From 66830878ef77fb7030de00ab6e302ef9936f0a3b Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 9 Nov 2012 15:32:04 +0000
Subject: [PATCH] more tweaking of static pages and rejigging applet parameter
 documentation for accessibility

---
 examples/appletParameters.html |  249 ++++++++++++++++++++--------------------
 examples/applets.html          |   11 +-
 examples/css/style.css         |   20 +++-
 3 files changed, 146 insertions(+), 134 deletions(-)

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 78a5eb7..9350c4b 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -163,129 +163,9 @@ document.onclick = mclose;
 								href="jalviewLiteJs.html">here</a></li>
 						</ul></strong>
 					</p>
-					
-        <h3 align="left">Useful to know!!</h3>
-        <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>
-            <font face="Courier New, Courier, mono" align="left">&lt;applet code=&quot;jalview.bin.JalviewLite&quot;<em><strong> 
-            archive=&quot;jalviewApplet.jar, mydata.zip&quot;</strong></em>&gt;<br>
-            </font></li>
-          <li> Use Jalview for input to a HTML form. For an example of how to 
-            code this using Javascript, click <a href="formComplete.html">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>
-        </ul>
-        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.8</font></strong></p>
-        <ul>
-        <li><font size="2">Normalised sequence logo display
-        </font></li>
-        <li><font size="2">RNA secondary structure annotation row
-        </font></li>
-<li><font size="2">Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></font></li>
-<li>To use Jmol as the structure viewer for Jalview, you must include 
-            the jar file in the applet archive argument thus:<br>
-            <pre>archive=&quot;jalviewApplet.jar,Jmol-12.2.4.jar&quot;</pre></font>
-          </li>
-          <li>Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have 
-            Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the 
-            original Jalview structure viewer will still be available. <br>
-          </li>
-          
-        </ul>
-        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7</font></strong></p>
-        <ul>
-        <li><font size="2">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></font>
-        </li>
-        <li><font size="2">New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
-        </font></li></ul>
-        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>
-        <ul>
-        <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series</font></li>
-          <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from 
-          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><font size="2">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).</font></li>
-		</ul>
-        <br><strong><font size="2">**NEW FEATURES** in Jalview 2.5</font></strong></p>
-        <ul>
-        <li><font size="2">New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</font></li>
-		</ul>        
-        <br><strong><font size="2">**NEW FEATURES** in Jalview 2.4</font></strong></p>
-        <ul>
-        <li><font size="2">New applet API methods for feature display control, views, and obtaining current selection via javascript.</font></li>
-          <li><font size="2">Group show and hide parameters:
-        &quot;showfeaturegroups&quot; and
-        &quot;hidefeaturegroups&quot;. Both take a list
-        of feature group names (separarated by &quot;|&quot; by default) to hide or show on the displayed
-        alignment.</font>
-        </li>
-        <li><font size="2">Regular expressions can be used in URL links for sequence IDs.</font></li>
-        <li><font size="2">&quot;debug&quot; parameter to control verbosity of the applet's console output.</font></li>
-        <li><font size="2">&quot;showbutton&quot; parameter to disable launch button and open JalviewLite immediatly.</font></li>
-        <li><font size="2">&quot;nojmol&quot; parameter to disable check for Jmol classes.</font></li>
-        </ul><br>
-        <strong><font size="2">**NEW FEATURES** in Jalview 2.3</font></strong></p>
-        <ul>
-          <li><font size="2">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 
-            multiple PDB files by adding an incremental value to PDBFile (up to 
-            10). It is also possible to map specific sequences to specific chains 
-            by using the following notation:<br>
-            <br>
-            &lt;param name=&quot;PDBFile&quot; value=&quot;First.pdb SeqA SeqB 
-            SeqC&quot;&gt; </font><br>
-            <font size="2">&lt;param name=&quot;PDBFile2&quot; value=&quot;Second.pdb 
-            A=SeqA B=SeqB C=SeqC&quot;&gt; </font><br>
-            <font size="2">&lt;param name=&quot;PDBFile3&quot; value=&quot;Third.pdb 
-            D=SeqX B=SeqY C=SeqZ&quot;&gt; </font> <br>
-          </li>
-          <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="../versions.html">versions archive if you want to download the old Jmol applet</a>.</li> 
-            <p>&nbsp;</p>
-          </li>
-        </ul>
-        <strong><font size="2">**NEW FEATURES** in Jalview 2.1</font></strong> 
-        <ul>
-          <li>Jalview Applet can read and display JNet secondary structure annotation 
-            directly via the <strong>jnetfile</strong> parameter. <br>
-          </li>
-          <li>Param <font face="Courier New, Courier, mono">UserDefinedColour</font><em> 
-            </em>- specify your own colours for each residue using a semi colon 
-            separated list. Multiple residues can be assigned the same colour 
-            using commas. eg:<br>
-            <font face="Courier New, Courier, mono">&lt;param name=&quot;userDefinedColour&quot; 
-            value=&quot;D,E=red; K,R,H=0022FF; C=yellow&quot;&gt;</font><br>
-          </li>
-          <li>Param <font face="Courier New, Courier, mono">showFeatureSettings</font>
-            - this will display the feature settings window when the applet starts.<br>
-          </li>
-          <li>Param <font face="Courier New, Courier, mono">Application_URL value=&quot;http://www.jalview.org/services/launchApp&quot;<br>
-            </font>This calls a servlet which creates a JNLP file with the alignment 
-            file, annotations file and features file of the applet as arguments. 
-            If the user has Java installed, the returned JNLP file should start 
-            up the full Jalview Application. BUT this does not currently work 
-            for alignment files added to the applet in a zip file.<br>
-          </li>
-          <li>Alignment file can be a series of parameters using eg PFAM format 
-            <br>
-            <font face="Courier New, Courier, mono">&lt;param name=&quot;sequence1&quot; 
-            value=&quot;Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI&quot;&gt;<br>
-            &lt;param name=&quot;sequence2&quot; value=&quot;FER1_PEA/14-29 TSFLRTQPMPMSVTTT&quot;&gt;<br>
-            </font>(All the usual Jalview File formats are valid, however each 
-            new line in an alignment file must be entered as a parameter)<font face="Courier New, Courier, mono"><br>
-            </font> </li>
-        </ul>
-        <a name="parameters"></a>        <table width="97%" border="1" align="center" >
+     <p>Additional <a href="#appletdeploymentnotes">applet deployment notes are 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> 
             <td width="103" height="23"><strong>&lt;param name=&quot;&quot;</strong></td>
             <td width="80" ><strong>value=&quot;&quot;&gt;</strong></td>
@@ -578,6 +458,129 @@ document.onclick = mclose;
           <td>Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format</td>
           </tr>
                   </table>
+                  <p><h2><a name="appletdeploymentnotes"/>Notes on applet deployment</h2><br/>
+        <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;<br>
+            </pre></li>
+          <li> Use Jalview for input to a HTML form. For an example of how to 
+            code this using Javascript, click <a href="formComplete.html">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>
+        </ul>
+        <p><strong>**NEW FEATURES** in Jalview 2.8</strong></p>
+        <ul>
+        <li>Normalised sequence logo display
+        </li>
+        <li>RNA secondary structure annotation row
+        </li>
+<li>Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></li>
+<li>To use Jmol as the structure viewer for Jalview, you must include 
+            the jar file in the applet archive argument thus:<br>
+            <pre>archive=&quot;jalviewApplet.jar,Jmol-12.2.4.jar&quot;</pre>
+          </li>
+          <li>Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have 
+            Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the 
+            original Jalview structure viewer will still be available. <br>
+          </li>
+          
+        </ul>
+        <p><strong>**NEW FEATURES** in Jalview 2.7</strong></p>
+        <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>
+        <li>New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
+        </li></ul>
+        <p><strong>**NEW FEATURES** in Jalview 2.6</strong></p>
+        <ul>
+        <li>Jmol compatibility updated to Jmol 12.1.x series</li>
+          <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from 
+          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>
+        <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
+        &quot;hidefeaturegroups&quot;. Both take a list
+        of feature group names (separarated by &quot;|&quot; by default) to hide or show on the displayed
+        alignment.
+        </li>
+        <li>Regular expressions can be used in URL links for sequence IDs.</li>
+        <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>
+          <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 
+            multiple PDB files by adding an incremental value to PDBFile (up to 
+            10). It is also possible to map specific sequences to specific chains 
+            by using the following notation:<br>
+            <br>
+            <pre>
+            &lt;param name=&quot;PDBFile&quot; value=&quot;First.pdb SeqA SeqB 
+            SeqC&quot;&gt;<br>
+            &lt;param name=&quot;PDBFile2&quot; value=&quot;Second.pdb 
+            A=SeqA B=SeqB C=SeqC&quot;&gt;<br>
+            &lt;param name=&quot;PDBFile3&quot; value=&quot;Third.pdb 
+            D=SeqX B=SeqY C=SeqZ&quot;&gt;<br>
+            </pre>
+          </li>
+          <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="../versions.html">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>
+          <li>Jalview Applet can read and display JNet secondary structure annotation 
+            directly via the <strong>jnetfile</strong> parameter. <br>
+          </li>
+          <li>Param &quot;UserDefinedColour&quot; - specify your own colours for each residue using a semi colon 
+            separated list. Multiple residues can be assigned the same colour 
+            using commas. eg:<br>
+            <pre>&lt;param name=&quot;userDefinedColour&quot; 
+            value=&quot;D,E=red; K,R,H=0022FF; C=yellow&quot;&gt;</pre>
+          </li>
+          <li>Param &quot;showFeatureSettings&quot;
+            - this will display the feature settings window when the applet starts.
+          </li>
+          <li>Param &quot;Application_URL&quot; value=&quot;http://www.jalview.org/services/launchApp&quot;<br/>
+            This calls a servlet which creates a JNLP file with the alignment 
+            file, annotations file and features file of the applet as arguments. 
+            If the user has Java installed, the returned JNLP file should start 
+            up the full Jalview Application. BUT this does not currently work 
+            for alignment files added to the applet in a zip file.
+            <br/>Look at the XML comments in the file downloaded from <a href="http://www.jalview.org/services/launchApp">The LaunchApp page</a> for full documentation.
+          </li>
+          <li>Alignment file can be a series of parameters using eg PFAM format 
+            <br>
+            <pre>&lt;param name=&quot;sequence1&quot; 
+            value=&quot;Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI&quot;&gt;<br>
+            &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>
+        
 </div>
 
