-<!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 ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
* 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>Applet Parameters</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-
-</head>
-
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" 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="jalviewLiteJs.html">Javascript API</a></li>
- <li class="jvlite-nav-small"><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="embedded.html">Embedded Alignment</a></li>
- <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="formComplete.html">Access from Javascript</a></li>
- <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
-
<!-- content start -->
<h2>JalviewLite Applet Parameter Documentation</h2>
The JalviewLite applet is configured through a series of applet parameters,
which are described <a href="#parameters"> below</a>. Once initialised,
the applet can be interacted with <em>via</em> its
-<a href="jalviewLiteJs.html">Javascript API</a>.
-</p><p><strong>Issues arising from tightening of Java Security default settings</strong><br/>JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java are not compatible with these settings, so if you find that you cannot see any of the examples on the left, try the <a href="u_applets.html">unsigned applet examples</a>.
-</p>
+<a href="javascript:doSubmit('jalviewLiteJs')">Javascript API</a>.
+</p><p><strong>Issues arising from tightening of Java Security default settings</strong><br/>JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java may not be compatible with these settings. </p>
<p>For additional deployment notes, <a href="#appletdeploymentnotes">see below</a>.</p>
<p><h2>Applet Parameters</h2><br/>The applet takes the following initialisation parameters.</p>
<a name="parameters"></a> <table width="97%" class="borderTable" align="center" >
archive="jalviewApplet.jar, mydata.zip"</strong></em>><br>
</pre></li>
<li> Use Jalview for input to a HTML form. For an example of how to
- code this using Javascript, click <a href="formComplete.html">here</a>.
+ code this using Javascript, click <a href="javascript:doSubmit('formComplete')">here</a>.
<br>
</li>
<li>Embed Jalview into the web page, without the "Start Jalview"
<param name="embedded"
value="true"> </li>
</ul>
- <p><strong>**NEW FEATURES** in Jalview 2.8</strong></p>
+ <p><strong>**NEW FEATURES** in Jalview 2.8</strong></p>
<ul>
<li>Normalised sequence logo display
</li>
<li>Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</li>
<li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (<param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul>
</li>
- <li>New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
+ <li>New <a href="javascript:doSubmit('jalviewLiteJs')">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
</li></ul>
<p><strong>**NEW FEATURES** in Jalview 2.6</strong></p>
<ul>
</pre>(All the usual Jalview File formats are valid, however each
new line in an alignment file must be entered as a parameter)</li>
</ul>
-
-
-<!-- content end -->
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
+<!-- content end -->
\ No newline at end of file
-<!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 ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
* 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>JalviewLite Examples</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-
-</head>
-
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
- </ul>
- <div style="clear:both"></div>
- </div>
-
- </div>
-<div id="pageWrap">
-
-<div id="sideNav">
- <ul>
- <li class="jvlite-nav-small"><a href="applets.html">JalviewLite Examples</a></li>
- <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="embedded.html">Embedded Alignment</a></li>
- <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="formComplete.html">Access from Javascript</a></li>
- <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
-
<!-- boiler plate link to alternate demopage -->
-
<div style="width: 100%">
<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Examples aren't working ?<br/>Try <a href="u_applets.html">the unsigned applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
+<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
</p></div>
</div>
<p align="left">
<h2>JalviewLite Button Examples</h2>
Try out JalviewLite by pressing one of the buttons below.<br/>
- For more information on how to use the applet in your website, see the <a href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+ For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
<p> </p><div align="center">
<p align="center">
<h2>Ferredoxins, chloroplast precursor related UniRef50
<table width="90%">
<tr>
<td width="10%" valign="center">
- <applet
- code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
-<param name="permissions" value="sandbox"/>
-<param name="file" value="uniref50.fa"/>
-<param name="treeFile" value="ferredoxin.nw"/>
-<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
-<param name="sortByTree" value="True"/>
-<param name="showSequenceLogo" value="true"/>
-<param name="showGroupConsensus" value="true"/>
-<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="EMBL-EBI Search"/>
- <param name="linkUrl_2"
- value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp"/>
-</applet>
+ <applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
+ <param name="permissions" value="sandbox"/>
+ <param name="file" value="uniref50.fa"/>
+ <param name="treeFile" value="ferredoxin.nw"/>
+ <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
+ <param name="sortByTree" value="True"/>
+ <param name="showSequenceLogo" value="true"/>
+ <param name="showGroupConsensus" value="true"/>
+ <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="EMBL-EBI Search"/>
+ <param name="linkUrl_2" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
+ </applet>
</td>
<td valign="center">User Defined Colours, loads an associated
Newick format tree file which is used to sort the alignment, and
</p>
<table width="90%">
<tr>
- <td width="10%" valign="center"><applet
+ <td width="10%" valign="center">
+<applet
code="jalview.bin.JalviewLite" width="140" height="35"
archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<td valign="center">Displays a split window view of protein and its related cDNA</td>
</tr>
</table>
-</div>
-<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
-<!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 ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
* 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>Embedded Alignment</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-
-</head>
-
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" 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="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li class="jvlite-nav-small"><a href="embedded.html">Embedded Alignment</a></li>
- <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="formComplete.html">Access from Javascript</a></li>
- <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
<!-- boiler plate link to alternate demopage -->
-
<div style="width: 100%">
<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Examples aren't working ?<br/>Try <a href="u_embedded.html">the unsigned applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
+<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
</p></div>
</div>
</applet>
</p>
<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
-<!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 ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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.
--->
+<!-- boiler plate link to alternate demopage -->
+
<head>
- <TITLE>Jalview and Jmol</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>
- <script>
+<script>
<!--//--><![CDATA[//><!--
var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
//--><!]]>
<script src="javascript/jquery.timer.js"></script>
<script src="javascript/jquery.blockUI.js"></script>
<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
-<!-- <script src="archive-min.js" language="javascript"></script>
--->
+
<script src="javascript/jalview.js" language="javascript"></script>
<script language="JavaScript">
// instead of this, we use a custom JmolApplet spec
}
window.location=href;
}
-</script>
-<script>
+
var loglevel=1;
function dbg(lvl,string) {
if (_console && lvl<=loglevel) {_console.value += string + "\n";}
jmolSetCallback("hoverCallback","_jmolhover");
