--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
+<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
+<head>\r
+<!-- InstanceBeginEditable name="doctitle" -->\r
+<TITLE>Embedded JalviewLite talking to externally managed Jmol</TITLE>\r
+<!-- InstanceEndEditable --> \r
+<meta http-equiv="content-type" content="text/html; charset=UTF-8">\r
+<meta http-equiv="keywords" content="protein,interaction,domain,alignment,barton group,structure,interface">\r
+<!-- InstanceBeginEditable name="head" -->\r
+<script src="http://www.java.com/js/deployJava.js"></script>\r
+<script src="jmol/Jmol.js"></script>\r
+<script src="javascript/jquery-1.4.4.min.js"></script>\r
+<script src="javascript/jquery.timer.js"></script>\r
+<script src="javascript/jquery.blockUI.js"></script>\r
+<script src="javascript/jshashtable-2.1.js" language="javascript"></script>\r
+<!-- <script src="archive-min.js" language="javascript"></script>\r
+-->\r
+<script src="javascript/jalview.js" language="javascript"></script>\r
+<script language="JavaScript">\r
+// instead of this, we use a custom JmolApplet spec\r
+// jmolInitialize('jmol');\r
+jmolInitialize("","JmolApplet-12.1.13.jar");\r
+function genHref()\r
+{\r
+ var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";\r
+ for(i=0; i<11; i++)\r
+ { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); \r
+ }\r
+ window.location=href;\r
+}\r
+</script>\r
+<script>\r
+ var loglevel=1;\r
+ function dbg(lvl,string) {\r
+ if (_console && lvl<=loglevel) {_console.value += string + "\n";}\r
+ }\r
+ var _lastTime=new Date();\r
+ var _path;\r
+ var _datazip;\r
+ var _zip;\r
+ var alignA;\r
+ var alignB;\r
+ var featuresA;\r
+ var featuresB;\r
+ var pairs;\r
+ var atompairs;\r
+ var structdata;\r
+ var jmolview;\r
+ var jvstructassoc;\r
+ var modeltofiles = new Array();\r
+\r
+ function lJvA() {\r
+ jvfollower = document.getElementById("jvA");\r
+ setConsole(document.getElementById("stdout"));\r
+ \r
+ sep = jvfollower.getSeparator();\r
+ //jvapp.setSeparator(""+jvapp.getSeparator());\r
+ linkJvJmol(jvfollower, "jmolView", modeltofiles);\r
+ };\r
+\r
+ var _jvA=new Object();\r
+ _jvA.attributes = {\r
+ code : 'jalview.bin.JalviewLite',\r
+ archive : 'jalviewApplet.jar',\r
+ width : '100%',\r
+ height : '35%',\r
+ mayscript : 'True',\r
+ scriptable: 'True',\r
+ id : 'jvA'\r
+ };\r
+ _jvA.parameters = {\r
+ java_arguments : "-Xmx256m",\r
+ externalstructureviewer : "true",\r
+ oninit : "lJvA",\r
+ automaticScrolling : "true",\r
+ defaultColour : "Strand Propensity",\r
+ file : "uniref50.fa",\r
+ \r
+ relaxedidmatch : "true",\r
+ debug : "true",\r
+ wrap : "false",\r
+ // separator : "^",\r
+ showAnnotation : "false",\r
+ embedded : "true",\r
+ showFullId : "false",\r
+ RGB : "F2F2FF",\r
+ linkLabel_1 : "SRS",\r
+ linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"\r
+ ,\r
+ linkLabel_2 : "Uniprot"\r
+ ,\r
+ linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",\r
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp",\r
+ PDBfile : "1gaq.txt FER1_MAIZE"\r
+ };\r
+ jmolSetCallback("hoverCallback","_jmolhover");\r
+ jmolSetCallback("pickCallback","_jmolpick");\r
+ modeltofiles+="1gaq.txt";\r
+</script>\r
+<!-- InstanceEndEditable --> \r
+<style type="text/css">\r
+<!--\r
+td {\r
+ font-family: Geneva, Arial, Helvetica, sans-serif;\r
+ font-size: 12px;\r
+}\r
+.plain {\r
+ font-family: Verdana, Arial, Helvetica, sans-serif;\r
+ font-size: 14px;\r
+ text-decoration: none;\r
+}\r
+.plain:hover{\r
+ background-color:#000000; color: #F2F2FF;\r
+}\r
+ \r
+-->\r
+</style>\r
+<script language="JavaScript">\r
+function genHref()\r
+{\r