 <div id ="footer">
diff --git a/examples/applets.html b/examples/applets.html
index 9437aed..8862db0 100755
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -162,15 +162,8 @@ document.onclick = mclose;
     saving files, and running web service jobs. This is mostly due to
     security restrictions imposed on applets.</p>
    <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
-      <p>Pressing one of the buttons below will load up JalviewLite,
-       a cut down version parameters.
-    </strong></a>
-   </p>
-   of Jalview, which runs within your web browser.
-   </p>
+    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>Ferredoxins, chloroplast precursor related UniRef50
diff --git a/examples/css/style.css b/examples/css/style.css
index 67d57a0..4dbb1a3 100644
--- a/examples/css/style.css
+++ b/examples/css/style.css
@@ -280,8 +280,15 @@ float:left;
 padding-top:29px;
 margin-right:50px;
 }
-
-
+#content ul
+{
+	list-style-type: disc;
+}
+#content li
+{
+	margin-left: 11px;
+	padding-bottom:11px;
+}
 	
 #sideNav li
 {
@@ -376,6 +383,15 @@ background: url("../images/train-arrow-3-normal.png") no-repeat scroll 0 0 trans
     padding-left: 5px;
 }
 
+#content .borderTable td
+{
+	border: 1px solid black;
+}
+#content .borderTable tr
+{
+	border-bottom: 2px solid black;
+}
+
 td
 {
     vertical-align: middle;
-- 
1.7.10.2