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JAL-1503 update version in GPL header
[jalview.git] / examples / applets.html
diff --git a/examples/applets.html b/examples/applets.html
index fcbcb9a..d715a4d 100755 (executable)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -1,21 +1,22 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
-    * 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/>.
-  -->
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
 <head>
   <TITLE>JalviewLite Examples</TITLE>
   <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /> 
@@ -151,7 +152,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
       <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
       <li ><a href="formComplete.html">Access from Javascript</a></li>
       <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
-      <li ><a href="linkedapplets_ng.html">Linked JalviewLite applets</a></li>
+      <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
   </ul>
 </div>
 
@@ -161,9 +162,13 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
 <!-- boiler plate link to alternate demopage -->
 
 <div style="width: 100%">
-<div style="float:left;">
-</div><div style="border: 2px solid black; align: left; float:right;">
- Working on Snow Leopard or Java out of date ? Try <a href="u_applets.html">the unsigned applet demos</a>
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Examples aren't working ?<br/>Try <a href="u_applets.html">the unsigned applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
 </div>
 </div>
 
@@ -173,8 +178,8 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
 <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>
-<div align="center">
-  <p>
+<p>&nbsp;</p><div align="center">
+  <p align="center">
     <h2>Ferredoxins, chloroplast precursor related UniRef50
       cluster</h2>
     <br /> (15 sequences x 150 residues)
@@ -185,7 +190,14 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
        <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="sortByTree" value="True"/><param name="showSequenceLogo" value="true"/><param name="showGroupConsensus" value="true"/><param name="showFullId" value="false"/>
+<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="sortByTree" value="True"/>
+<param name="showSequenceLogo" value="true"/>
+<param name="showGroupConsensus" value="true"/>
+<param name="showFullId" value="false"/>
    <param name="linkLabel_1" value="Uniprot"/>
    <param name="linkUrl_1"
      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
@@ -204,7 +216,15 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
       <td width="10%" valign="center"><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="showFullId" value="false"/><param name="windowHeight" value="500"/><param name="windowWidth" value="650"/><param name="showFeatureSettings" value="true"/><param name="wrap" value="true"/><param name="showAnnotation" value="false"/>
+<param name="permissions" value="sandbox"/>
+<param name="file" value="uniref50.fa"/>
+<param name="features" value="exampleFeatures.txt"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="500"/>
+<param name="windowWidth" value="650"/>
+<param name="showFeatureSettings" value="true"/>
+<param name="wrap" value="true"/>
+<param name="showAnnotation" value="false"/>
    <param name="linkLabel_1" value="Uniprot"/>
    <param name="linkUrl_1"
      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
@@ -221,7 +241,15 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
       <td width="10%" valign="center"><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="showFullId" value="false"/><param name="windowHeight" value="500"/><param name="windowWidth" value="650"/><param name="wrap" value="true"/><param name="showAnnotation" value="false"/><param name="defaultColour" value="Strand Propensity"/>
+<param name="permissions" value="sandbox"/>
+<param name="file" value="uniref50.fa"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="500"/>
+<param name="windowWidth" value="650"/>
+<param name="wrap" value="true"/>
+<param name="showAnnotation" value="false"/>
+<param name="defaultColour" value="Strand Propensity"/>
+<param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
    <param name="linkLabel_1" value="Uniprot"/>
    <param name="linkUrl_1"
      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
@@ -239,7 +267,14 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
       <td width="10%" valign="center"><applet
    code="jalview.bin.JalviewLite" width="140" height="35"
    archive="jalviewApplet.jar">
-<param name="file" value="jpred_msa.fasta"/><param name="showFullId" value="false"/><param name="windowHeight" value="515"/><param name="windowWidth" value="650"/><param name="showAnnotation" value="true"/><param name="defaultColour" value="Clustal"/>
+<param name="permissions" value="sandbox"/>
+<param name="file" value="jpred_msa.fasta"/>
+<param name="jnetfile" value="jpred_msa.seq.concise"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="515"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" value="true"/>
+<param name="defaultColour" value="Clustal"/>
    <param name="linkLabel_1" value="Uniprot"/>
    <param name="linkUrl_1"
      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
@@ -263,7 +298,13 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
       <td width="10%" valign="center"><applet
    code="jalview.bin.JalviewLite" width="140" height="35"
    archive="jalviewApplet.jar">
-<param name="file" value="RF00031_folded.stk"/><param name="showFullId" value="false"/><param name="windowHeight" value="515"/><param name="windowWidth" value="650"/><param name="showAnnotation" value="true"/><param name="defaultColour" value="Purine/Pyrimidine"/>
+<param name="permissions" value="sandbox"/>
+<param name="file" value="RF00031_folded.stk"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="515"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" value="true"/>
+<param name="defaultColour" value="Purine/Pyrimidine"/>
    <param name="APPLICATION_URL"
      value="http://www.jalview.org/services/launchApp"/>
 </applet>