1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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2 <html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
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4 <!-- InstanceBeginEditable name="doctitle" -->
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5 <TITLE>Embedded JalviewLite talking to externally managed Jmol</TITLE>
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6 <!-- InstanceEndEditable -->
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7 <meta http-equiv="content-type" content="text/html; charset=UTF-8">
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8 <meta http-equiv="keywords" content="protein,interaction,domain,alignment,barton group,structure,interface">
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9 <!-- InstanceBeginEditable name="head" -->
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10 <script src="javascript/deployJava.js"></script>
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11 <script src="jmol/Jmol.js"></script>
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12 <script src="javascript/jquery-1.4.4.min.js"></script>
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13 <script src="javascript/jquery.timer.js"></script>
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14 <script src="javascript/jquery.blockUI.js"></script>
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15 <script src="javascript/jshashtable-2.1.js" language="javascript"></script>
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16 <!-- <script src="archive-min.js" language="javascript"></script>
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18 <script src="javascript/jalview.js" language="javascript"></script>
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19 <script language="JavaScript">
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20 // instead of this, we use a custom JmolApplet spec
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21 // jmolInitialize('jmol');
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22 jmolInitialize("","JmolApplet-12.1.13.jar");
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25 var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
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27 { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
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29 window.location=href;
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34 function dbg(lvl,string) {
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35 if (_console && lvl<=loglevel) {_console.value += string + "\n";}
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37 var _lastTime=new Date();
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50 var modeltofiles = new Array();
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53 jvfollower = document.getElementById("jvA");
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54 setConsole(document.getElementById("stdout"));
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56 sep = jvfollower.getSeparator();
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57 //jvapp.setSeparator(""+jvapp.getSeparator());
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58 linkJvJmol(jvfollower, "jmolView", modeltofiles);
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61 var _jvA=new Object();
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63 code : 'jalview.bin.JalviewLite',
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64 archive : 'jalviewApplet.jar',
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72 java_arguments : "-Xmx256m",
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73 externalstructureviewer : "true",
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75 automaticScrolling : "true",
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76 // <!-- defaultColour : "Strand Propensity", -->
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77 file : "uniref50_mz.fa",
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79 relaxedidmatch : "true",
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83 showAnnotation : "false",
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85 showFullId : "false",
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87 linkLabel_1 : "SRS",
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88 linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
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90 linkLabel_2 : "Uniprot"
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92 linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
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93 APPLICATION_URL : "http://www.jalview.org/services/launchApp",
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94 PDBfile : "1gaq.txt FER1_MAIZE"
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96 jmolSetCallback("hoverCallback","_jmolhover");
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97 jmolSetCallback("pickCallback","_jmolpick");
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98 modeltofiles+="1gaq.txt";
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100 <!-- InstanceEndEditable -->
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101 <style type="text/css">
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104 font-family: Geneva, Arial, Helvetica, sans-serif;
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108 font-family: Verdana, Arial, Helvetica, sans-serif;
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110 text-decoration: none;
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113 background-color:#000000; color: #F2F2FF;
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118 <script language="JavaScript">
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121 var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
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123 {href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
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124 window.location=href;
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126 function getEventTarget(e)
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132 return e.srcElement;
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136 <body alink="#000000" vlink="#000000" link="#000000">
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137 <script type="text/javascript">
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138 var gaJsHost = (("https:" == document.location.protocol) ?
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139 "https://ssl." : "http://www.");
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140 document.write(unescape("%3Cscript src='" + gaJsHost +
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141 "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
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143 <script type="text/javascript">
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145 var pageTracker = _gat._getTracker("UA-9060947-1");
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146 pageTracker._trackPageview();
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149 <div align="left">
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150 <table width="805" height="100" cellpadding="5">
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152 <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>
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155 <table width="805" border="0" cellpadding="5" cellspacing="5">
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157 <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
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159 <div align="center">
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160 <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
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162 <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
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165 <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
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168 <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
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171 <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
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175 <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
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178 <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
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181 <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
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184 <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
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188 <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
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192 <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
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195 <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
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198 <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
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199 Mailing List</a></td>
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202 <td align="left" valign="middle"><a
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203 href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
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204 class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
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205 bug reports to the discussion list.</em></td>
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209 <!--<td align="left" valign="middle"><br>
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210 Please send problems<br>and
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211 bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
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215 <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
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216 <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
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219 <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
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220 <!-- <a onclick="colourStructs();">Colour from jalviews</a>
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224 jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
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227 deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
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233 <!-- <form name="console" id="console">
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234 <textarea name="output" id="stdout" rows="3" cols="80"
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235 >Messages will appear here.</textarea></form>
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237 <!-- InstanceEndEditable --></td>
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242 <!-- InstanceEnd --></html>
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