+ </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>
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