jmolSetCallback("pickCallback","_jmolpick");
modeltofiles+="1gaq.txt";
-</script>
-
+</script>
</head>
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" 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="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="embedded.html">Embedded Alignment</a></li>
- <li class="jvlite-nav-small"><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="formComplete.html">Access from Javascript</a></li>
- <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
-
-
-<!-- boiler plate link to alternate demopage -->
-
<div style="width: 100%">
<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Examples aren't working ?<br/>Try <a href="u_embeddedWJmol.html">the unsigned applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
+<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
</p></div>
</div>
deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
</script>
</center>
-<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
+<!-- content template end -->
\ No newline at end of file
-<!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 ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
* 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>Access from Javascript</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-
-</head>
-
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" 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="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="embedded.html">Embedded Alignment</a></li>
- <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
- <li class="jvlite-nav-small"><a href="formComplete.html">Access from Javascript</a></li>
- <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
<!-- boiler plate link to alternate demopage -->
-
<div style="width: 100%">
<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Examples aren't working ?<br/>Try <a href="u_formComplete.html">the unsigned applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
+<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
</p></div>
</div>
</div>
<!-- content template start -->
-<h2><a href="jalviewLiteJs.html">JalviewLite API</a> Demo</h2>
+<h2><a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite API</a> Demo</h2>
<p>Using the Javascript API to fill out forms using data from JalviewLite
<br/>Click the Javascript buttons below to interact with the Applet
instance on the page.</p>
View the source in your browser to see how it has been done. <br/>
-<a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
+<a name="api">View the full <a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite API documentation</a>.</a>
<applet code="jalview.bin.JalviewLite" width="0" height="0"
archive="jalviewApplet.jar,JmolApplet-12.2.4.jar" name="Jalview">
</form>
</div>
<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
--- /dev/null
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+-->
+
+
+ <footer id="section-footer" class="section section-footer">
+ <div id="zone-footer-wrapper" class="zone-wrapper zone-footer-wrapper clearfix">
+ <div id="zone-footer" class="zone zone-footer clearfix container-12">
+ <div class="grid-12 region region-footer-first" id="region-footer-first">
+ <div class="region-inner region-footer-first-inner">
+ <div class="block block-block citation-block block-3 block-block-3 odd block-without-title" id="block-block-3">
+ <div class="block-inner clearfix">
+
+ <div class="content clearfix">
+ <p>If you use Jalview in your work, please cite this publication:</p>
+<p>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)<br />"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"<br />Bioinformatics25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a></p>
+<p><a href="https://twitter.com/jalview" target="_blank"><img alt="" class="media-image" style="width: 45px; height: 40px;" typeof="foaf:Image" src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/styles/large/public/Twitter_bird_1.png?itok=pRhs111L" width="172" height="139" /></a><a href="https://www.facebook.com/Jalview" target="_blank"><img alt="" class="media-image" style="width: 45px; height: 45px;" typeof="foaf:Image" src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/styles/large/public/facebook1.png?itok=NZOm8lnL" width="225" height="225" /></a></p>
+ </div>
+ </div>
+</div><div class="block block-block footer-icons block-11 block-block-11 even block-without-title" id="block-block-11">
+ <div class="block-inner clearfix">
+
+ <div class="content clearfix">
+ <p><a href="http://www.compbio.dundee.ac.uk/" target="_blank"><img alt="" class="media-image" height="98" width="80" typeof="foaf:Image" src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/gb_0.jpg" /></a><a href="http://www.wellcome.ac.uk/" target="_blank"><img alt="" class="media-image" height="98" width="248" typeof="foaf:Image" src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/wt.jpg" /></a><a href="http://www.bbsrc.ac.uk/home/home.aspx" target="_blank"><img alt="" class="media-image" height="98" width="186" typeof="foaf:Image" src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/bbsrc.jpg" /></a><a href="http://www.dundee.ac.uk/" target="_blank"><img alt="" class="media-image" height="98" width="97" typeof="foaf:Image" src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/uni.jpg" /></a></p>
+<p><a href="http://creativecommons.org/licenses/by-sa/3.0/" style="fg: white">Published under CC SA v3</a></p>
+ </div>
+ </div>
+</div> </div>
+</div> </div>
+</div></footer> </div>
+
+
+ </body>
+</html>
+
--- /dev/null
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+-->
+
+
+<body
+ class="html not-front not-logged-in page-node page-node- page-node-18 node-type-basic-page context-about">
+ <div id="skip-link">
+ <a href="#main-content" class="element-invisible element-focusable">Skip
+ to main content</a>
+ </div>
+ <div class="page clearfix" id="page">
+ <header id="section-header" class="section section-header">
+ <div id="zone-branding-wrapper"
+ class="zone-wrapper zone-branding-wrapper clearfix">
+ <div id="zone-branding"
+ class="zone zone-branding clearfix container-12">
+ <div class="grid-6 region region-branding" id="region-branding">
+ <div class="region-inner region-branding-inner">
+ <div
+ class="block block-views block-main-logo-block block-views-main-logo-block odd block-without-title"
+ id="block-views-main-logo-block">
+ <div class="block-inner clearfix">
+ <div class="content clearfix">
+ <div
+ class="view view-main-logo view-id-main_logo view-display-id-block view-dom-id-1828f18ab2b5b41781dad3bdfec6156b">
+ <div class="view-content">
+ <div class="item-list">
+ <ul>
+ <li
+ class="views-row views-row-1 views-row-odd views-row-first views-row-last">
+ <div class="views-field views-field-field-logo-image">
+ <div class="field-content">
+ <a href="http://www.jalview.org/"><img
+ class="adaptive-image" typeof="foaf:Image"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/styles/adaptive/adaptive-image/public/jalviewHome_0.jpg?itok=xoZsVtTd"
+ alt="" /></a>
+ </div>
+ </div>
+ </li>
+ </ul>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ <div class="grid-6 region region-launch-buttons"
+ id="region-launch-buttons">
+ <div class="region-inner region-launch-buttons-inner">
+ <div
+ class="block block-views block-launch-buttons-block block-views-launch-buttons-block odd block-without-title"
+ id="block-views-launch-buttons-block">
+ <div class="block-inner clearfix">
+ <div class="content clearfix">
+ <div
+ class="view view-launch-buttons view-id-launch_buttons view-display-id-block view-dom-id-be0b33b57f9a461aaaf77cdeab66e60c">
+ <div class="view-content">
+ <div class="item-list">
+ <ul>
+ <li
+ class="views-row views-row-1 views-row-odd views-row-first">
+ <div class="views-field views-field-field-button-image">
+ <div class="field-content">
+ <a href="http://www.jalview.org/webstart/jalview.jnlp"><img
+ typeof="foaf:Image"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/desk.jpg"
+ width="250" height="40" alt="" /></a>
+ </div>
+ </div>
+ </li>
+ <li
+ class="views-row views-row-2 views-row-even views-row-last">
+ <div class="views-field views-field-field-button-image">
+ <div class="field-content">
+ <a href="http://www.jalview.org/examples/applets.html"><img
+ typeof="foaf:Image"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/applet.jpg"
+ width="250" height="40" alt="" /></a>
+ </div>
+ </div>
+ </li>
+ </ul>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ <div id="zone-menu-wrapper"
