JAL-1996 added link for viewing example source codes, changed release history outline...

diff --git a/examples/appletDeployment.html b/examples/appletDeployment.html
index 0301225..7fcca00 100644 (file)
--- a/examples/appletDeployment.html
+++ b/examples/appletDeployment.html
@@ -46,7 +46,7 @@
   </tr>
 </table>
 
-<p>The snippet below shows a mininmal code for embeding Jalview applet into a web page.    
+<p>To run Jalview applet in your web page download the Jars listed above. The snippet below shows a minimal code for embedding Jalview applet into a web page.    
 <pre><code>
 &lt;applet code="jalview.bin.JalviewLite" width="756" height="560" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar"&gt;
        &lt;param name="permissions" value="sandbox" /&gt;
@@ -63,26 +63,38 @@
 &lt;/applet&gt;
 </code></pre> 
 
-For more information and advanced options, see the <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters page</strong></a>, and other documentation in the links to the left. 
-  <ul>
-          <li>Package all your data files into a single (or multiple) zip / jar 
-            files. This is very useful to reduce download time of large data files. 
-            The applet archive tag can take multiple entries separated by commas, 
-            eg<br>
-            <pre>&lt;applet code=&quot;jalview.bin.JalviewLite&quot;<em><strong> archive=&quot;jalviewApplet.jar, mydata.zip&quot;</strong></em>&gt;
-            </pre></li>
-          <li> Use Jalview for input to a HTML form. For an example of how to 
-            code this using Javascript, click <a href="javascript:doSubmit('formComplete')">here</a>. 
-            <br>
-          </li>
-          <li>Embed Jalview into the web page, without the &quot;Start Jalview&quot; 
-            button by setting the embed parameter to true;<br>
-            &lt;param name=&quot;embedded&quot;
-          value=&quot;true&quot;&gt; </li>
-       <li><a href="javascript:doSubmit('appletParameters')">View full list of supported parameters here.</a> </li>
-        </ul>
-        
-        <p><strong>**NEW FEATURES** in Jalview 2.9</strong></p> 
+
+
+
+<ul>
+       <li>View full list of <a href="javascript:doSubmit('appletParameters')"> supported applet parameters here.</a></li>
+       <li>Package all your data files into a single (or multiple) zip /
+               jar files. This is very useful to reduce download time of large data
+               files. The applet archive tag can take multiple entries separated by
+               commas, eg<br> <pre>&lt;applet code=&quot;jalview.bin.JalviewLite&quot;<em><strong> archive=&quot;jalviewApplet.jar, mydata.zip&quot;</strong></em>&gt;
+            </pre>
+       </li>
+       <li>Use Jalview for input to a HTML form. For an example of how to
+               code this using Javascript, click <a
+               href="javascript:doSubmit('formComplete')">here</a>. <br>
+       </li>
+       <li>Embed Jalview into the web page, without the &quot;Start
+               Jalview&quot; button by setting the embed parameter to true;<br>
+               &lt;param name=&quot;embedded&quot; value=&quot;true&quot;&gt;
+       </li>
+       <li>For more examples, see the links to the left.</li>
+</ul>
+
+<table border="1" width=80%>
+       <tr><th colspan="2">Applet Release History</th>
+       <tr>
+               <th>Release</th>
+
+               <th>New Features / required changes</th>
+       </tr>
+       <tr>
+               <td><strong>2.9<br>(Latest)</strong></td>
+               <td>
         <ul>
         <li>Split Views for cDNA and Protein alignments<br/>Specify second alignment with 'file2' parameter, and set cDNA/Protein column scaling with scaleProteinAsCdna
         </li>
@@ -95,9 +107,11 @@ For more information and advanced options, see the <a href="javascript:doSubmit(
             <pre>archive=&quot;jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,<font color="red">java-json.jar,json_simple-1.1.jar</font>&quot;</pre>              
        </li>
         </ul>
-        </p>
-        <p><strong>**NEW FEATURES** in Jalview 2.8</strong></p> 
-        <ul>
+               </td>
+       </tr>
+       <tr>
+               <td><strong>2.8</strong></td>
+               <td><ul>
         <li>Normalised sequence logo display
         </li>
         <li>RNA secondary structure annotation row
@@ -112,9 +126,11 @@ For more information and advanced options, see the <a href="javascript:doSubmit(
             original Jalview structure viewer will still be available. <br>
           </li>
           
