Merge branch 'JAL-1286' into Release_2_8_Branch
[jalview.git] / examples / applets.html
index 2ab29a3..255f104 100755 (executable)
@@ -79,7 +79,11 @@ function mcancelclosetime()
 document.onclick = mclose; 
 // -->
 </script>
-
+<script>
+<!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+</script>
 </head>
 
 
@@ -87,10 +91,10 @@ document.onclick = mclose;
 
 
 <div id="header">
-<div id="logo"><a href="/" title="Home"></a></div>
+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
 <ul id="buttons">
 <li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
+<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
 </ul>
 </div>
 
@@ -99,39 +103,38 @@ document.onclick = mclose;
 <div id="navInner">
 
 <ul id="sddm">
- <li><a href="#">Home</a></li>
- <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
   <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Documentation</a>
-  <a href="#">Publications</a>
-  <a href="#">Credits</a>
-  <a href="#">Screenshots</a>
+  <a href="http://www.jalview.org/about/documentation">Documentation</a>
+  <a href="http://www.jalview.org/about/citation">Publications</a>
+  <a href="http://www.jalview.org/about/credits">Credits</a>
   </div>
  </li>
- <li><a href="#">FAQ</a></li>
- <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
   <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">News Mailing List</a>
-  <a href="#">Discussion Mailing List</a>
-  <a href="#">Links</a>
-  <a href="#">Community News</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+  <a href="http://www.jalview.org/community/links">Links</a>
+  <a href="http://www.jalview.org/community/community-news">Community News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
   <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Release History</a>
-  <a href="#">Jalview Bug Tracker</a>
-  <a href="#">Jalview Git Web</a>
-  <a href="#">Development News</a>
+  <a href="http://www.jalview.org/development/release-history">Release History</a>
+  <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+  <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+  <a href="http://www.jalview.org/development/development-news">Development News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
   <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Training Courses</a>
-  <a href="#">Training News</a>
+  <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+  <a href="http://www.jalview.org/training/training-news">Training News</a>
   </div>
  </li>
- <li><a href="#" class="download-right">Download</a></li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 </ul>
 <div style="clear:both"></div>
 </div>
@@ -139,193 +142,176 @@ document.onclick = mclose;
 </div>
 
 
-<div id="pageWrap">
+ <div id="pageWrap">
 
-<div id="sideNav">
-<ul>
-<li class="jvlite-nav-title"><a href="applets.html">JalviewLite Examples</a></li>
-<li><a href="appletParameters.html">Applet Parameters</a></li>
-<li><a href="jalviewLiteJs.html">Javascript API</a></li>
-<li><a href="formComplete.html">in-page API demo</a></li>
-<li><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
-<li><a href="embeddedWJmol.html">Sequence And Structure demo</a></li>
-</ul>
-</div>
+  <div id="sideNav">
+   <ul>
+    <li class="jvlite-nav-title"><a href="applets.html">JalviewLite
+      Examples</a></li>
+    <li><a href="appletParameters.html">Applet Parameters</a></li>
+    <li><a href="jalviewLiteJs.html">Javascript API</a></li>
+    <li><a href="formComplete.html">in-page API demo</a></li>
+    <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
+    <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
+   </ul>
+  </div>
 
-<div id="content" class="content">
-        <p>JalviewLite is a web based version of Jalview, which runs as a Java applet in or on a web page. It's one of the easiest ways of providing an interactive
-          display for precalculated alignments, features and annotations files.
-          It lacks some functionality available in the Jalview Desktop, however, such
-          as making images, saving files, and running web service jobs. This is mostly due to security
-          restrictions imposed on applets.</p>
-        <p align="left">For more information on how to use the applet in your
-          website, see <a href="appletParameters.html"><strong>full list of applet
-          parameters.</strong></a></p>
-        <p> Pressing one of the buttons below will load up JalviewLite, a cut down version
-          of Jalview, which runs within your web browser. </p>
-        <H4 align="center"> Ferredoxins, chloroplast precursor related UniRef50
-          cluster<br>
-          (15 sequences x 150 residues)</H4>
-        <div align="center"> </div>
-        <div align="center">
-          <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="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">
-                        <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?$SEQUENCE_ID$">
-                                               <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
-                      </applet></td>
-                    <td width="165">User Defined Colours, loads an associated Newick
-                      format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment.</td>
-                  </tr>
-                </table></td>
-            </tr>
-          </table>
-          <p>&nbsp;</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="uniref50.fa">
-                        <param name="features" value="exampleFeatures.txt">
-                        <param name="showFeatureSettings" value="true">
-                        <param name="wrap" value="true">
-                        <param name="showAnnotation" value="false">
-                        <param name="windowHeight" value="500">
-                        <param name="windowWidth" value="650">
-                        <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 features file on the alignment</td>
-                  </tr>
-                </table></td>
-            </tr>
-          </table>
-            <p>&nbsp;</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,JmolApplet-12.2.4.jar">
-                        <param name="file" value="uniref50.fa">
-                        <!-- <param name="debug" value="true">
+  <div id="content" class="content">
+   <p>JalviewLite is a web based version of Jalview, which runs as a
+    Java applet in or on a web page. It's one of the easiest ways of
+    providing an interactive display for precalculated alignments,
+    features and annotations files. It lacks some functionality
+    available in the Jalview Desktop, however, such as making images,
+    saving files, and running web service jobs. This is mostly due to
+    security restrictions imposed on applets.</p>
+   <p align="left">
+    Try out JalviewLite by pressing one of the buttons below. For more information on how to use the applet in your website, see the <a
+     href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+   <div align="center">
+    <p>
+     <h2>Ferredoxins, chloroplast precursor related UniRef50
+      cluster</h2>
+     <br /> (15 sequences x 150 residues)
+    </p>
+    <table width="90%">
+     <tr>
+      <td width="10%" valign="center"><applet
+        code="jalview.bin.JalviewLite" width="140" height="35"
+        archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox">
+       <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="sortByTree" value="True">
+        <param name="showSequenceLogo" value="true">
+         <param name="showGroupConsensus" value="true">
+          <param name="linkLabel_1" value="Uniprot">
+           <param name="linkUrl_1"
+            value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+            <param name="linkLabel_2" value="Expasy">
+             <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 valign="center">User Defined Colours, loads an associated
+       Newick format tree file which is used to sort the alignment, and
+       group consensus and sequence logos are shown below the alignment.</td>
+     </tr>
+     <tr>
+      <td width="10%" valign="center"><applet
+        code="jalview.bin.JalviewLite" width="140" height="35"
+        archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox">
+       <param name="file" value="uniref50.fa">
+        <param name="features" value="exampleFeatures.txt">
+         <param name="showFeatureSettings" value="true">
+          <param name="wrap" value="true">
+           <param name="showAnnotation" value="false">
+            <param name="windowHeight" value="500">
+             <param name="windowWidth" value="650">
+              <param name="showFullId" value="false">
+       <param name="linkLabel_1" value="Uniprot">
+        <param name="linkUrl_1"
+         value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+         <param name="linkLabel_2" value="Expasy">
+          <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 valign="center">Displays a features file on the alignment</td>
+     </tr>
+     <tr>
+      <td width="10%" valign="center"><applet
+        code="jalview.bin.JalviewLite" width="140" height="35"
+        archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+<param name="permissions" value="sandbox">
+       <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">
-                        <param name="windowWidth" value="650">
-                        <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">
-                        <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
-                      </applet> </td>
-                    <td width="165">Associates PDB file 1GAQ with sequence FER1_MAIZE</td>
-                  </tr>
-                </table></td>
-            </tr>
-          </table>
-          <p>&nbsp;</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>&nbsp;</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>&nbsp;</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>
-</div>
+        <param name="defaultColour" value="Strand Propensity">
+         <param name="wrap" value="true">
+          <param name="showAnnotation" value="false">
+           <param name="windowHeight" value="500">
+            <param name="windowWidth" value="650">
+             <param name="showFullId" value="false">
+       <param name="linkLabel_1" value="Uniprot">
+        <param name="linkUrl_1"
+         value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+         <param name="linkLabel_2" value="Expasy">
+          <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">
+        <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
+       </applet></td>
+      <td valign="center">Associates PDB file 1GAQ with sequence
+       FER1_MAIZE</td>
+     </tr>
+     <tr>
+      <td width="10%" valign="middle"><applet
+        code="jalview.bin.JalviewLite" width="140" height="35"
+        archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox">
+       <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="linkLabel_1" value="Uniprot">
+        <param name="linkUrl_1"
+         value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+         <param name="linkLabel_2" value="Expasy">
+          <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 valign="center">Displays a Multiple Sequence Alignment
+       Based JNet Prediction for a Sequence</td>
+     </tr>
+    </table>
+    <p>
+    <h2>RF00031 RFAM Alignment with per sequence secondary
+     structure</h2>
+    </p>
+    <table width="90%">
+     <tr>
+      <td width="10%" valign="center"><applet
+        code="jalview.bin.JalviewLite" width="140" height="35"
+        archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox">
+       <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="APPLICATION_URL"
+        value="http://www.jalview.org/services/launchApp">
+       </applet></td>
+      <td valign="center">Displays an RFAM RNA fold family with
+       secondary structure annotation</td>
+     </tr>
+    </table>
+   </div>
+  </div>
+ </div>
 
 <div id ="footer">
 <div id="innerFooter">
-<div id="copyright"><p>Copyright all rights reserved 2012</p></div>
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
 <div id="cite">
 <p>
 If you use Jalview in your work, please cite this publication:
@@ -334,11 +320,11 @@ If you use Jalview in your work, please cite this publication:
 <p>
 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
-Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
 </p>
 </div>
 </div>
 </div>
 </body>
 </html>
-          
\ No newline at end of file
+