From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 9 Sep 2015 11:55:43 +0000 (+0100)
Subject: JAL-1684 clarification of which alignment will be used to guide the reconstruction... 
X-Git-Tag: Release_2_10_0~457^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=85c6a9ff7bb1e0711b4c8503f10186bb083fb871;p=jalview.git

JAL-1684 clarification of which alignment will be used to guide the reconstruction of the linked alignment
---

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 6dd26e2..8daa4ee 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>