-<html>\r
-<!--\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
--->\r
-<head>\r
-<title>The VARNA RNA Viewer</title>\r
-</head>\r
-<body>\r
-<p><strong>The VARNA RNA Viewer</strong></p>\r
-<p>Since Jalview\r
-2.7.1, <a href="http://varna.lri.fr/index.html">VARNA</a> has been\r
-integrated into Jalview for interactively viewing structures opened by\r
-selecting the <strong>"Structure→View\r
-Structure:"</strong> option in\r
-the <a href="../menus/popupMenu.html">sequence id pop-up menu</a> (if\r
-you can't see this, then no RNA structure is associated with your\r
-sequence or alignment. In the pop-up menu all structures that\r
-are associated with this sequence and all sequences that are\r
-associated with the alignment are available.\r
-\r
-<p><strong>Different structures</strong></p>\r
-<ul>\r
- <li>\r
- <b>Alignment structures</b>:\r
- Structures associated with the alignment are marked by having "consensus" attached to their name. VARNA contains two different entries for consensus structures.\r
- <ul>\r
- <li>Consensus structure: the individual sequence folded into the consensus structure</li>\r
- <li>Trimed consensus structure: the individual sequence\r
- folded into the the gap-free consensus structure. That means all\r
- columns that contained gaps in the individual sequence were\r
- removed. If this breaks a base-pair the pairing is removed also.\r
- This can be considered as an approximation for the individual structure.\r
- </ul>\r
- </li>\r
- <li>\r
- <b>Individual structures</b>:\r
- this is a structure associated with the individual sequence and therefore not related to the alignment \r
- </li>\r
-\r
-<p><strong>Controls</strong><br>\r
-<ul>\r
-<li>Rotate view - Left Click and drag</li>\r
-<li>Zoom in - Press '+'</li>\r
-<li>Zoom out - Press '-'</li>\r
-<li>Choose a different structure - Left click on structure in the left hand panel</li>\r
-<li>Highlighting bases - Move mouse over columns in the Jalview alignment panel</li>\r
-</ul>\r
-\r
-<p><strong>Functionality provided by Jmol</strong></p>\r
-<p>VARNA's own functions are accessed by right-clicking in the\r
-structure display area. That will open the VARNA pop-up menu,\r
-which provides access to a number of features like different draw algorithm, color highlighting or annotations. \r
-</p>\r
-<p><strong>More Information</strong></p>\r
-<p>VARNA is a very powerful RNA viewer on it's own. Only the\r
-essentials have been described here - the interested reader is\r
-referred to <a href="http://varna.lri.fr/usermanual.html">VARNA's own\r
-comprehensive online documentation</a>.</p>\r
-</body>\r
-</html>\r
+<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>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>
+ 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>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>
git://source.jalview.org / jalview.git / blobdiff