Merge branch 'JAL-957_jbake' into Release_2_8_Branch

diff --git a/examples-jbake/content/appletParameters.html b/examples-jbake/content/appletParameters.html
index 7ed46b9..e02a7be 100644 (file)
--- a/examples-jbake/content/appletParameters.html
+++ b/examples-jbake/content/appletParameters.html
@@ -2,14 +2,15 @@ title=Applet Parameters
 type=page
 status=published
 ~~~~~~
+<h2>JalviewLite Applet Parameter Documentation</h2>
 <p>
-<ul>
-<li>Parameters are described <a href="#parameters">below</a></li>
-<li>The javascript API is described <a
-href="jalviewLiteJs.html">here</a></li>
-</ul></strong>
+The JalviewLite applet is configured through a series of applet parameters,
+which are described <a href="#parameters"> below</a>. Once initialised,
+the applet can be interacted with <em>via</em> its 
+<a href="jalviewLiteJs.html">Javascript API</a>.
+</p><p><strong>Issues arising from tightening of Java Security default settings</strong><br/>JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java are not compatible with these settings, so if you find that you cannot see any of the examples on the left, try the <a href="u_applets.html">unsigned applet examples</a>.
 </p>
-    <p>Additional <a href="#appletdeploymentnotes">applet deployment notes are below</a>.</p>
+    <p>For additional deployment notes, <a href="#appletdeploymentnotes">see below</a>.</p>
            <p><h2>Applet Parameters</h2><br/>The applet takes the following initialisation parameters.</p>
         <a name="parameters"></a>        <table width="97%" class="borderTable" align="center" >
           <tr> 

diff --git a/examples-jbake/templates/jvl_examples.ftl b/examples-jbake/templates/jvl_examples.ftl
index fc21388..f2bf8b1 100644 (file)
--- a/examples-jbake/templates/jvl_examples.ftl
+++ b/examples-jbake/templates/jvl_examples.ftl
@@ -3,8 +3,8 @@
 <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)

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 167df36..84f61e4 100644 (file)
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -159,14 +159,15 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
 
 
 <!-- content start -->
+<h2>JalviewLite Applet Parameter Documentation</h2>
 <p>
-<ul>
-<li>Parameters are described <a href="#parameters">below</a></li>
-<li>The javascript API is described <a
-href="jalviewLiteJs.html">here</a></li>
-</ul></strong>
+The JalviewLite applet is configured through a series of applet parameters,
+which are described <a href="#parameters"> below</a>. Once initialised,
+the applet can be interacted with <em>via</em> its 
+<a href="jalviewLiteJs.html">Javascript API</a>.
+</p><p><strong>Issues arising from tightening of Java Security default settings</strong><br/>JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java are not compatible with these settings, so if you find that you cannot see any of the examples on the left, try the <a href="u_applets.html">unsigned applet examples</a>.
 </p>
-    <p>Additional <a href="#appletdeploymentnotes">applet deployment notes are below</a>.</p>
+    <p>For additional deployment notes, <a href="#appletdeploymentnotes">see below</a>.</p>
            <p><h2>Applet Parameters</h2><br/>The applet takes the following initialisation parameters.</p>
         <a name="parameters"></a>        <table width="97%" class="borderTable" align="center" >
           <tr> 

diff --git a/examples/applets.html b/examples/applets.html
index 05a50ae..a57efb7 100755 (executable)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -177,8 +177,8 @@ 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)

diff --git a/examples/u_applets.html b/examples/u_applets.html
index f49c38a..93164cb 100644 (file)
--- a/examples/u_applets.html
+++ b/examples/u_applets.html
@@ -177,8 +177,8 @@ 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)