+ class="zone-wrapper zone-menu-wrapper clearfix">
+ <div id="zone-menu" class="zone zone-menu clearfix container-12">
+ <div class="grid-12 region region-menu" id="region-menu">
+ <div class="region-inner region-menu-inner">
+ <section
+ class="block block-nice-menus block-1 block-nice-menus-1 odd"
+ id="block-nice-menus-1">
+ <div class="block-inner clearfix">
+ <h2 class="block-title">
+ <span class="nice-menu-hide-title">Main menu</span>
+ </h2>
+ <div class="content clearfix">
+ <ul class="nice-menu nice-menu-down" id="nice-menu-1">
+ <li class="menu-346 menu-path-front first odd "><a
+ href="/" title="">Home</a></li>
+ <li
+ class="menu-355 menuparent menu-path-node-18 active-trail even "><a
+ href="/About">About</a>
+ <ul>
+ <li class="menu-356 menu-path-node-19 first odd "><a
+ href="/about/citation">Publications</a></li>
+ <li class="menu-357 menu-path-node-20 even "><a
+ href="/about/credits">Credits</a></li>
+ <li class="menu-494 menu-path-node-310 odd last "><a
+ href="/about/jalview-scientific-advisory-committee">Advisory
+ Committee</a></li>
+ </ul></li>
+ <li class="menu-437 menuparent menu-path-node-340 odd "><a
+ href="/Help" class="help-colour-scheme">Help</a>
+ <ul>
+ <li class="menu-579 menu-path-node-576 first odd "><a
+ href="/Help/Getting-Started"
+ title="Getting Starting with jalview">Getting Started</a></li>
+ <li class="menu-511 menu-path-faq even "><a
+ href="/faq">FAQ</a></li>
+ <li class="menu-513 menu-path-node-2 odd "><a
+ href="/about/documentation">Documentation</a></li>
+ <li
+ class="menu-514 menu-path-jalvieworg-mailman-listinfo-jalview-discuss even "><a
+ href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
+ class="new-window" target="_blank">Discussion Mailing
+ List</a></li>
+ <li class="menu-773 menu-path-node-618 odd last "><a
+ href="/Help/About-Jalview" title="About Jalview">Other
+ Resources</a></li>
+ </ul></li>
+ <li class="menu-363 menuparent menu-path-node-25 even "><a
+ href="/community" class="community">Community</a>
+ <ul>
+ <li
+ class="menu-364 menu-path-jalvieworg-mailman-listinfo-jalview-announce first odd "><a
+ href="http://www.jalview.org/mailman/listinfo/jalview-announce"
+ class="new-window" target="_blank">News Mailing List</a></li>
+ <li
+ class="menu-365 menu-path-jalvieworg-mailman-listinfo-jalview-discuss even "><a
+ href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
+ class="new-window" target="_blank">Discussion Mailing
+ List</a></li>
+ <li class="menu-441 menu-path-community-links odd "><a
+ href="/community/links">Links</a></li>
+ <li
+ class="menu-457 menu-path-community-community-news even last "><a
+ href="/community/community-news">Community News</a></li>
+ </ul></li>
+ <li class="menu-366 menuparent menu-path-node-26 odd "><a
+ href="/development" class="development active">Development</a>
+ <ul>
+ <li
+ class="menu-436 menu-path-issuesjalvieworg-secure-Dashboardjspa first odd "><a
+ href="http://issues.jalview.org/secure/Dashboard.jspa"
+ name="new-window" class="new-window" target="_blank">Jalview
+ Bug Tracker</a></li>
+ <li class="menu-367 menu-path-node-27 even "><a
+ href="/development/development-builds">Development
+ Version</a></li>
+ <li
+ class="menu-453 menu-path-sourcejalvieworg-gitweb-pjalviewgit;asummary odd "><a
+ href="http://source.jalview.org/gitweb/?p=jalview.git;a=summary"
+ class="new-window" target="_blank">Jalview Git Web</a></li>
+ <li class="menu-512 menu-path-node-341 even "><a
+ href="/development/Version-Archive">Version Archive</a></li>
+ <li
+ class="menu-462 menu-path-development-release-history odd "><a
+ href="/development/release-history">Release History</a></li>
+ <li
+ class="menu-456 menu-path-development-development-news even last "><a
+ href="/development/development-news">Development News</a></li>
+ </ul></li>
+ <li class="menu-369 menuparent menu-path-node-29 even "><a
+ href="/training" class="training">Training</a>
+ <ul>
+ <li
+ class="menu-440 menu-path-training-training-courses first odd "><a
+ href="/training/training-courses">Training Courses</a></li>
+ <li class="menu-1374 menu-path-node-654 even "><a
+ href="/training/Training-Videos"
+ title="Jalview Online Training Videos">Training Videos</a></li>
+ <li class="menu-458 menu-path-training-training-news odd "><a
+ href="/training/training-news">Training News</a></li>
+ <li class="menu-610 menu-path-node-606 even last "><a
+ href="/ISMB-2014-Presentation">Jalview & JABA Slides</a></li>
+ </ul></li>
+ <li class="menu-358 menu-path-node-21 odd last "><a
+ href="/Download" class="download-right">Download</a></li>
+ </ul>
+ </div>
+ </div>
+ </section>
+ </div>
+ </div>
+ </div>
+ </div>
+ <div id="zone-header-wrapper"
+ class="zone-wrapper zone-header-wrapper clearfix">
+ <div id="zone-header" class="zone zone-header clearfix container-12">
+ <div class="grid-12 region region-header-first"
+ id="region-header-first">
+ <div class="region-inner region-header-first-inner">
+ <div
+ class="block block-menu-block primary-nav block-3 block-menu-block-3 odd block-without-title"
+ id="block-menu-block-3">
+ <div class="block-inner clearfix">
+
+ <div class="content clearfix">
+ <div
+ class="menu-block-wrapper menu-block-3 menu-name-main-menu parent-mlid-0 menu-level-1">
+ <ul class="menu">
+ <li class="first leaf menu-mlid-346"><a href="/"
+ title="">Home</a></li>
+ <li class="expanded active-trail active menu-mlid-355"><a
+ href="/About" class="active-trail active">About</a>
+ <ul class="menu">
+ <li class="first leaf menu-mlid-356"><a
+ href="/about/citation">Publications</a></li>
+ <li class="leaf menu-mlid-357"><a
+ href="/about/credits">Credits</a></li>
+ <li class="last leaf menu-mlid-494"><a
+ href="/about/jalview-scientific-advisory-committee">Advisory
+ Committee</a></li>
+ </ul></li>
+ <li class="expanded menu-mlid-437"><a href="/Help"
+ class="help-colour-scheme">Help</a>
+ <ul class="menu">
+ <li class="first leaf menu-mlid-579"><a
+ href="/Help/Getting-Started"
+ title="Getting Starting with jalview">Getting Started</a></li>
+ <li class="leaf menu-mlid-511"><a href="/faq">FAQ</a></li>
+ <li class="leaf menu-mlid-513"><a
+ href="/about/documentation">Documentation</a></li>
+ <li class="leaf menu-mlid-514"><a
+ href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
+ class="new-window" target="_blank">Discussion Mailing
+ List</a></li>
+ <li class="last leaf menu-mlid-773"><a
+ href="/Help/About-Jalview" title="About Jalview">Other
+ Resources</a></li>
+ </ul></li>
+ <li class="expanded menu-mlid-363"><a href="/community"
+ class="community">Community</a>
+ <ul class="menu">
+ <li class="first leaf menu-mlid-364"><a
+ href="http://www.jalview.org/mailman/listinfo/jalview-announce"
+ class="new-window" target="_blank">News Mailing List</a></li>
+ <li class="leaf menu-mlid-365"><a
+ href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
+ class="new-window" target="_blank">Discussion Mailing
+ List</a></li>
+ <li class="leaf menu-mlid-441"><a
+ href="/community/links">Links</a></li>
+ <li class="last leaf menu-mlid-457"><a
+ href="/community/community-news">Community News</a></li>
+ </ul></li>
+ <li class="expanded menu-mlid-366"><a
+ href="/development" class="development">Development</a>
+ <ul class="menu">
+ <li class="first leaf menu-mlid-436"><a
+ href="http://issues.jalview.org/secure/Dashboard.jspa"
+ name="new-window" class="new-window" target="_blank">Jalview
+ Bug Tracker</a></li>
+ <li class="leaf menu-mlid-367"><a
+ href="/development/development-builds">Development
+ Version</a></li>
+ <li class="leaf menu-mlid-453"><a
+ href="http://source.jalview.org/gitweb/?p=jalview.git;a=summary"
+ class="new-window" target="_blank">Jalview Git Web</a></li>
+ <li class="leaf menu-mlid-512"><a
+ href="/development/Version-Archive">Version Archive</a></li>
+ <li class="leaf menu-mlid-462"><a
+ href="/development/release-history">Release History</a></li>
+ <li class="last leaf menu-mlid-456"><a
+ href="/development/development-news">Development News</a></li>
+ </ul></li>
+ <li class="expanded menu-mlid-369"><a href="/training"
+ class="training">Training</a>
+ <ul class="menu">
+ <li class="first leaf menu-mlid-440"><a
+ href="/training/training-courses">Training Courses</a></li>
+ <li class="leaf menu-mlid-1374"><a
+ href="/training/Training-Videos"
+ title="Jalview Online Training Videos">Training Videos</a></li>
+ <li class="leaf menu-mlid-458"><a
+ href="/training/training-news">Training News</a></li>
+ <li class="last leaf menu-mlid-610"><a
