X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=90280a354ee5393625acb3f6863c4b95cd27c033;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=fdcdb33ddfca222f15169d86821e1b316f5ccbe7;hpb=1d415c4766233d4710950f6b5384eab64bb629bb;p=jalview.git

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index fdcdb33..90280a3 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -1,6 +1,6 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -17,6 +17,9 @@
  * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
 
+
+<div id="view_decorated" name="view_decorated"  style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#appletParameters"> here</a> to view decorated page</b></div>
+
 <!-- content start -->
 <h2>JalviewLite Applet Parameter Documentation</h2>
 <p>
@@ -43,11 +46,23 @@ the applet can be interacted with <em>via</em> its
             <td>fileName</td>
             <td>The file to open, must be on same server as the applet.</td>
           </tr>
-          <tr> 
-            <td>file2</td>
-            <td>fileName</td>
-            <td>A second file to open. If one file is nucleotide and the other peptide, and at least one peptide sequence
-            is the translation of one of the nucleotide sequences, then alignments will be displayed linked in a split frame (<em>since 2.9</em>).</td>
+              <tr>
+                <td>file2</td>
+                <td>fileName</td>
+                <td>A second file to open and show linked in a Split Frame
+                  view. If one file is nucleotide and the other peptide, and at
+                  least one peptide sequence matches the translation of one of the
+                  nucleotide sequences, then gaps will be inserted into the
+                  sequences in this file to match the aligned columns for
+                  corresponding positions in the primary alignment file. This
+                  parameter is ignored if enableSplitFrame is set to false (<em>since
+                    2.9</em>).
+                </td>
+              </tr>
+            <tr> 
+            <td>enableSplitFrame</td>
+            <td>true or false (default true)</td>
+            <td>Enable or disable the display of linked cDNA and Protein alignments in a split frame (<em>since 2.9</em>).</td>
           </tr>
           <tr> 
             <td>sequence1,<br>
@@ -103,6 +118,14 @@ the applet can be interacted with <em>via</em> its
             <td>Default is no colour.</td>
           </tr>
           <tr> 
+            <td>defaultColourNuc</td>
+            <td>A colour scheme (from the list above) to apply to Nucleotide alignments</td><td>This overrides defaultColour if it is specified.</td>
+          </tr>
+          <tr> 
+            <td>defaultColourProt</td>
+            <td>A colour scheme (from the list above) to apply to Peptide alignments</td><td>This overrides defaultColour if it is specified.</td>
+          </tr>
+          <tr> 
             <td>userDefinedColour</td>
             <td><p><em>Example:</em><br>
                 D,E=red; K,R,H=0022FF; c=yellow</p></td>
@@ -352,6 +375,13 @@ the applet can be interacted with <em>via</em> its
             &lt;param name=&quot;embedded&quot;
           value=&quot;true&quot;&gt; </li>
         </ul>
+        
+        <p><strong>**NEW FEATURES** in Jalview 2.9</strong></p> 
+        <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>
+        </ul>
+        </p>
         <p><strong>**NEW FEATURES** in Jalview 2.8</strong></p> 
         <ul>
         <li>Normalised sequence logo display
@@ -456,4 +486,4 @@ the applet can be interacted with <em>via</em> its
             </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>
-<!-- content end -->
\ No newline at end of file
+<!-- content end -->