-        </ul>
-        <p><strong>**NEW FEATURES** in Jalview 2.7</strong></p>
-        <ul>
+        </ul></td>
+       </tr>
+       <tr>
+               <td><strong>2.7</strong></td>
+               <td><ul>
         <li>Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</li>
         <li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (&lt;param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul>
         </li>
@@ -127,13 +143,17 @@ For more information and advanced options, see the <a href="javascript:doSubmit(
           the Jmol binary distribution available at the Jmol Sourceforge site, 
           or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
           <li>Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</li>
-  </ul>
-        <br><strong>**NEW FEATURES** in Jalview 2.5</strong></p>
-        <ul>
-        <li>New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</li>
-  </ul>        
-        <br><strong>**NEW FEATURES** in Jalview 2.4</strong></p>
-        <ul>
+  </ul></td>
+       </tr>
+       <tr>
+               <td><strong>2.5</strong></td>
+               <td><ul>
+        <li>New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</li>  </ul>
+    </td>
+       </tr>
+       <tr>
+               <td><strong>2.4</strong></td>
+               <td><ul>
         <li>New applet API methods for feature display control, views, and obtaining current selection via javascript.</li>
           <li>Group show and hide parameters:
         &quot;showfeaturegroups&quot; and
@@ -145,9 +165,11 @@ For more information and advanced options, see the <a href="javascript:doSubmit(
         <li>&quot;debug&quot; parameter to control verbosity of the applet's console output.</li>
         <li>&quot;showbutton&quot; parameter to disable launch button and open JalviewLite immediatly.</li>
         <li>&quot;nojmol&quot; parameter to disable check for Jmol classes.</li>
-        </ul><br>
-        <strong>**NEW FEATURES** in Jalview 2.3</strong></p>
-        <ul>
+        </ul></td>
+       </tr>
+       <tr>
+               <td><strong>2.3</strong></td>
+               <td><ul>
           <li>Note that Parameter &quot;PDBFile&quot; now takes 
             the PDB file followed by a space separated list of alignment sequence 
             ids to associate the structure to. It is also possible to associate 
@@ -167,11 +189,12 @@ For more information and advanced options, see the <a href="javascript:doSubmit(
           <li>Note parameter &quot;PDBSeq&quot; is no longer required.<br>
           </li>
           <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="/development">versions archive if you want to download the old Jmol applet</a>.</li> 
-            <p>&nbsp;</p>
-          </li>
-        </ul>
-        <strong>**NEW FEATURES** in Jalview 2.1</strong> 
-        <ul>
+          
+        </ul></td>
+       </tr>
+       <tr>
+               <td><strong>2.1</strong></td>
+               <td><ul>
           <li>Jalview Applet can read and display JNet secondary structure annotation 
             directly via the <strong>jnetfile</strong> parameter. <br>
           </li>
@@ -199,5 +222,9 @@ For more information and advanced options, see the <a href="javascript:doSubmit(
             &lt;param name=&quot;sequence2&quot; value=&quot;FER1_PEA/14-29 TSFLRTQPMPMSVTTT&quot;&gt;<br>
             </pre>(All the usual Jalview File formats are valid, however each 
             new line in an alignment file must be entered as a parameter)</li>
-        </ul>
+        </ul></td>
+       </tr>
+</table>
+
+        
 <!-- content end -->

diff --git a/examples/applets.html b/examples/applets.html
index 02d1d09..fd18098 100644 (file)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -27,7 +27,8 @@
 
 <p align="left">
 <h2>JalviewLite Button Examples</h2>
-Try out JalviewLite by pressing one of the buttons below.<br/>
+Try out JalviewLite by pressing one of the buttons below. 
+  <a href="view-source:http://www.jalview.org/builds/develop/examples/applets.html" target="_blank">View the source for the examples below here</a><br/>
  For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletDeployment')"><strong>applet deployment,</strong></a> <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters,</strong></a> and other documentation in the links to the left.</p>
 <p>&nbsp;</p><div align="center">
   <p align="center">

diff --git a/examples/embedded.html b/examples/embedded.html
index d4e00f9..77b5b5a 100644 (file)
--- a/examples/embedded.html
+++ b/examples/embedded.html
@@ -37,6 +37,7 @@
     <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
       Jalview Alignment Annotations File</li>
   </ul>
+  <a href="view-source:http://www.jalview.org/builds/develop/examples/embedded.html" target="_blank">View the source code for this example here</a><p>
   <applet
    code="jalview.bin.JalviewLite" width="756" height="560"
    archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">

diff --git a/examples/formComplete.html b/examples/formComplete.html
index dc651fb..97d28ea 100644 (file)
--- a/examples/formComplete.html
+++ b/examples/formComplete.html
@@ -33,7 +33,7 @@
 <p>Using the Javascript API to fill out forms using data from JalviewLite
 <br/>Click the Javascript buttons below to interact with the Applet
 instance on the page.</p>
-View the source in your browser to see how it has been done. <br/>
+  <a href="view-source:http://www.jalview.org/builds/develop/examples/embedded.html" target="_blank">View the source here to see how it has been done</a><br/>
 <a name="api">View the full <a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite API documentation</a>.</a>
 <applet code="jalview.bin.JalviewLite" width="0" height="0"
        archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar" name="Jalview">

diff --git a/examples/javascriptLaunch.html b/examples/javascriptLaunch.html
index 47f60e8..8d1b1a6 100644 (file)
--- a/examples/javascriptLaunch.html
+++ b/examples/javascriptLaunch.html
@@ -115,7 +115,7 @@ archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_
 <param name="showbutton" value="false"/>
 </applet>
 
-<h2>Javascript Launch Button</h2><p>The button below demonstrates how JalviewLite can be launched via a javascript action.</p>
+<h2>Javascript Launch Button</h2><p>The button below demonstrates how JalviewLite can be launched via a javascript action.  <a href="view-source:http://www.jalview.org/builds/develop/examples/javascriptLaunch.html" target="_blank">View the source here to see how it has been done</a></p>
 
   <input type="button" name="Button1" value="Start"
 onClick="startJalview('plantfdx.fa','Button1.alignment','alwvar')"/>

diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index 4df08fc..c6b9ed2 100644 (file)
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -34,7 +34,7 @@
 
     <h2>JalviewLite Linked Applets Demo</h2>
     <p>The two applets below use <a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
-    </p>
+    <a href="view-source:http://www.jalview.org/builds/develop/examples/linkedapplets_ng.html" target="_blank">View the source here to see how it has been done</a></p>
 
 
 <applet