From 023d23abaad346f745b93fced2407d7342ab7171 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 27 Aug 2015 12:33:55 +0100
Subject: [PATCH] JAL-1701 help page for Split Frame view linked in

---
 help/help.jhm                     |    1 +
 help/helpTOC.xml                  |    1 +
 help/html/features/splitView.html |    7 ++++---
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/help/help.jhm b/help/help.jhm
index 2cfe8d8..a450473 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -74,6 +74,7 @@
    <mapID target="edit" url="html/editing/index.html"/>
    <mapID target="jalarchive" url="html/features/jalarchive.html"/>
    <mapID target="multipleviews" url="html/features/multipleViews.html"/>
+   <mapID target="splitframe" url="html/features/splitView.html"/>
    <mapID target="trees" url="html/calculations/tree.html"/>
    <mapID target="treeviewer" url="html/calculations/treeviewer.html"/>
    <mapID target="sorting" url="html/calculations/sorting.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 345cb51..4ce9892 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -29,6 +29,7 @@
 		<tocitem text="Making Figures" target="export" />
 		<tocitem text="Hidden Regions" target="hiddenRegions" />
 		<tocitem text="Multiple Views" target="multipleviews" />
+		<tocitem text="Split Frame View" target="splitframe" />
 		<tocitem text="Viewing Trees" target="treeviewer" expand="false" />
 		<tocitem text="Fetching Sequences" target="seqfetch" />
 		<tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
diff --git a/help/html/features/splitView.html b/help/html/features/splitView.html
index c9ce093..16d6c10 100644
--- a/help/html/features/splitView.html
+++ b/help/html/features/splitView.html
@@ -43,7 +43,8 @@ This consensus may reveal variation in nucleotides coding for conserved protein
 <p><strong><em>Add Sequences</em></strong></p>
 <p>If you add (coding) DNA sequences to an open peptide alignment, or vice versa, <em>and</em> at least one DNA sequence translates to one of the
 peptide sequences, then the option to open in a split window is offered. The DNA may include start and/or stop codons, but no non-coding (intron)
-sequence.</p> 
+sequence.<br>
+If more than one cDNA variant is present in the alignment, Jalview will first try to match these to protein sequences based on any retrieved cross-references, and failing that, pairwise as they are ordered in the alignments. 
 
 <p>This option is available in Jalview Desktop (when adding sequences by any supported method), and Jalview applet (adding from textbox).
 The additional options below apply to Jalview Desktop only.</p>
@@ -56,7 +57,7 @@ calculated protein product in a Split Frame view.</p>
 <p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate | Get Cross-References"</a></strong> is available for fetched sequences which have cross-references to other databases.
 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 Split View</em></strong></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>
@@ -69,6 +70,6 @@ Split Frame.</p>
 </ul> 
   
 
-<p><em>Split Frame Views were introduced in Jalview 2.?.?</em></p>
+<p><em>Split Frame Views were introduced in Jalview 2.9</em></p>
 </body>
 </html>
-- 
1.7.10.2