+ href="/ISMB-2014-Presentation">Jalview & JABA
+ Slides</a></li>
+ </ul></li>
+ <li class="last expanded menu-mlid-358"><a
+ href="/Download" class="download-right">Download</a></li>
+ </ul>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ <div class="grid-6 region region-header-second"
+ id="region-header-second">
+ <div class="region-inner region-header-second-inner">
+ <div
+ class="block block-delta-blocks block-breadcrumb block-delta-blocks-breadcrumb odd block-without-title"
+ id="block-delta-blocks-breadcrumb">
+ <div class="block-inner clearfix">
+
+ <div class="content clearfix">
+ <div id="breadcrumb" class="clearfix">
+ <ul class="breadcrumb">
+ <li class="depth-1 odd first"><a href="/">Home</a></li>
+ <li class="depth-2 even last"><a href="/About"
+ class="active">About</a></li>
+ </ul>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </header>
+
+
+ <form name="custom_form" id="custom_form" action="jalview_examples.php" method="post">
+ <input type="hidden" name="target" id="target" value="APPLETS"><br>
+ </form>
--- /dev/null
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+-->
+
+<ul id="menu" class="menu">
+ <li id="applets" class="first leaf menu-mlid-1001">
+ <a id="applets" href="javascript:doSubmit('applets')" class=" ">JalviewLite Examples</a></li>
+
+ <li id="jalviewLiteJs" class="leaf menu-mlid-1002">
+ <a id="jalviewLiteJs" href="javascript:doSubmit('jalviewLiteJs')" class=" ">Javascript API</a></li>
+
+ <li id="appletParameters" class="leaf menu-mlid-1003">
+ <a id="appletParameters" href="javascript:doSubmit('appletParameters')" class=" ">Applet Parameters</a></li>
+
+ <li id="embedded" class="leaf menu-mlid-1004">
+ <a id="embedded" href="javascript:doSubmit('embedded')" class=" ">Embedded Alignment</a></li>
+
+ <li id="embeddedWJmol" class="leaf menu-mlid-1005">
+ <a id="embeddedWJmol" href="javascript:doSubmit('embeddedWJmol')" class=" ">Jalview and Jmol</a></li>
+
+ <li id="formComplete" class="leaf menu-mlid-1006">
+ <a id="formComplete" href="javascript:doSubmit('formComplete')" class=" ">Access from Javascript</a></li>
+
+ <li id="javascriptLaunch" class="leaf menu-mlid-1007">
+ <a id="javascriptLaunch" href="javascript:doSubmit('javascriptLaunch')" class=" ">Javascript Launch</a></li>
+
+ <li id="linkedapplets_ng" class="last leaf menu-mlid-1008">
+ <a id="linkedapplets_ng" href="javascript:doSubmit('linkedapplets_ng')" class=" ">Linked JalviewLites</a></li>
+ </ul>
+
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML+RDFa 1.1//EN">
+<html lang="en" dir="ltr" version="HTML+RDFa 1.1"
+ xmlns:content="http://purl.org/rss/1.0/modules/content/"
+ xmlns:dc="http://purl.org/dc/terms/"
+ xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:og="http://ogp.me/ns#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:sioc="http://rdfs.org/sioc/ns#"
+ xmlns:sioct="http://rdfs.org/sioc/types#"
+ xmlns:skos="http://www.w3.org/2004/02/skos/core#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#">
+<head profile="http://www.w3.org/1999/xhtml/vocab">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<link rel="shortcut icon"
+ href="http://www.jalview.org/sites/all/themes/jalview/favicon.ico"
+ type="image/vnd.microsoft.icon" />
+<meta name="viewport"
+ content="width=device-width, initial-scale=1, maximum-scale=1, minimum-scale=1, user-scalable=no" />
+<meta content="" about="/About" property="dc:title" />
+<link rel="shortlink" href="/node/18" />
+<meta name="Generator" content="Drupal 7 (http://drupal.org)" />
+<link rel="canonical" href="/About" />
+<title>Development | jalview.org</title>
+<link type="text/css" rel="stylesheet"
+ href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_pbm0lsQQJ7A7WCCIMgxLho6mI_kBNgznNUWmTWcnfoE.css"
+ media="all" />
+<link type="text/css" rel="stylesheet"
+ href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_gUtVu-PFpNy2iKRzspQnPE665qK-eDx99tAc6O2EKBs.css"
+ media="all" />
+<link type="text/css" rel="stylesheet"
+ href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_HByEx9XzXH_VOfr3lfyJmXRKhQdq8UyyslSu9odJFaw.css"
+ media="all" />
+<link type="text/css" rel="stylesheet"
+ href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_Rj_Ai4KdTE0qt75bSUOfQPNak90tBSJRVjZIjglGhlM.css"
+ media="all" />
+
+<!--[if lte IE 6]>
+<link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/all/themes/jalview/css/ie6.css?nqc8th" media="all" />
+<![endif]-->
+
+<!--[if lte IE 7]>
+<link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/all/themes/jalview/css/ie7.css?nqc8th" media="all" />
+<![endif]-->
+
+<!--[if lte IE 8]>
+<link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/all/themes/jalview/css/ie8.css?nqc8th" media="all" />
+<![endif]-->
+
+<!--[if (lt IE 9)&(!IEMobile)]>
+<link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_ybf1eloQwwauLFbDPh5-J2RvDVEM4Gsh1NsAC0ynfNs.css" media="all" />
+<![endif]-->
+
+<!--[if gte IE 9]><!-->
+<link type="text/css" rel="stylesheet"
+ href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_kD8qBi2CLfQkl16-SgdHuwlYq_NUjXsjCxmpeidlT0I.css"
+ media="all" />
+<!--<![endif]-->
+<script type="text/javascript">
+<!--//--><![CDATA[//><!--
+ document.cookie = 'adaptive_image=' + Math.max(screen.width, screen.height)
+ + '; path=/';
+ //--><!]]>
+</script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_0gj6QcpfRH2jzTbCQqf7kEkm4MXY0UA_sRhwPc8jC1o.js"></script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/all/modules/lightbox2/js/lightbox.js?1434966756"></script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_SoFDHsgxDY2cLYbZ6HeW4SLlU_sLxsgGT6tSFwfsHGY.js"></script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/all/modules/mobile_navigation/js/mobile_menu.js?nqc8th"></script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/all/modules/mobile_navigation/mobile_navigation.js?nqc8th"></script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_IDBX5SzkJ9gGNq7x-qOE_2DZsexqguTJQGMKvi4w-Uw.js"></script>
+<script type="text/javascript">
+<!--//--><![CDATA[//><!--
+ var _gaq = _gaq || [];
+ _gaq.push([ "_setAccount", "UA-9060947-1" ]);
+ _gaq.push([ "_trackPageview" ]);
+ (function() {
+ var ga = document.createElement("script");
+ ga.type = "text/javascript";
+ ga.async = true;
+ ga.src = ("https:" == document.location.protocol ? "https://ssl"
+ : "http://www")
+ + ".google-analytics.com/ga.js";
+ var s = document.getElementsByTagName("script")[0];
+ s.parentNode.insertBefore(ga, s);
+ })();
+ //--><!]]>
+</script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_tnUY-Xr0uSK3E1mkrZ6ON7OmxH4PiVjShebnFJ8E-9c.js"></script>
+<script type="text/javascript"
+ src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_43n5FBy8pZxQHxPXkf-sQF7ZiacVZke14b0VlvSA554.js"></script>
+
+<script type="text/javascript">
+<!--//--><![CDATA[//><!--
+jQuery.extend(Drupal.settings, {"basePath":"\/","pathPrefix":"","ajaxPageState":{"theme":"jalview","theme_token":"wip-WGy4TPV1wdu4Sdq6IXFdriaYrLsrzHuYbaCEpD8","js":{"0":1,"sites\/all\/modules\/jquery_update\/replace\/jquery\/1.7\/jquery.min.js":1,"misc\/jquery.once.js":1,"misc\/drupal.js":1,"sites\/all\/modules\/lightbox2\/js\/lightbox.js":1,"sites\/all\/modules\/nice_menus\/superfish\/js\/superfish.js":1,"sites\/all\/modules\/nice_menus\/superfish\/js\/jquery.bgiframe.min.js":1,"sites\/all\/modules\/nice_menus\/superfish\/js\/jquery.hoverIntent.minified.js":1,"sites\/all\/modules\/nice_menus\/nice_menus.js":1,"sites\/all\/modules\/mobile_navigation\/js\/mobile_menu.js":1,"sites\/all\/modules\/mobile_navigation\/mobile_navigation.js":1,"sites\/all\/modules\/google_analytics\/googleanalytics.js":1,"1":1,"sites\/all\/themes\/jalview\/js\/jalview_ga_event_tracking.js":1,"sites\/all\/themes\/omega\/omega\/js\/jquery.formalize.js":1,"sites\/all\/themes\/omega\/omega\/js\/omega-mediaqueries.js":1},"css":{"modules\/system\/system.base.css":1,"modules\/system\/system.menus.css":1,"modules\/system\/system.messages.css":1,"modules\/system\/system.theme.css":1,"sites\/all\/modules\/adaptive_image\/css\/adaptive-image.css":1,"sites\/all\/modules\/date\/date_api\/date.css":1,"sites\/all\/modules\/date\/date_popup\/themes\/datepicker.1.7.css":1,"modules\/field\/theme\/field.css":1,"modules\/node\/node.css":1,"modules\/poll\/poll.css":1,"modules\/search\/search.css":1,"modules\/user\/user.css":1,"sites\/all\/modules\/views\/css\/views.css":1,"sites\/all\/modules\/ctools\/css\/ctools.css":1,"sites\/all\/modules\/lightbox2\/css\/lightbox.css":1,"sites\/all\/modules\/nice_menus\/nice_menus.css":1,"sites\/all\/modules\/nice_menus\/nice_menus_default.css":1,"sites\/all\/modules\/mobile_navigation\/mobile_navigation.css":1,"sites\/all\/themes\/omega\/alpha\/css\/alpha-reset.css":1,"sites\/all\/themes\/omega\/alpha\/css\/alpha-mobile.css":1,"sites\/all\/themes\/omega\/alpha\/css\/alpha-alpha.css":1,"sites\/all\/themes\/omega\/omega\/css\/formalize.css":1,"sites\/all\/themes\/omega\/omega\/css\/omega-text.css":1,"sites\/all\/themes\/omega\/omega\/css\/omega-branding.css":1,"sites\/all\/themes\/omega\/omega\/css\/omega-menu.css":1,"sites\/all\/themes\/omega\/omega\/css\/omega-forms.css":1,"sites\/all\/themes\/omega\/omega\/css\/omega-visuals.css":1,"sites\/all\/themes\/jalview\/css\/mobile.css":1,"sites\/all\/themes\/jalview\/css\/global.css":1,"sites\/all\/themes\/jalview\/css\/ie6.css":1,"sites\/all\/themes\/jalview\/css\/ie7.css":1,"sites\/all\/themes\/jalview\/css\/ie8.css":1,"ie::normal::sites\/all\/themes\/jalview\/css\/jalview-alpha-default.css":1,"ie::normal::sites\/all\/themes\/jalview\/css\/jalview-alpha-default-normal.css":1,"ie::normal::sites\/all\/themes\/omega\/alpha\/css\/grid\/alpha_default\/normal\/alpha-default-normal-12.css":1,"narrow::sites\/all\/themes\/jalview\/css\/jalview-alpha-default.css":1,"narrow::sites\/all\/themes\/jalview\/css\/jalview-alpha-default-narrow.css":1,"sites\/all\/themes\/omega\/alpha\/css\/grid\/alpha_default\/narrow\/alpha-default-narrow-12.css":1,"normal::sites\/all\/themes\/jalview\/css\/jalview-alpha-default.css":1,"normal::sites\/all\/themes\/jalview\/css\/jalview-alpha-default-normal.css":1,"sites\/all\/themes\/omega\/alpha\/css\/grid\/alpha_default\/normal\/alpha-default-normal-12.css":1,"wide::sites\/all\/themes\/jalview\/css\/jalview-alpha-default.css":1,"wide::sites\/all\/themes\/jalview\/css\/jalview-alpha-default-wide.css":1,"sites\/all\/themes\/omega\/alpha\/css\/grid\/alpha_default\/wide\/alpha-default-wide-12.css":1}},"lightbox2":{"rtl":0,"file_path":"\/(\\w\\w\/)public:\/","default_image":"\/sites\/all\/modules\/lightbox2\/images\/brokenimage.jpg","border_size":10,"font_color":"000","box_color":"fff","top_position":"","overlay_opacity":"0.8","overlay_color":"000","disable_close_click":1,"resize_sequence":0,"resize_speed":100,"fade_in_speed":100,"slide_down_speed":100,"use_alt_layout":0,"disable_resize":0,"disable_zoom":0,"force_show_nav":0,"show_caption":1,"loop_items":0,"node_link_text":"View Image Details","node_link_target":0,"image_count":"Image !current of !total","video_count":"Video !current of !total","page_count":"Page !current of !total","lite_press_x_close":"press \u003Ca href=\u0022#\u0022 onclick=\u0022hideLightbox(); return FALSE;\u0022\u003E\u003Ckbd\u003Ex\u003C\/kbd\u003E\u003C\/a\u003E to close","download_link_text":"","enable_login":false,"enable_contact":false,"keys_close":"c x 27","keys_previous":"p 37","keys_next":"n 39","keys_zoom":"z","keys_play_pause":"32","display_image_size":"original","image_node_sizes":"()","trigger_lightbox_classes":"","trigger_lightbox_group_classes":"","trigger_slideshow_classes":"","trigger_lightframe_classes":"","trigger_lightframe_group_classes":"","custom_class_handler":0,"custom_trigger_classes":"","disable_for_gallery_lists":true,"disable_for_acidfree_gallery_lists":true,"enable_acidfree_videos":true,"slideshow_interval":5000,"slideshow_automatic_start":true,"slideshow_automatic_exit":true,"show_play_pause":true,"pause_on_next_click":false,"pause_on_previous_click":true,"loop_slides":false,"iframe_width":600,"iframe_height":400,"iframe_border":1,"enable_video":0},"nice_menus_options":{"delay":"800","speed":"fast"},"mobile_navigation":{"breakpoint":"all and (min-width: 740px) and (min-device-width: 740px), (max-device-width: 800px) and (min-width: 740px) and (orientation:landscape)","menuSelector":".primary-nav","menuPlugin":"accordion","showEffect":"expand_down","showItems":"all","tabHandler":1,"menuWidth":"100","specialClasses":0,"mainPageSelector":"#page","useMask":1,"menuLabel":"","expandActive":1},"googleanalytics":{"trackOutbound":1,"trackMailto":1,"trackDownload":1,"trackDownloadExtensions":"7z|aac|arc|arj|asf|asx|avi|bin|csv|doc|exe|flv|gif|gz|gzip|hqx|jar|jpe?g|js|mp(2|3|4|e?g)|mov(ie)?|msi|msp|pdf|phps|png|ppt|qtm?|ra(m|r)?|sea|sit|tar|tgz|torrent|txt|wav|wma|wmv|wpd|xls|xml|z|zip"},"omega":{"layouts":{"primary":"normal","order":["narrow","normal","wide"],"queries":{"narrow":"all and (min-width: 740px) and (min-device-width: 740px), (max-device-width: 800px) and (min-width: 740px) and (orientation:landscape)","normal":"all and (min-width: 980px) and (min-device-width: 980px), all and (max-device-width: 1024px) and (min-width: 1024px) and (orientation:landscape)","wide":"all and (min-width: 1220px)"}}}});
+//--><!]]>
+</script>
+<!--[if lt IE 9]><script src="http://html5shiv.googlecode.com/svn/trunk/html5.js"></script><![endif]-->
+<script src="javascript/jquery-1.4.4.min.js"></script>
+
+<script src="javascript/jvcontroller.js"> </script>
+
+
+
+
+
+
+</head>
+
+
+
+<div id="header"></div>
+<section id="section-content" class="section section-content">
+ <div id="zone-content-wrapper"
+ class="zone-wrapper zone-content-wrapper clearfix">
+
+ <div id="zone-content" class="zone zone-content clearfix container-12">
+ <!— — — — — — — — — — — side bar — — — — — — — — — — —>
+ <aside class="grid-3 region region-sidebar-first"
+ id="region-sidebar-first">
+ <div class="region-inner region-sidebar-first-inner">
+ <section
+ class="block block-menu-block block-1 block-menu-block-1 odd"
+ id="block-menu-block-1">
+ <div class="block-inner clearfix">
+ <h2 class="block-title">
+ <a href="/development" class="development active-trail">Development</a>
+ </h2>
+ <div class="content clearfix">
+ <div class="menu-block-wrapper menu-block-1 menu-name-main-menu parent-mlid-0 menu-level-2">
+ <div id="nav" class="nav">nav</div>
+ </div>
+ </div>
+ </div>
+ </section>
+ <section
+ class="block block-menu-block block-2 block-menu-block-2 even"
+ id="block-menu-block-2">
+ <div class="block-inner clearfix">
+ <h2 class="block-title">
+ <a href="/About" class="active-trail active">About</a>
+ </h2>
+
+ <div class="content clearfix">
+ <div
+ class="menu-block-wrapper menu-block-2 menu-name-main-menu parent-mlid-0 menu-level-2">
+ <div id="nav" class="nav">nav</div>
+ </div>
+ </div>
+ </div>
+ </section>
+ </div>
+ </aside>
+ <!- — - - - - - - - - - - - - end of sidebar — — — — —>
+
+ <div class="grid-9 region region-content" id="region-content">
+ <div class="region-inner region-content-inner">
+ <a id="main-content"></a>
+ <div
+ class="block block-system block-main block-system-main odd block-without-title"
+ id="block-system-main">
+ <div class="block-inner clearfix">
+ <div class="content clearfix">
+ <article about="/About" typeof="sioc:Item foaf:Document"
+ class="node node-basic-page node-published node-not-promoted node-not-sticky author-admin odd clearfix"
+ id="node-basic-page-18">
+ <div class="content clearfix">
+ <div
+ class="field field-name-body field-type-text-with-summary field-label-hidden">
+ <div class="field-items">
+ <div class="field-item even" property="content:encoded">
+ <div id="content"></div>
+ </div>
+ </div>
+ </div>
+ </div>
+ <div class="clearfix">
+ <nav class="links node-links clearfix"></nav>
+ </div>
+ </article>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+</section>
+
+<div id="footer"></div>
+
+
-<!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 ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
* 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>Javascript API</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-
-</head>
-
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" 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 class="jvlite-nav-small"><a href="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="embedded.html">Embedded Alignment</a></li>
- <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="formComplete.html">Access from Javascript</a></li>
- <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
-
<!-- content start -->
-
-
- <p>The jalviewLite applet's application programming interface (API) includes two components. A <a href="javascript/jalview.js">JalviewLite Javascript Library</a> and the <a href="#api">public methods on the JalviewLite applet</a>.
+<p>The jalviewLite applet's application programming interface (API) includes two components. A <a href="javascript/jalview.js">JalviewLite Javascript Library</a> and the <a href="#api">public methods on the JalviewLite applet</a>.
