X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=1e45aae5d5483f661652d5c9a2ea7494bfe9e275;hb=5fd2be21a60c72ae4941970a525679677044f572;hp=6dd26e2b03370085d081b43c5473b9fdfd3a6226;hpb=47cbe0d4a22563312b7a841d08cf81b823c4cb39;p=jalview.git

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 6dd26e2..1e45aae 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -46,13 +46,20 @@ 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
-            matches the translation of one of the nucleotide sequences, then alignments will be displayed linked in a Split Frame. Parameter is ignored if enableSplitFrame is set to false (<em>since 2.9</em>).</td>
-          </tr>
-          <tr> 
+              <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>
@@ -111,6 +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>