X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Fapplets.html;h=1086416406c94cdd44f45e6a2570998726251cfc;hb=ee1c37b3e5d47128cb71ec2aa51c6e4a69dddbbe;hp=eeb0d8725bab74226bfbbe07977ba58572f3a86d;hpb=6fa12685f5a274baad0f65db6241de29b7e5dbbf;p=jalview.git

diff --git a/examples/applets.html b/examples/applets.html
index eeb0d87..1086416 100755
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -15,7 +15,7 @@
         <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 a cut down version
+        <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>
@@ -29,19 +29,17 @@
                     <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="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="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?$SEQUENCE_ID$">
 						<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</td>
+                      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>
@@ -74,16 +72,16 @@
                 </table></td>
             </tr>
           </table>
-          <p>&nbsp;</p>
+            <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-12.1.13.jar">
-                        <param name="file" value="uniref50.fa">
-                        <param name="defaultColour" value="Strand Propensity">
+			       	archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+                        <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">
@@ -102,36 +100,5 @@
                 </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>
-        </div>
+          <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>
         <!-- InstanceEndEditable --></td>
    </tr>
  </table>
</div>
</body>
<!-- InstanceEnd --></html>
\ No newline at end of file