-<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\r
-<html xmlns="http://www.w3.org/1999/xhtml">\r
-<title>\r
-Embedded viewing of Alignments\r
-</title>\r
-<body>\r
-<h1>Embedded viewing of Alignments</h1>\r
-<p>The alignment below was generated from the following files:\r
-<ul>\r
- <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in\r
- FASTA format</li>\r
- <li><a href="plantfdx.features">plantfdx.features</a> - Jalview\r
- Format Sequence Features file</li>\r
- <li><a href="plantfdx.annotations">plantfdx.annotations</a> -\r
- Jalview Alignment Annotations File</li>\r
-</ul>\r
-<applet code="jalview.bin.JalviewLite"\r
- width="756" height="560" archive="../../jalviewApplet.jar">\r
- <param name="file" value="plantfdx.fa">\r
- <param name="annotations" value="plantfdx.annotations">\r
- <param name="features" value="plantfdx.features">\r
- <param name="embedded" value="true">\r
- <param name="userDefinedColour"\r
- value="C=yellow; R,K,H=FF5555; D,E=5555FF">\r
- <param name="showFullId" value="false">\r
- <param name="RGB" value="F2F2FF">\r
- <param name="linkLabel_1" value="SRS">\r
- <param name="linkUrl_1"\r
- value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">\r
- <param name="linkLabel_2" value="Uniprot">\r
- <param name="linkUrl_2"\r
- value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">\r
- <param name="APPLICATION_URL"\r
- value="http://www.jalview.org/services/launchApp">\r
- </applet>\r
-</p>\r
-</body>\r
-</html>\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>Embedded viewing of Alignments
+</title>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+<![endif]-->
+
+<!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+<![endif]-->
+
+<!-- dd menu -->
+<script type="text/javascript">
+<!--
+var timeout = 500;
+var closetimer = 0;
+var ddmenuitem = 0;
+
+// open hidden layer
+function mopen(id)
+{
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+}
+// close showed layer
+function mclose()
+{
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+}
+
+// go close timer
+function mclosetime()
+{
+ closetimer = window.setTimeout(mclose, timeout);
+}
+
+// cancel close timer
+function mcancelclosetime()
+{
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+}
+
+// close layer when click-out
+document.onclick = mclose;
+// -->
+</script>
+
+</head>
+
+
+<body>
+
+
+<div id="header">
+<div id="logo"><a href="/" title="Home"></a></div>
+<ul id="buttons">
+<li id="applet"><a href="applets.html" title="applet"></a></li>
+<li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
+</ul>
+</div>
+
+
+<div id ="nav">
+<div id="navInner">
+
+<ul id="sddm">
+ <li><a href="#">Home</a></li>
+ <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Documentation</a>
+ <a href="#">Publications</a>
+ <a href="#">Credits</a>
+ <a href="#">Screenshots</a>
+ </div>
+ </li>
+ <li><a href="#">FAQ</a></li>
+ <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">News Mailing List</a>
+ <a href="#">Discussion Mailing List</a>
+ <a href="#">Links</a>
+ <a href="#">Community News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Release History</a>
+ <a href="#">Jalview Bug Tracker</a>
+ <a href="#">Jalview Git Web</a>
+ <a href="#">Development News</a>
+ </div>
+ </li>
+ <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="#">Training Courses</a>
+ <a href="#">Training News</a>
+ </div>
+ </li>
+ <li><a href="#" class="download-right">Download</a></li>
+</ul>
+<div style="clear:both"></div>
+</div>
+
+</div>
+
+
+<div id="pageWrap">
+
+<div id="sideNav">
+<ul>
+<li><a href="applets.html">JalviewLite Examples</a></li>
+<li><a href="appletParameters.html">Applet Parameters</a></li>
+<li><a href="jalviewLiteJs.html">Javascript API</a></li>
+<li><a href="formComplete.html">in-page API demo</a></li>
+<li class="jvlite-nav-small"><a href="embedded.html">Embedded applet demo</a></li>
+<li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
+<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
+</ul>
+</div>
+
+<div id="content" class="content">
+<h1>Embedded viewing of Alignments</h1>
+<p>The alignment below was generated from the following files:
+<ul>
+ <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
+ FASTA format</li>
+ <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
+ Format Sequence Features file</li>
+ <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
+ Jalview Alignment Annotations File</li>
+</ul>
+<applet code="jalview.bin.JalviewLite"
+ width="756" height="560" archive="jalviewApplet.jar">
+ <param name="file" value="plantfdx.fa">
+ <param name="annotations" value="plantfdx.annotations">
+ <param name="features" value="plantfdx.features">
+ <param name="embedded" value="true">
+ <param name="userDefinedColour"
+ value="C=yellow; R,K,H=FF5555; D,E=5555FF">
+ <param name="showFullId" value="false">
+ <param name="linkLabel_1" value="Uniprot">
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+ <param name="linkLabel_2" value="Expasy">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp">
+ </applet>
+</p>
+</div>
+</div>
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
+</div>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff