-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML+RDFa 1.1//EN">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
--->
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-<meta http-equiv="keywords" content="protein,interaction,domain,alignment,barton group,structure,interface">
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+ * 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.
+ -->
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+ type="image/vnd.microsoft.icon" />
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+ content="width=device-width, initial-scale=1, maximum-scale=1, minimum-scale=1, user-scalable=no" />
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+<link rel="shortlink" href="/node/18" />
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+<script type="text/javascript"
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+
+
<script src="javascript/deployJava.js"></script>
-<script src="jmol/Jmol.js"></script>
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<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 src="javascript/jvcontroller.js"> </script>
+
+
+
+</head>
+
+
+
+<div id="header"></div>
+<section id="section-content" class="section section-content">
+ <div id="zone-content-wrapper"
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+
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+ <!— — — — — — — — — — — 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">
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+ </div>
+ </section>
+ <section
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+ id="block-menu-block-2">
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+ </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">
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+ id="node-basic-page-18">
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+
+
+
+
+
+
+
+<div>
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+
<script language="JavaScript">
// instead of this, we use a custom JmolApplet spec
// jmolInitialize('jmol');
-jmolInitialize("","JmolApplet-12.2.4.jar");
-function genHref()
-{
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</script>
<script>
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-// <!-- defaultColour : "Strand Propensity", -->
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- RGB : "F2F2FF",
- linkLabel_1 : "SRS",
- linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
- ,
- linkLabel_2 : "Uniprot"
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- PDBfile : "1gaq.txt FER1_MAIZE"
- };
- jmolSetCallback("hoverCallback","_jmolhover");
+ 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"));
+ linkJvJmol(jvfollower, "jmolView", modeltofiles);
+ };
+
+ var _jvA=new Object();
+ _jvA.attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : 'jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.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>
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+</script>
+<div style="width: 100%">
+
+</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>
+
+
+<div>
+ <script>
+ jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; background black; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;set hoverDelay 0.001; select 0","jmolView");
+ </script>
+</div>
+<div>
+<applet
+ code="jalview.bin.JalviewLite" width="500" height="350" id="jvA" mayscript="mayscript" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
+<param name="permissions" value="sandbox"/>
+<param name="java_arguments" value="-Xmx256m"/>
+<param name="externalstructureviewer" value="true"/>
+<param name="oninit" value="lJvA"/>
+<param name="automaticScrolling" value="true"/>
+<param name="file" value="uniref50_mz.fa"/>
+<param name="relaxedidmatch" value="true"/>
+<param name="debug" value="true"/>
+<param name="wrap" value="false"/>
+<param name="showAnnotation" value="false"/>
+<param name="embedded" value="true"/>
+<param name="showFullId" value="false"/>
+<param name="RGB" value="F2F2FF"/>
+<param name="linkLabel_1" value="EMBL-EBI Search"/>
+<param name="linkUrl_1" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+<param name="linkLabel_2" value="Uniprot"/>
+<param name="linkUrl_2" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+<param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
+<param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
+</applet>
+
+</div>
+
+<!-- content template end -->
+
--->
-</style>
-<script language="JavaScript">
-function genHref()
-{
-var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
-for(i=0; i<8; i++)
-{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
-window.location=href;
-}
-function getEventTarget(e)
-{
-if(!e)
-e = window.event;
-if(e.target)
-return e.target;
-return e.srcElement;
-}
-</script>
-</head>
-<body alink="#000000" vlink="#000000" link="#000000">
-<script type="text/javascript">
-var gaJsHost = (("https:" == document.location.protocol) ?
-"https://ssl." : "http://www.");
-document.write(unescape("%3Cscript src='" + gaJsHost +
-"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
-</script>
-<script type="text/javascript">
-try{
-var pageTracker = _gat._getTracker("UA-9060947-1");
-pageTracker._trackPageview();
-} catch(err) {}
-</script>
-<div align="left">
- <table width="805" height="100" cellpadding="5">
- <tr>
- <td background="../jalview.gif"> <a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>
- </tr>
- </table>
- <table width="805" border="0" cellpadding="5" cellspacing="5">
- <tr>
- <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
-
- <div align="center">
- <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
- <tr>
- <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
- Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
- history</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
- Code</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
- Mailing List</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a
- href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
- class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
- bug reports to the discussion list.</em></td>
- </tr>
- <tr></tr>
- <tr>
- <!--<td align="left" valign="middle"><br>
- Please send problems<br>and
- bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
- </tr>
- </table>
- </div>
- <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
- <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
- </div>
- </td>
- <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
-<!-- <a onclick="colourStructs();">Colour from jalviews</a>
- -->
- <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>
- </td>
- </tr>
- </table>
-<!-- <form name="console" id="console">
- <textarea name="output" id="stdout" rows="3" cols="80"
- >Messages will appear here.</textarea></form>
- --></div>
- <!-- InstanceEndEditable --></td>
- </tr>
- </table>
</div>
-</body>
-<!-- InstanceEnd --></html>
-
+
+
+
+
+
+
+
+
+
+
+</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>
+
+
git://source.jalview.org / jalview.git / blobdiff