-<!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" -->
+<!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>Jalview - Applets</TITLE>
-<!-- InstanceEndEditable -->
\r<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta http-equiv="keywords" content="jalview,multiple,sequence,alignment,editor,viewer,java,download,barton group,protein,dna,das,distributed annotation system">
\r<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
\r<style type="text/css">
\r<!--
\rtd {
\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\r<script language="JavaScript">
\rfunction genHref()
\r{
\rvar s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
\rfor(i=0; i<8; i++)
\r{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
\rwindow.location=href;
\r}
\rfunction getEventTarget(e)
\r{
\rif(!e)
\re = window.event;
\rif(e.target)
\rreturn e.target;
\rreturn e.srcElement;
\r}
\r\r</script>
\r</head>
\r\r<body alink="#000000" vlink="#000000" link="#000000">
\r<script type="text/javascript">
\rvar gaJsHost = (("https:" == document.location.protocol) ?
\r"https://ssl." : "http://www.");
\rdocument.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">
\rtry{
\rvar pageTracker = _gat._getTracker("UA-9060947-1");
\rpageTracker._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\r </div>
\r\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" -->
+<!-- InstanceEndEditable -->
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta http-equiv="keywords" content="jalview,multiple,sequence,alignment,editor,viewer,java,download,barton group,protein,dna,das,distributed annotation system">
+<!-- InstanceBeginEditable name="head" --><!-- 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" -->
<p>Jalview comes in two distinct flavours.<br>
<br>
The main application allows connection to multiple web services provided
<td width="100"> <applet code="jalview.bin.JalviewLite"
width="140" height="35"
archive="jalviewApplet.jar">
- <param name="file" value="uniref50.fa">
\r <param name="treeFile" value="ferredoxin.nw">
+ <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="showFullId" value="false">
- <param name="RGB" value="F2F2FF">
\r <param name="sortByTree" value="True">
\r <param name="showSequenceLogo" value="true">
\r <param name="showGroupConsensus" value="true">
\r <param name="linkLabel_1" value="SRS">
+ <param name="RGB" value="F2F2FF">
+ <param name="sortByTree" value="True">
+ <param name="showSequenceLogo" value="true">
+ <param name="showGroupConsensus" value="true">
+ <param name="linkLabel_1" value="SRS">
<param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
<param name="linkLabel_2" value="Uniprot">
<param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
<td width="100"> <applet code="jalview.bin.JalviewLite"
width="140" height="35"
archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
- <param name="file" value="uniref50.fa">
\r <!-- <param name="debug" value="true">
- -->
\r <param name="defaultColour" value="Strand Propensity">
+ <param name="file" value="uniref50.fa">
+ <!-- <param name="debug" value="true">
+ -->
+ <param name="defaultColour" value="Strand Propensity">
<param name="wrap" value="true">
<param name="showAnnotation" value="false">
<param name="windowHeight" value="500">
</table></td>
</tr>
</table>
- <p> </p>
\r <table width="300" border="1" cellspacing="0" cellpadding="0">
\r <tr>
\r <td><table width="300" border="0" cellspacing="0"
\r cellpadding="0">
\r <tr>
\r <td width="100"><applet code="jalview.bin.JalviewLite"
\r width="140" height="35" archive="jalviewApplet.jar">
\r <param name="file" value="jpred_msa.fasta">
\r <param name="jnetfile" value="jpred_msa.seq.concise">
\r <param name="defaultColour" value="Clustal">
\r <param name="showAnnotation" value="true">
\r <param name="windowHeight" value="515">
\r <param name="windowWidth" value="650">
\r <param name="showConservation" value="false">
\r <param name="showQuality" value="false">
\r <param name="showConsensus" value="false">
\r <param name="showFullId" value="false">
\r <param name="RGB" value="F2F2FF">
\r <param name="linkLabel_1" value="SRS">
\r <param name="linkUrl_1"
\r value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
\r <param name="linkLabel_2" value="Uniprot">
\r <param name="linkUrl_2"
\r value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
\r <param name="APPLICATION_URL"
\r value="http://www.jalview.org/services/launchApp">
\r </applet></td>
\r <td width="165">Displays a Multiple Sequence Alignment
\r Based JNet Prediction for a Sequence</td>
\r </tr>
\r </table></td>
\r </tr>
\r </table>
\r <p> </p>
\r <table width="300" border="1" cellspacing="0" cellpadding="0">
\r <tr>
\r <td><table width="300" border="0" cellspacing="0" cellpadding="0">
\r <tr>
\r <td width="100"> <applet code="jalview.bin.JalviewLite"
\r width="140" height="35"
\r archive="jalviewApplet.jar">
\r <param name="file" value="RF00031_folded.stk">
\r <param name="defaultColour" value="Purine/Pyrimidine">
\r <param name="showAnnotation" value="true">
\r <param name="windowHeight" value="515">
\r <param name="windowWidth" value="650">
\r <param name="showConservation" value="false">
\r <param name="showQuality" value="false">
\r <param name="showConsensus" value="true">
\r <param name="showFullId" value="false">
\r <param name="RGB" value="F2F2FF">
\r <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
\r </applet> </td>
\r <td width="165">Displays an RFAM RNA fold family with secondary structure annotation</td>
\r </tr>
\r </table></td>
\r </tr>
\r </table>
\r </div>
\r <p> </p>
\r <p>For more JalviewLite examples, follow the links below.
