From cb231b238443611effe9ed859f1e9d4370882f9b Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 2 Sep 2015 12:10:01 +0100
Subject: [PATCH] JAL-1619 additions, standardised menu item symbols

---
 help/html/features/splitView.html |   26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/help/html/features/splitView.html b/help/html/features/splitView.html
index 16d6c10..5b48ec3 100644
--- a/help/html/features/splitView.html
+++ b/help/html/features/splitView.html
@@ -27,13 +27,17 @@
 <p/></p>Coding DNA (cDNA) and its protein product can be displayed in a split view, with cDNA above and protein below. The two alignments are
 linked, with these features supported:
 <ul>
-<li>mouseover or scrolling of either alignment is followed by the other (unless you turn off <strong><a href="../menus/alwview.html">"View | Automatic Scrolling"</a></strong>)</li>
+<li>mouseover or scrolling of either alignment is followed by the other (unless you turn off <strong><a href="../menus/alwview.html">"View&#8594;Automatic Scrolling"</a></strong>)</li>
 <li>on selecting rows, columns or regions in one alignment, the corresponding selection is made in the other</li>
-<li>sequence ordering in one alignment (using the cursor, or <strong><a href="../calculate/sorting.html">"Calculate | Sort")</a></strong> is also applied to the other</li>
+<li>sequence ordering in one alignment (using the cursor, or <strong><a href="../calculate/sorting.html">"Calculate&#8594;Sort")</a></strong> is also applied to the other</li>
 <li>editing (gap insertion / deletion) in the protein alignment is reflected in the cDNA (but not vice versa)</li>
 <li>on <strong><a href="../calculations/tree.html">"Calculate Tree"</a></strong> in either alignment, grouping, colouring and sorting by tree are applied to both</li>
-<li>the <strong><a href="../menus/alwformat.html">"Format | Font"</a></strong> menu option has an option 'Scale protein residues to codons'; select this option to make each protein residue
+<li>the <strong><a href="../menus/alwformat.html">"Format&#8594;Font"</a></strong> menu option has an option 'Scale protein residues to codons'; select this option to make each protein residue
 the same width as a DNA codon (so the alignments 'line up' vertically)</li>
+<li>menu option <strong>"View&#8594;Protein"</strong> (in the cDNA panel) or <strong>"View&#8594;Nucleotide"</strong> (in the protein panel) allows you to show or hide the complementary alignment</li>
+<li>you can adjust panel heights by dragging the divider between them using the mouse</li>
+<li>menu options <a href="menus/alwview.html"><strong>"View&#8594;New View / Expand Views / Gather Views"</strong></a> behave as for a normal alignment window, but always create new views
+as split frames</li> 
 </ul>
 <p>An alignment annotation row on the protein alignment shows the <strong><a href="../calculations/consensus.html">cDNA consensus</a></strong> for each peptide column.<br/>
 This consensus may reveal variation in nucleotides coding for conserved protein residues.</p>
@@ -50,11 +54,11 @@ If more than one cDNA variant is present in the alignment, Jalview will first tr
 The additional options below apply to Jalview Desktop only.</p>
 
 <p><strong><em>Translate as cDNA</em></strong></p>
-<p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate | Translate as cDNA"</a></strong> is available for a nucleotide alignment. Selecting this option shows the DNA and its 
+<p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate&#8594;Translate as cDNA"</a></strong> is available for a nucleotide alignment. Selecting this option shows the DNA and its 
 calculated protein product in a Split Frame view.</p>
 
 <p><strong><em>Get Cross-References</em></strong></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.
+<p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate&#8594;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 a Split View</em></strong></p>
@@ -68,7 +72,17 @@ Split Frame.</p>
     </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><em>Split Frame Views were introduced in Jalview 2.9</em></p>
 </body>
-- 
1.7.10.2