</p>
<h3>Notes</h3>
<ul>
public static boolean debug
</pre>
-
-
-<!-- content end -->
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
+<!-- content end -->
\ No newline at end of file
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
+
+
+
+
+
+
+
+
// default console to report messages
var _console = document.getElementById("stdout");
var _jvapps = new Array();
--- /dev/null
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ */
+
+
+ var currentPage = (readCookie("current_page")) ? readCookie("current_page") : "applets";
+ var signedJars = "jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar";
+ var unsignedJars = "u_jalviewApplet.jar,u_JmolApplet-12.2.4.jar,u_java-json.jar,u_json_simple-1.1.jar";
+ setOrUpdateCookie('jv_applet_mode', 'false', '1');
+ var isSignedAppletMode = readCookie("jv_applet_mode");
+ var appletJars = (isSignedAppletMode === 'true') ? signedJars : unsignedJars;
+ //alert(unsigned);
+
+
+ function createAppletTag(code, name, archive, width, height, params){
+ var app = document.createElement('applet');
+ app.code= code;
+ app.width = width;
+ app.height = height;
+ app.archive = archive;
+
+ var arrayLength = params.length;
+ for (var i = 0; i < arrayLength; i++) {
+ //console.log('name : '+ params[i][0] + ' code : '+ params[i][1]);
+ var param = document.createElement('param');
+ param.name = params[i][0];
+ param.value = params[i][1];
+ app.appendChild(param);
+ }
+ return app;
+ }
+
+ function readCookie(name) {
+ var nameEQ = name + "=";
+ var ca = document.cookie.split(';');
+ for(var i=0;i < ca.length;i++) {
+ var c = ca[i];
+ while (c.charAt(0)==' ') c = c.substring(1,c.length);
+ if (c.indexOf(nameEQ) == 0) return c.substring(nameEQ.length,c.length);
+ }
+ return null;
+ }
+
+ function setOrUpdateCookie(name, value, days) {
+ var expires;
+ if (days) {
+ var date = new Date();
+ date.setTime(date.getTime() + (days * 24 * 60 * 60 * 1000));
+ expires = "; expires=" + date.toGMTString();
+ }
+ else {
+ expires = "";
+ }
+ document.cookie = name + "=" + value + expires + "; path=/";
+ }
+
+ $(function(){
+ //var currentPage = (readCookie("current_page")) ? readCookie("current_page") : "applets.html";
+ //alert("cur page : " + currentPage);
+ $('#header').load("includes/header_jv.html");
+ $('#content').load(currentPage+".html");
+ $('#nav').load("includes/nav_jv.html");
+ $('#footer').load("includes/footer_jv.html");
+ $('#'+ currentPage).addClass('active-trail active');
+ });
+
+ $(document).ready(function(){
+ //var currentPage = (readCookie("current_page")) ? readCookie("current_page") : "applets.html";
+ //updateLinks(currentPage);
+ var params = [["file","uniref50.fa"],
+ ["treeFile","ferredoxin.nw"],
+ ["userDefinedColour","C=yellow; R,K,H=FF5555; D,E=5555F"],
+ ["sortByTree","True"],
+ ["showSequenceLogo","true"],
+ ["showGroupConsensus","true"],
+ ["showFullId","false"],
+ ["linkLabel_1","Uniprot"],
+ ["linkUrl_1","http://www.uniprot.org/uniprot/$SEQUENCE_ID$"],
+ ["linkLabel_2","EMBL-EBI Search"],
+ ["linkUrl_2","http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"],
+ ["APPLICATION_URL","http://www.jalview.org/services/launchApp"]];
+ var app = createAppletTag('jalview.bin.JalviewLite','',appletJars,'140','35', params);
+ console.log('—————————> app ———————> ' + app);
+ //var appDiv = document.getElementById("applet_div");
+ //var appDiv = document.getElementById("applet_div");
+ //appDiv.appendChild(app);
+ $("<div class='newbox'>I'm new box by appendTo</div>").appendTo('.applet_div');
+ //$(‘.applet_div').append(app);
+ });
+
+function doSubmit(target){
+ setOrUpdateCookie('current_page', target, '1');
+ //alert('current page : ' + readCookie("current_page"));
+ var currentPage = target+'.html';
+ $('#content').load(currentPage);
+ updateLinks(target);
+}
+
+function updateLinks(target) {
+ var ul = document.getElementById("menu");
+ var items = ul.getElementsByTagName("li");
+ for (var i = 0; i < items.length; ++i) {
+ removeClass(items[i], "active-trail active");
+ }
+ $('#'+ target).addClass('active-trail active');
+}
+
+function hasClass(ele,cls) {
+ return !!ele.className.match(new RegExp('(\\s|^)'+cls+'(\\s|$)'));
+}
+
+function addClass(ele,cls) {
+ if (!hasClass(ele,cls)) ele.className += " "+cls;
+}
+
+function removeClass(ele,cls) {
+ if (hasClass(ele,cls)) {
+ var reg = new RegExp('(\\s|^)'+cls+'(\\s|$)');
+ ele.className=ele.className.replace(reg,' ');
+ }
+}
-<!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 ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
* 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>Javascript Launch</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-
-</head>
-
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" 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="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="embedded.html">Embedded Alignment</a></li>
- <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="formComplete.html">Access from Javascript</a></li>
- <li class="jvlite-nav-small"><a href="javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
-
<!-- boiler plate link to alternate demopage -->
-
<div style="width: 100%">
<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Examples aren't working ?<br/>Try <a href="u_javascriptLaunch.html">the unsigned applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
+
+<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
</p></div>
</div>
onClick="startJalview('plantfdx.fa','Button1.alignment','alwvar')"/>
</form>
<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
-<!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 ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
* 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>Linked JalviewLites</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-
-</head>
-
-
-<body>
-
-
-<div id="header">
-<div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" 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="jalviewLiteJs.html">Javascript API</a></li>
-<li><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="embedded.html">Embedded Alignment</a></li>
- <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="formComplete.html">Access from Javascript</a></li>
- <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
- <li class="jvlite-nav-small"><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
-</ul>
-</div>
-
-<div id="content" class="content">
-
<!-- boiler plate link to alternate demopage -->
-
<div style="width: 100%">
<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Examples aren't working ?<br/>Try <a href="u_linkedapplets_ng.html">the unsigned applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
+<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
</p></div>
</div>
};
</script>
<h2>JalviewLite Linked Applets Demo</h2>
- <p>The two applets below use <a href="jalviewLiteJs.html">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
+ <p>The two applets below use <a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
</p>
<script>
var attributes = {
id="stdout" rows="20" cols="80">Messages will appear here.</textarea></form>
<br>
</p>
-<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
+<!-- content template end -->
\ No newline at end of file
+++ /dev/null
-<!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 ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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>JalviewLite Examples</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-
-</head>
-
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
- </ul>
- <div style="clear:both"></div>
- </div>
-
- </div>
-<div id="pageWrap">
-
-<div id="sideNav">
- <ul>
- <li class="jvlite-nav-small"><a href="u_applets.html">JalviewLite Examples</a></li>
- <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="u_embedded.html">Embedded Alignment</a></li>
- <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="u_formComplete.html">Access from Javascript</a></li>
- <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
-
-
-<!-- boiler plate link to alternate demopage -->
-
-<div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Scary Java warnings ?<br/>Try <a href="applets.html">the signed applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
-<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
-</p></div>
-</div>
-</div>
-
-<!-- content template start -->
-
-<p align="left">
-<h2>JalviewLite Button Examples</h2>
-Try out JalviewLite by pressing one of the buttons below.<br/>
- For more information on how to use the applet in your website, see the <a href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
-<p> </p><div align="center">
- <p align="center">
- <h2>Ferredoxins, chloroplast precursor related UniRef50
- cluster</h2>
- <br /> (15 sequences x 150 residues)
- </p>
- <table width="90%">
- <tr>
- <td width="10%" valign="center">
- <applet
- code="jalview.bin.JalviewLite" width="140" height="35"
- archive="u_jalviewApplet.jar">
-<param name="file" value="uniref50.fa"/>
-<param name="treeFile" value="ferredoxin.nw"/>
-<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
-<param name="sortByTree" value="True"/>
-<param name="showSequenceLogo" value="true"/>
-<param name="showGroupConsensus" value="true"/>
-<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="EMBL-EBI Search"/>
- <param name="linkUrl_2"
- value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp"/>
-</applet>
-</td>
- <td valign="center">User Defined Colours, loads an associated
- Newick format tree file which is used to sort the alignment, and
- group consensus and sequence logos are shown below the alignment.</td>
- </tr>
- <tr>
- <td width="10%" valign="center"><applet
- code="jalview.bin.JalviewLite" width="140" height="35"
- archive="u_jalviewApplet.jar">
-<param name="file" value="uniref50.fa"/>
-<param name="features" value="exampleFeatures.txt"/>
-<param name="showFullId" value="false"/>
-<param name="windowHeight" value="500"/>
-<param name="windowWidth" value="650"/>
-<param name="showFeatureSettings" value="true"/>
-<param name="wrap" value="true"/>
-<param name="showAnnotation" 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="EMBL-EBI Search"/>
- <param name="linkUrl_2"
- value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp"/>
-</applet>
-</td>
- <td valign="center">Displays a features file on the alignment</td>
- </tr>
- <tr>
- <td width="10%" valign="center"><applet
- code="jalview.bin.JalviewLite" width="140" height="35"
- archive="u_jalviewApplet.jar,u_JmolApplet-12.2.4.jar">
-<param name="file" value="uniref50.fa"/>
-<param name="showFullId" value="false"/>
-<param name="windowHeight" value="500"/>
-<param name="windowWidth" value="650"/>
-<param name="wrap" value="true"/>
-<param name="showAnnotation" value="false"/>
-<param name="defaultColour" value="Strand Propensity"/>
-<param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
- <param name="linkLabel_1" value="Uniprot"/>
- <param name="linkUrl_1"
- value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
- <param name="linkLabel_2" value="EMBL-EBI Search"/>
- <param name="linkUrl_2"
- value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp"/>
-</applet>
-</td>
- <td valign="center">Associates PDB file 1GAQ with sequence
- FER1_MAIZE</td>
- </tr>
- <tr>
- <td width="10%" valign="center"><applet
- code="jalview.bin.JalviewLite" width="140" height="35"
- archive="u_jalviewApplet.jar">
-<param name="file" value="jpred_msa.fasta"/>
-<param name="jnetfile" value="jpred_msa.seq.concise"/>
-<param name="showFullId" value="false"/>
-<param name="windowHeight" value="515"/>