+var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";\r
+for(i=0; i<8; i++)\r
+{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }\r
+window.location=href;\r
+}\r
+function getEventTarget(e)\r
+{\r
+if(!e)\r
+e = window.event;\r
+if(e.target)\r
+return e.target;\r
+return e.srcElement;\r
+}\r
+</script>\r
+</head>\r
+<body alink="#000000" vlink="#000000" link="#000000">\r
+<script type="text/javascript">\r
+var gaJsHost = (("https:" == document.location.protocol) ? \r
+"https://ssl." : "http://www.");\r
+document.write(unescape("%3Cscript src='" + gaJsHost + \r
+"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));\r
+</script>\r
+<script type="text/javascript">\r
+try{\r
+var pageTracker = _gat._getTracker("UA-9060947-1");\r
+pageTracker._trackPageview();\r
+} catch(err) {}\r
+</script>\r
+<div align="left"> \r
+ <table width="805" height="100" cellpadding="5">\r
+ <tr>\r
+ <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>\r
+ </tr>\r
+ </table>\r
+ <table width="805" border="0" cellpadding="5" cellspacing="5">\r
+ <tr> \r
+ <td width="183" valign="top" bgcolor="#F2F2FF" border="5"> \r
+ \r
+ <div align="center">\r
+ <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">\r
+ <tr> \r
+ <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>\r
+ </tr>\r
+ <tr> \r
+ <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>\r
+ </tr>\r
+ <tr> \r
+ <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>\r
+ </tr>\r
+ <tr> \r
+ <td align="left" valign="middle"><a href="applets.html" class="plain">Applet \r
+ Version</a></td>\r
+ </tr>\r
+ <tr> \r
+ <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>\r
+ </tr>\r
+ <tr> \r
+ <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>\r
+ </tr>\r
+ <tr> \r
+ <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>\r
+ </tr>\r
+ <tr>\r
+ <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release \r
+ history</a></td>\r
+ </tr>\r
+ <tr> \r
+ <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source \r
+ Code</a></td>\r
+ </tr>\r
+ <tr> \r
+ <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>\r
+ </tr>\r
+ <tr> \r
+ <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>\r
+ </tr>\r
+ <tr> \r
+ <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News \r
+ Mailing List</a></td>\r
+ </tr>\r
+ <tr>\r
+ <td align="left" valign="middle"><a\r
+ href="http://www.jalview.org/mailman/listinfo/jalview-discuss"\r
+ class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and\r
+ bug reports to the discussion list.</em></td>\r
+ </tr>\r
+ <tr></tr>\r
+ <tr>\r
+ <!--<td align="left" valign="middle"><br>\r
+ Please send problems<br>and\r
+ bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->\r
+ </tr>\r
+ </table>\r
+ </div>\r
+ <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>\r
+ <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a> \r
+ </div>\r
+ </td>\r
+ <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->\r
+<!-- <a onclick="colourStructs();">Colour from jalviews</a>\r
+ -->\r
+ <script>\r
+ jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; backbone 0.01; restrict; center *; set selectionhalos true;select 0","jmolView");\r
+</script>\r
+ <script>\r
+ deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');\r
+ </script>\r
+ \r
+ </td>\r
+ </tr>\r
+ </table>\r
+<form name="console" id="console">\r
+ <textarea name="output" id="stdout" rows="3" cols="80"\r
+ >Messages will appear here.</textarea></form>\r
+ </div>\r
+ <!-- InstanceEndEditable --></td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+</body>\r
+<!-- InstanceEnd --></html>\r
+
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff