X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples-jbake%2Ftemplates%2Fjvl_examples.ftl;h=d0e40bf07b86574314735f6cde33cdd531e6d04c;hb=7431a6e01992d55b94a0b4113e19ef65932ca723;hp=9468ab4195b481295b39a3730be87f25c571f1d9;hpb=b9117af25fa6c759fd626717557cc04a68400185;p=jalview.git

diff --git a/examples-jbake/templates/jvl_examples.ftl b/examples-jbake/templates/jvl_examples.ftl
index 9468ab4..d0e40bf 100644
--- a/examples-jbake/templates/jvl_examples.ftl
+++ b/examples-jbake/templates/jvl_examples.ftl
@@ -1,9 +1,10 @@
 
 <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>JalviewLite Button Examples</h2>
+Try out JalviewLite by pressing one of the buttons below.<br/>
+ 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>
+<p>&nbsp;</p><div align="center">
+  <p align="center">
     <h2>Ferredoxins, chloroplast precursor related UniRef50
       cluster</h2>
     <br /> (15 sequences x 150 residues)
@@ -11,7 +12,7 @@
   <table width="90%">
     <tr>
       <td width="10%" valign="center">
-	<@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"uniref50.fa"
+	<@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions" , "file":"uniref50.fa"
 		       , "treeFile":"ferredoxin.nw"
 		       , "userDefinedColour":"C=yellow; R,K,H=FF5555; D,E=5555FF"
 		       , "showFullId":"false"
@@ -23,7 +24,7 @@
 	group consensus and sequence logos are shown below the alignment.</td>
     </tr>
     <tr>
-      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions",
+      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions",
        "file":"uniref50.fa"
 						     , "features":"exampleFeatures.txt"
 						     , "showFeatureSettings":"true"
@@ -48,7 +49,7 @@
 	FER1_MAIZE</td>
     </tr>
     <tr>
-      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
+      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
 						       , "file":"jpred_msa.fasta"
 						       , "jnetfile":"jpred_msa.seq.concise"
 						       , "defaultColour":"Clustal"
@@ -70,7 +71,7 @@
   </p>
   <table width="90%">
     <tr>
-      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
+      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
 						     , "file":"RF00031_folded.stk"
 						     , "defaultColour":"Purine/Pyrimidine"
 						     , "showAnnotation":"true"
@@ -84,3 +85,20 @@
 	secondary structure annotation</td>
     </tr>
   </table>
+  <p>
+    <h2>Linked amino acid and cDNA alignments for homologous proteins</h2>
+  </p>
+  <table width="90%">
+    <tr>
+      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
+						     , "file":"estrogenReceptorCdna.fa"
+						     , "file2":"estrogenReceptorProtein.fa"
+						     , "defaultColour":"Purine/Pyrimidine"
+						     , "showAnnotation":"false"
+						     , "windowHeight":"300"
+						     , "windowWidth":"800"
+						     , "showFullId":"false"} prots=true /></td>
+      <td valign="center">Displays a split window view of protein and its related cDNA</td>
+    </tr>
+  </table>
+</div>