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
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11 * of the License, or (at your option) any later version.
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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.
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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>
35 <li>HTML<br> <em>for viewing in a web browser</em>
37 <li>PNG - a Portable Networks Graphics image<br> <em>For
38 low quality diagrams and powerpoint presentations</em>
40 <li>EPS - an Encapsulated Postscript Document<br> <em>For
41 high quality diagrams and publications.</em>
42 <li>SVG - a Scalable Vector Graphics document<br> <em>For
43 high quality diagrams in publications and on the web.</em>
45 <li>BioJS MSA - A JavaScript based multiple sequence alignment
46 viewer. <br> <em>For interactive alignment data
47 visualisation in a web browser.<br />Get more info about the
48 BioJS MSA viewer at <a href="http://msa.biojs.net/">http://msa.biojs.net/</a>
54 <strong>PNG Export Options</strong>
57 <em>Since Jalview 2.11.3</em> it is possible to specify options when <a
58 href="../features/clarguments-reference.html#exportingimagefiles">exporting
59 figures via the command line</a> to increase the resolution of the
60 exported PNG, and configure maximum width and height settings.
62 <p>You can also configure default export settings by adding the
65 <pre>.jalview_properties</pre>
66 <pre>BITMAP_SCALE=<Scale factor multiplied by 10>
67 BITMAP_WIDTH=Width of export in pixels
68 BITMAP_HEIGHT=Height of figure export in pixels
70 When scale is not set, the figure will be scaled to fit in the smallest
71 specified dimension. Scale will be ignored if it results in an image
72 dimension greater than the smallest specified dimension.
74 <a name="htmlexport" /><p>
75 <strong>Exporting alignments as Web Pages</strong>
77 In Jalview 2.9, new HTML exporting options were introduced. The
78 standard HTML export option displays alignments as SVG documents
79 embedded as scrollable panes. Exported pages can optionally also
80 include <a href="../features/bioJsonFormat.html">BioJSON</a> data,
81 which allows Jalview to extract the original data used to create the
82 page. Jalview can also generate HTML pages which embed BioJSON data
83 and the BioJS MSA viewer, a pure javascript alignment viewer that
84 provides a range of interactive analysis capabilities.
88 <strong>Tips for working with EPS Files</strong>
90 <li>The EPS file generated by Jalview contains vector graphics
91 which are directly editable in graphics applications such as Adobe
93 <li>EPS files can be produced as "Text" or
94 "Lineart". Use "Text" if you want the final
95 document to be MUCH smaller in diskspace and be able to search, edit
96 and select text. Use "Lineart" if you want an exact image
97 of the alignment as displayed in Jalview. This is useful if a 3rd
98 Party EPS viewer does not have the same Font which the EPS file was
100 <li>When importing an EPS file into a Microsoft office document,
101 a snapshot image of the file will be displayed which often looks
102 blurred. Right-click the image and choose "Edit image." to
103 convert it to word drawing objects which give a truer WYSIWIG
105 <li>EPS does not support colour transparency, so will not reproduce this
106 if used for <a href="../features/featuresettings.html#transparency">feature colouring</a>.</li>
107 <li>Mac OSX users will find that eps files are automatically
108 converted into PDF files.</li>