-<param name="windowWidth" value="650"/>
-<param name="showAnnotation" value="true"/>
-<param name="defaultColour" value="Clustal"/>
- <param name="linkLabel_1" value="Uniprot"/>
- <param name="linkUrl_1"
- value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
- <param name="linkLabel_2" value="EMBL-EBI Search"/>
- <param name="linkUrl_2"
- value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp"/>
-</applet>
- </td>
- <td valign="middle">Displays a Multiple Sequence Alignment
- Based JNet Prediction for a Sequence</td>
- </tr>
- </table>
- <p>
- <h2>RF00031 RFAM Alignment with per sequence secondary
- structure</h2>
- </p>
- <table width="90%">
- <tr>
- <td width="10%" valign="center"><applet
- code="jalview.bin.JalviewLite" width="140" height="35"
- archive="u_jalviewApplet.jar">
-<param name="file" value="RF00031_folded.stk"/>
-<param name="showFullId" value="false"/>
-<param name="windowHeight" value="515"/>
-<param name="windowWidth" value="650"/>
-<param name="showAnnotation" value="true"/>
-<param name="defaultColour" value="Purine/Pyrimidine"/>
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp"/>
-</applet>
-</td>
- <td valign="center">Displays an RFAM RNA fold family with
- secondary structure annotation</td>
- </tr>
- </table>
-</div>
-<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
+++ /dev/null
-<!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 ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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>Embedded Alignment</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-
-</head>
-
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
- </ul>
- <div style="clear:both"></div>
- </div>
-
- </div>
-<div id="pageWrap">
-
-<div id="sideNav">
- <ul>
- <li ><a href="u_applets.html">JalviewLite Examples</a></li>
- <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li class="jvlite-nav-small"><a href="u_embedded.html">Embedded Alignment</a></li>
- <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="u_formComplete.html">Access from Javascript</a></li>
- <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
-
-
-<!-- boiler plate link to alternate demopage -->
-
-<div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Scary Java warnings ?<br/>Try <a href="embedded.html">the signed applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
-<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
-</p></div>
-</div>
-</div>
-
-<!-- content template start -->
-<h2>Embedded viewing of Alignments</h2>
-<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="u_jalviewApplet.jar">
-<param name="file" value="plantfdx.fa"/>
-<param name="features" value="plantfdx.features"/>
-<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
-<param name="showFullId" value="false"/>
-<param name="embedded" value="true"/>
- <param name="linkLabel_1" value="Uniprot"/>
- <param name="linkUrl_1"
- value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
- <param name="linkLabel_2" value="EMBL-EBI Search"/>
- <param name="linkUrl_2"
- value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp"/>
-</applet>
-</p>
-<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
+++ /dev/null
-<!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 ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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>Jalview and Jmol</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-<script src="javascript/deployJava.js"></script>
-<script src="jmol/Jmol.js"></script>
-<script src="javascript/jquery-1.4.4.min.js"></script>
-<script src="javascript/jquery.timer.js"></script>
-<script src="javascript/jquery.blockUI.js"></script>
-<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
-<!-- <script src="archive-min.js" language="javascript"></script>
--->
-<script src="javascript/jalview.js" language="javascript"></script>
-<script language="JavaScript">
-// instead of this, we use a custom JmolApplet spec
-// jmolInitialize('jmol');
-jmolInitialize("","u_JmolApplet-12.2.4.jar");
-function genHref()
-{
- var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
- for(i=0; i<11; i++)
- { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
- }
- window.location=href;
-}
-</script>
-<script>
- var loglevel=1;
- function dbg(lvl,string) {
- if (_console && lvl<=loglevel) {_console.value += string + "\n";}
- }
- var _lastTime=new Date();
- var _path;
- var _datazip;
- var _zip;
- var alignA;
- var alignB;
- var featuresA;
- var featuresB;
- var pairs;
- var atompairs;
- var structdata;
- var jmolview;
- var jvstructassoc;
- var modeltofiles = new Array();
-
- function lJvA() {
- jvfollower = document.getElementById("jvA");
- setConsole(document.getElementById("stdout"));
-
- sep = jvfollower.getSeparator();
- //jvapp.setSeparator(""+jvapp.getSeparator());
- linkJvJmol(jvfollower, "jmolView", modeltofiles);
- };
-
- var _jvA=new Object();
- _jvA.attributes = {
- code : 'jalview.bin.JalviewLite',
- archive : 'u_jalviewApplet.jar',
- width : '500',
- height : '350',
- mayscript : 'True',
- scriptable: 'True',
- id : 'jvA'
- };
- _jvA.parameters = {
- java_arguments : "-Xmx256m",
- externalstructureviewer : "true",
- oninit : "lJvA",
- automaticScrolling : "true",
-// <!-- defaultColour : "Strand Propensity", -->
- file : "uniref50_mz.fa",
-
- relaxedidmatch : "true",
- debug : "true",
- wrap : "false",
- // separator : "^",
- showAnnotation : "false",
- embedded : "true",
- showFullId : "false",
- RGB : "F2F2FF",
- linkLabel_1 : "EMBL-EBI Search",
- linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
- ,
- linkLabel_2 : "Uniprot"
- ,
- linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
- APPLICATION_URL : "http://www.jalview.org/services/launchApp",
- PDBfile : "1gaq.txt FER1_MAIZE",
- permissions : "sandbox"
- };
- jmolSetCallback("hoverCallback","_jmolhover");
- jmolSetCallback("pickCallback","_jmolpick");
- modeltofiles+="1gaq.txt";
-</script>
-
-</head>
-
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
- </ul>
- <div style="clear:both"></div>
- </div>
-
- </div>
-<div id="pageWrap">
-
-<div id="sideNav">
- <ul>
- <li ><a href="u_applets.html">JalviewLite Examples</a></li>
- <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="u_embedded.html">Embedded Alignment</a></li>
- <li class="jvlite-nav-small"><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="u_formComplete.html">Access from Javascript</a></li>
- <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
-
-
-<!-- boiler plate link to alternate demopage -->
-
-<div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Scary Java warnings ?<br/>Try <a href="embeddedWJmol.html">the signed applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
-<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
-</p></div>
-</div>
-</div>
-
-<!-- content template start -->
-<h2>Structure and Alignment</h2>
-<p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
-<center>
- <script>
- jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
- </script>
- <script>
- deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
- </script>
-</center>
-<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
+++ /dev/null
-<!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 ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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>Access from Javascript</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-
-</head>
-
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
- </ul>
- <div style="clear:both"></div>
- </div>
-
- </div>
-<div id="pageWrap">
-
-<div id="sideNav">
- <ul>
- <li ><a href="u_applets.html">JalviewLite Examples</a></li>
- <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="u_embedded.html">Embedded Alignment</a></li>
- <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
- <li class="jvlite-nav-small"><a href="u_formComplete.html">Access from Javascript</a></li>
- <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
-
-
-<!-- boiler plate link to alternate demopage -->
-
-<div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Scary Java warnings ?<br/>Try <a href="formComplete.html">the signed applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
-<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
-</p></div>
-</div>
-</div>
-
-<!-- content template start -->
-<h2><a href="jalviewLiteJs.html">JalviewLite API</a> Demo</h2>
-<p>Using the Javascript API to fill out forms using data from JalviewLite
-<br/>Click the Javascript buttons below to interact with the Applet
-instance on the page.</p>
-View the source in your browser to see how it has been done. <br/>
-<a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
-<applet code="jalview.bin.JalviewLite" width="0" height="0"
- archive="u_jalviewApplet.jar" name="Jalview">
-
- <param name="file" value="plantfdx.fa"/>
- <param name="features" value="plantfdx.features"/>
- <param name="wrap" value="true"/>
- <param name="showAnnotation" value="false"/>
- <param name="windowHeight" value="500"/>
- <param name="windowWidth" value="650"/>
- <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="hidefeaturegroups" value="uniprot" />
- <param name="showbutton" value="false" />
-</applet>
-<form name="exampleForm"><br/>
- <br/>
- <center><strong>Using the Jalview Applet for Input
- to an HTML Form</strong></center>
- <div align="center"><input type="button"
- onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
- value="Fill Form from Jalview" /> <br/>
- <br/>
- <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
-</form>
-<center><strong>Make a new View and Get and Set
- Group Display List</strong></center>
-<form name="groupForm">
- <div align="center"><input type="button"
- onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
- value="Get groups" /> <input type="button"
- onClick="document.applets.Jalview.newView()" value="new View" /> <br/>
- <textarea name="groups" cols="55" rows="9"></textarea> <br/>
- <input type="button"
- onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
- value="Display groups" /> <input type="button"
- onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
- value="Hide groups" /></div>
-</form>
-</div>
-<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
+++ /dev/null
-<!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 ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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>Javascript Launch</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-
-</head>
-
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
- </ul>
- <div style="clear:both"></div>
- </div>
-
- </div>
-<div id="pageWrap">
-
-<div id="sideNav">
- <ul>
- <li ><a href="u_applets.html">JalviewLite Examples</a></li>
- <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="u_embedded.html">Embedded Alignment</a></li>
- <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="u_formComplete.html">Access from Javascript</a></li>
- <li class="jvlite-nav-small"><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
-
-
-<!-- boiler plate link to alternate demopage -->
-
-<div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Scary Java warnings ?<br/>Try <a href="javascriptLaunch.html">the signed applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
-<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
-</p></div>
-</div>
-</div>
-
-<!-- content template start -->
- <SCRIPT type="text/javascript">
- /* <![CDATA[ // */
-// From http://snipplr.com/view.php?codeview&id=1272
-//----------------------------------------
-//Wrapper function for constructing a request object.
