-<html>\r
-<!--\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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>Trimmed 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 VARNA</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 its 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 2.8.2b1)
+ * Copyright (C) 2014 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><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/usermanual.html">VARNA's own
+comprehensive online documentation</a>.</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff