From 8392c56e80d73084bd8eac9276979bdf28f462a2 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 8 Sep 2015 17:59:41 +0100
Subject: [PATCH] JAL-1645 JAL-1701 fix up split frame docs and add a bit more
 info about reconstructed alignments. maybe we need a
 screenshot here too.

---
 help/html/features/splitView.html |   51 +++++++++++++++----------------------
 1 file changed, 21 insertions(+), 30 deletions(-)

diff --git a/help/html/features/splitView.html b/help/html/features/splitView.html
index 80e27b0..59894f6 100644
--- a/help/html/features/splitView.html
+++ b/help/html/features/splitView.html
@@ -62,37 +62,28 @@ calculated protein product in a Split Frame view.</p>
 On selecting protein cross-references (for a cDNA alignment), or DNA xrefs (for peptide), a Split Frame view is opened showing cDNA and peptide.</p>
 
 <p><strong><em>Realign a Split View</em></strong></p>
-<p>If you invoke a web service to realign either half of a Split Frame, then the resulting realignment is displayed in a new
-Split Frame.</p> 
-<ul>
-<li>the alignment you chose to realign (for example, peptide) is displayed as aligned by the external web service</li>
-<li>Jalview 'aligns' its complement (in this case, cDNA) similarly, by inserting corresponding gaps
-    <ul>
-    <li>NB this is <em>not</em> the same as aligning the complement using the external service, which may give different results</li> 
-    </ul>
-</li>
-</ul> 
-
-<p><strong><em>Applet</em></strong></p>
-<p>To see a split frame view in the Jalview applet, provide these applet parameters:
-<table border="1">
-<tr><th>Parameter</th><th>Value</th><th>Description</th>
-<tr><td>file</td><td>path to an alignment file</td><td>a cDNA (or protein) alignment</td>
-<tr><td>file</td><td>path to an alignment file</td><td>a protein (or cDNA) alignment</td>
-<tr><td>enableSplitFrame</td><td>true</td><td>to enable the Split Frame feature</td>
-</table>
-<p/>If compatible sequences are present in the input alignments, Jalview will open a Split Frame view.<br/>
-If not, only the first alignment will be opened (an error message is written to the Java console).
-
-	<p>
+  <p>If you invoke a web service to realign either half of a Split
+    Frame, then the resulting realignment is displayed in a new Split
+    Frame.
+  </p>
+  <ul>
+    <li>the alignment you chose to realign (for example, peptide)
+      is displayed as aligned by the external web service</li>
+    <li>Jalview reconstructs the alignment of its complement (in
+      this case, cDNA) by inserting gaps in the corresponding positions</li>
+  </ul>
+  <p><strong>Reconstructed Alignments</strong>
+    Reconstructed alignments are typically <em>not</em>
+    the same as the alignment produced by aligning the complement
+    sequence set directly with the external service. However, in the
+    case of protein alignments, a reconstructed cDNA alignment is often
+    more reliable than one calculated without coding information.
+    Reconstructed cDNA alignments are also more informative than the
+    original protein alignment when calculating phylogenetic trees or
+    performing other kinds of molecular evolution analysis.
+  </p>
+  <p>
 		<em>Split Frame Views were introduced in Jalview 2.9</em>
 	</p>
-	<p>
-		Example files for cDNA/Protein: <a
-			href="http://www.jalview.org/builds/nextrel/examples/estrogenReceptorProtein.fa">estrogenReceptorProtein.fa</a>
-		and <a
-			href="http://www.jalview.org/builds/nextrel/examples/estrogenReceptorCdna.fa">estrogenReceptorCdna.fa</a>
-		taken from xxx.
-	</p>
 </body>
 </html>
-- 
1.7.10.2