\r <ul>
\r <li><a href="embedded.html">JalviewLite embedded in the web page</a></li>
\r <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>
\r <li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other</a></li>
\r <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page.</a></li>
\r </ul>
- <!-- InstanceEndEditable --></td>\r </tr>\r </table>\r</div>\r</body>\r<!-- InstanceEnd --></html>\r
\ No newline at end of file
+ <p> </p>
+ <table width="300" border="1" cellspacing="0" cellpadding="0">
+ <tr>
+ <td><table width="300" border="0" cellspacing="0"
+ cellpadding="0">
+ <tr>
+ <td width="100"><applet code="jalview.bin.JalviewLite"
+ width="140" height="35" archive="jalviewApplet.jar">
+ <param name="file" value="jpred_msa.fasta">
+ <param name="jnetfile" value="jpred_msa.seq.concise">
+ <param name="defaultColour" value="Clustal">
+ <param name="showAnnotation" value="true">
+ <param name="windowHeight" value="515">
+ <param name="windowWidth" value="650">
+ <param name="showConservation" value="false">
+ <param name="showQuality" value="false">
+ <param name="showConsensus" value="false">
+ <param name="showFullId" value="false">
+ <param name="RGB" value="F2F2FF">
+ <param name="linkLabel_1" value="SRS">
+ <param name="linkUrl_1"
+ value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
+ <param name="linkLabel_2" value="Uniprot">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp">
+ </applet></td>
+ <td width="165">Displays a Multiple Sequence Alignment
+ Based JNet Prediction for a Sequence</td>
+ </tr>
+ </table></td>
+ </tr>
+ </table>
+ <p> </p>
+ <table width="300" border="1" cellspacing="0" cellpadding="0">
+ <tr>
+ <td><table width="300" border="0" cellspacing="0" cellpadding="0">
+ <tr>
+ <td width="100"> <applet code="jalview.bin.JalviewLite"
+ width="140" height="35"
+ archive="jalviewApplet.jar">
+ <param name="file" value="RF00031_folded.stk">
+ <param name="defaultColour" value="Purine/Pyrimidine">
+ <param name="showAnnotation" value="true">
+ <param name="windowHeight" value="515">
+ <param name="windowWidth" value="650">
+ <param name="showConservation" value="false">
+ <param name="showQuality" value="false">
+ <param name="showConsensus" value="true">
+ <param name="showFullId" value="false">
+ <param name="RGB" value="F2F2FF">
+ <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
+ </applet> </td>
+ <td width="165">Displays an RFAM RNA fold family with secondary structure annotation</td>
+ </tr>
+ </table></td>
+ </tr>
+ </table>
+ </div>
+ <p> </p>
+ <p>For more JalviewLite examples, follow the links below.
+ <ul>
+ <li><a href="embedded.html">JalviewLite embedded in the web page</a></li>
+ <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>
+ <li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other</a></li>
+ <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page.</a></li>
+ </ul>
+ <!-- InstanceEndEditable --></td>
+ </tr>
+ </table>
+</div>
+</body>
+<!-- InstanceEnd --></html>
git://source.jalview.org / jalview.git / blobdiff