<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<title>The VARNA RNA Viewer</title>
</head>
<body>
-<p><strong>The VARNA RNA Viewer</strong></p>
-<p><a href="http://varna.lri.fr/index.html">VARNA</a> was
-integrated into Jalview 2.8 to allow interactive viewing of RNA secondary structure annotation. It is opened by
-selecting the <strong>"Structure→View
-Structure:"</strong> option in
-the <a href="../menus/popupMenu.html">sequence id pop-up menu</a> (if
-you can't see this, then no RNA structure is associated with your
-sequence or alignment. In the pop-up menu all structures that
-are associated with this sequence and all sequences that are
-associated with the alignment are available.
+ <p>
+ <strong>The VARNA RNA Viewer</strong>
+ </p>
+ <p>
+ <a href="http://varna.lri.fr/index.html">VARNA</a> was integrated
+ into Jalview 2.8 to allow interactive viewing of RNA secondary
+ structure annotation. It is opened by selecting the <strong>"Structure→View
+ Structure:"</strong> option in the <a href="../menus/popupMenu.html">sequence
+ id pop-up menu</a> (if you can't see this, then no RNA structure is
+ associated with your sequence or alignment). In the pop-up menu all
+ structures that are associated with this sequence and all sequences
+ that are associated with the alignment are available.
+ <p>
+ Saving a Jalview session as a project file includes the state of any
+ Varna viewers, which are reopened when the project is reloaded <em>(since
+ Jalview 2.9)</em>.
+ <p>
+ <strong>Different structures</strong>
+ </p>
+ <ul>
+ <li><b>Alignment structures</b>: Structures associated with the
+ alignment are marked by having "consensus" attached to
+ their name. VARNA contains two different entries for consensus
+ structures.
+ <ul>
+ <li>Consensus structure: the individual sequence folded
+ into the consensus structure</li>
+ <li>Trimmed consensus structure: the individual sequence
+ folded into the the gap-free consensus structure. That means
+ all columns that contained gaps in the individual sequence
+ were removed. If this breaks a base-pair the pairing is
+ removed also. This can be considered as an approximation for
+ the individual structure.
+ </ul></li>
+ <li><b>Individual structures</b>: this is a structure
+ associated with the individual sequence and therefore not related
+ to the alignment</li>
+ </ul>
+ <p>
+ <strong>Controls</strong><br>
+ <ul>
+ <li>Rotate view - Left Click and drag</li>
+ <li>Zoom in - Press '+'</li>
+ <li>Zoom out - Press '-'</li>
+ <li>Choose a different structure - Left click on structure in
+ the left hand panel</li>
+ <li>Highlighting bases - Move mouse over columns in the Jalview
+ alignment panel</li>
+ </ul>
-<p><strong>Different structures</strong></p>
-<ul>
- <li>
- <b>Alignment structures</b>:
- Structures associated with the alignment are marked by having "consensus" attached to their name. VARNA contains two different entries for consensus structures.
- <ul>
- <li>Consensus structure: the individual sequence folded into the consensus structure</li>
- <li>Trimmed consensus structure: the individual sequence
- folded into the the gap-free consensus structure. That means all
- columns that contained gaps in the individual sequence were
- removed. If this breaks a base-pair the pairing is removed also.
- This can be considered as an approximation for the individual structure.
- </ul>
- </li>
- <li>
- <b>Individual structures</b>:
- this is a structure associated with the individual sequence and therefore not related to the alignment
- </li>
-
-<p><strong>Controls</strong><br>
-<ul>
-<li>Rotate view - Left Click and drag</li>
-<li>Zoom in - Press '+'</li>
-<li>Zoom out - Press '-'</li>
-<li>Choose a different structure - Left click on structure in the left hand panel</li>
-<li>Highlighting bases - Move mouse over columns in the Jalview alignment panel</li>
-</ul>
-
-<p><strong>Functionality provided by VARNA</strong></p>
-<p>VARNA's own functions are accessed by right-clicking in the
-structure display area. That will open the VARNA pop-up menu,
-which provides access to a number of features like different draw algorithm, color highlighting or annotations.
-</p>
-<p><strong>More Information</strong></p>
-<p>VARNA is a very powerful RNA viewer on its own. Only the
-essentials have been described here - the interested reader is
-referred to <a href="http://varna.lri.fr/usermanual.html">VARNA's own
-comprehensive online documentation</a>.</p>
+ <p>
+ <strong>Functionality provided by VARNA</strong>
+ </p>
+ <p>VARNA's own functions are accessed by right-clicking in the
+ structure display area. That will open the VARNA pop-up menu, which
+ provides access to a number of features like different draw
+ algorithm, color highlighting or annotations.</p>
+ <p>
+ <strong>More Information</strong>
+ </p>
+ <p>
+ VARNA is a very powerful RNA viewer on its own. Only the essentials
+ have been described here - the interested reader is referred to <a
+ href="http://varna.lri.fr/index.php?page=manual&css=varna"
+ >VARNA's own comprehensive online documentation</a>.
+ </p>
</body>
</html>
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