-// Parameters:
-// reqType: The HTTP request type, such as GET or POST.
-// url: The URL of the server program.
-// asynch: Whether to send the request asynchronously or not.
-//----------------------------------------
-
-function httpRequest(reqType,url,asynch,respHandle) {
-
- // Mozilla-based browsers
- if (window.XMLHttpRequest) {
- request = new XMLHttpRequest();
- } else if (window.ActiveXObject) {
- request = new ActiveXObject("Msxml2.XMLHTTP");
- if (!request) {
- request = new ActiveXObject("Microsoft.XMLHTTP");
- }
- }
-
- // Request could still be null if neither ActiveXObject
- // initialization succeeded
- if (request) {
- // If the reqType param is POST, then the fifth arg is the POSTed data
- if (reqType.toLowerCase() != "post") {
- initReq(reqType, url, asynch, respHandle);
- } else {
- // The POSTed data
- var args = arguments[5];
- if (args != null && args.length > 0) {
- initReq(reqType, url, asynch, respHandle, args);
- }
- }
- } else {
- alert("Your browser does not permit the use of all " +
- "of this application's features!");
- }
-
-}
-
-//----------------------------------------
-//Initialize a request object that is already constructed
-//----------------------------------------
-
-function initReq(reqType, url, bool, respHandle) {
- try {
- // Specify the function that will handle the HTTP response
- request.onreadystatechange = respHandle;
- request.open(reqType, url, bool);
- // If the reqType param is POST, then the
- // fifth argument to the function is the POSTed data
- if (reqType.toLowerCase() == "post") {
- // Set the Content-Type header for a POST request
- request.setRequestHeader("Content-Type", "application/x-ww-form-urlencoded; charset=UTF-8");
- request.send(arguments[4]);
- } else {
- request.send(null);
- }
- } catch (errv) {
- alert("The application cannot contact the server at the moment. " +
- "Please try again in a few seconds.\n" +
- "Error detail: " + errv.message);
- }
-}
-
-// jalview launching with fetched data
-
-function startJalview(aligURL,title,alwvar) {
- var aligment = "";
- httpRequest("get",aligURL,true,function() {
- if (request.readyState == 4) {
- alignment = request.responseText;
- eval("var "+alwvar+" = document.JalviewLite.loadAlignment(alignment,title)");
- }
- })
-
-}
-
-/* ]]> */
-</SCRIPT>
- <form name="Form1">
-<applet name="JalviewLite" code="jalview.bin.JalviewLite"
-archive="u_jalviewApplet.jar" width="0" height="0">
-<param name="debug" value="true"/>
-<param name="showbutton" value="false"/>
-</applet>
-
-<h2>Javascript Launch Button</h2><p>The button below demonstrates how JalviewLite can be launched via a javascript action.</p>
-
- <input type="button" name="Button1" value="Start"
-onClick="startJalview('plantfdx.fa','Button1.alignment','alwvar')"/>
- </form>
-<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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>
+++ /dev/null
-<!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 ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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>Linked JalviewLites</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>
- <script>
- <!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
- </script>
-
-</head>
-
-
-<body>
-
-
- <div id="header">
- <div id="logo"><a href="http://www.jalview.org" 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="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
- </ul>
- <div style="clear:both"></div>
- </div>
-
- </div>
-<div id="pageWrap">
-
-<div id="sideNav">
- <ul>
- <li ><a href="u_applets.html">JalviewLite Examples</a></li>
- <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="u_embedded.html">Embedded Alignment</a></li>
- <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
- <li ><a href="u_formComplete.html">Access from Javascript</a></li>
- <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
- <li class="jvlite-nav-small"><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
- </ul>
-</div>
-
-<div id="content" class="content">
-
-
-<!-- boiler plate link to alternate demopage -->
-
-<div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
- Scary Java warnings ?<br/>Try <a href="linkedapplets_ng.html">the signed applet demos</a>
-</div>
-<div style="margin:8px; padding:10px; align: left;">
-<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
-</p></div>
-</div>
-</div>
-
-<!-- content template start -->
-<script src="http://www.java.com/js/deployJava.js"></script>
-<script src="javascript/jalview.js" language="javascript"></script>
-<script> //deployJava.debug="true";
-
- function lJvApp() {
- var jvapp = document.getElementById("jvapp");
- var jvfollower = document.getElementById("jvfollower");
- setConsole(document.getElementById("stdout"));
- //jvapp.setSeparator(""+jvapp.getSeparator());
- linkJvJmol(jvapp);
- };
-
- function lJvFollow() {
- var jvapp = document.getElementById("jvapp");
- var jvfollower = document.getElementById("jvfollower");
- //jvfollower.setSeparator(""+jvfollower.getSeparator());
- linkJvJmol(jvfollower);
- };
-</script>
- <h2>JalviewLite Linked Applets Demo</h2>
- <p>The two applets below use <a href="jalviewLiteJs.html">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
- </p>
- <script>
- var attributes = {
- code : 'jalview.bin.JalviewLite',
- archive : 'u_jalviewApplet.jar',
- width : 800,
- height : 300,
- mayscript : 'True', scriptable: 'True',
- id : 'jvapp'
- };
- var parameters = {
- oninit : "lJvApp",
- automaticScrolling : "true",
- file : "plantfdx.fa",
- annotations : "plantfdx.annotations",
- debug : "true",
- wrap : "false",
- // separator : "^",
- showAnnotation : "true",
- embedded : "true",
- showFullId : "false",
- RGB : "F2F2FF",
- linkLabel_1 : "EMBL-EBI Search",
- linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
- ,
- linkLabel_2 : "Uniprot"
- ,
- linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
- permissions : 'sandbox',
- APPLICATION_URL : "http://www.jalview.org/services/launchApp"
- };
-
- deployJava.runApplet(attributes, parameters, '1.6');
-</script>
-<script>
- var attributes = {
- code : 'jalview.bin.JalviewLite',
- archive : 'u_jalviewApplet.jar',
- width : 800,
- height : 300,
- mayscript : 'True', scriptable: 'True',
- id : "jvfollower"
- };
- var parameters = {
- oninit : "lJvFollow",
- file : "plantfdx.fa",
- annotations : "plantfdx.annotations",
- automaticScrolling : "true",
- debug : "true",
- wrap : "false",
- // separator : "^",
- showAnnotation : "true",
- embedded : "true",
- showFullId : "false",
- RGB : "F2F2FF",
- linkLabel_1 : "EMBL-EBI Search",
- linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
- ,
- linkLabel_2 : "Uniprot"
- ,
- linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
- permissions : 'sandbox',
- APPLICATION_URL : "http://www.jalview.org/services/launchApp"
- };
- deployJava.runApplet(attributes, parameters, '1.6');
-</script>
- <p>
-<!-- <a href="javascript:linkJvJmol()">Click Me If you don't see any messages below</a>
- <br>
- -->
-<form name="console" id="console">
-<textarea name="output"
- id="stdout" rows="20" cols="80">Messages will appear here.</textarea></form>
- <br>
-</p>
-<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<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 / commitdiff