-<!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="javascript/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-12.2.4.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 : '500',\r
- height : '350',\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_mz.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
- <center>\r
- <script>\r
- jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");\r
-</script>\r
- <script>\r
- deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');\r
- </script>\r
- </center>\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
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//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
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<!-- InstanceBeginEditable name="doctitle" -->
+<TITLE>Embedded JalviewLite talking to externally managed Jmol</TITLE>
+<!-- InstanceEndEditable -->
+<meta http-equiv="content-type" content="text/html; charset=UTF-8">
+<meta http-equiv="keywords" content="protein,interaction,domain,alignment,barton group,structure,interface">
+<!-- InstanceBeginEditable name="head" -->
+<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("","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 : '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 : "SRS",
+ linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
+ ,
+ linkLabel_2 : "Uniprot"
+ ,
+ linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp",
+ PDBfile : "1gaq.txt FER1_MAIZE"
+ };
+ jmolSetCallback("hoverCallback","_jmolhover");
+ jmolSetCallback("pickCallback","_jmolpick");
+ modeltofiles+="1gaq.txt";
+</script>
+<!-- InstanceEndEditable -->
+<style type="text/css">
+<!--
+td {
+ font-family: Geneva, Arial, Helvetica, sans-serif;
+ font-size: 12px;
+}
+.plain {
+ font-family: Verdana, Arial, Helvetica, sans-serif;
+ font-size: 14px;
+ text-decoration: none;
+}
+.plain:hover{
+ background-color:#000000; color: #F2F2FF;
+}
+
+-->
+</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>
+
git://source.jalview.org / jalview.git / blobdiff