From 94115f9af30575885ef1e3f843e0dd381e579e08 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 17 Jun 2016 14:23:57 +0100
Subject: [PATCH] JAL-1557 selection from annotation (and group annotation)
 added to help

---
 help/html/calculations/consensus.html    |    5 +++++
 help/html/calculations/conservation.html |    7 ++++++-
 help/html/features/annotation.html       |   19 +++++++++++++++++++
 3 files changed, 30 insertions(+), 1 deletion(-)

diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html
index 0a0214e..c870887 100644
--- a/help/html/calculations/consensus.html
+++ b/help/html/calculations/consensus.html
@@ -55,6 +55,11 @@
   <strong>Normalise Consensus Logo</strong> to scale all columns of the
   logo to the same height.
 
+    <p>
+    <strong>Group Consensus</strong><br>
+    If sequence groups have been defined, then selecting option 'Group Consensus' in the <a href="../menus/alwannotation.html">Annotations menu</a> will 
+    result in Consensus being calculated for each group, as well as the alignment as a whole.
+  </p>
   <p>
     <strong>cDNA Consensus</strong>
   </p>
diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html
index df8b5ff..9cb8ce1 100755
--- a/help/html/calculations/conservation.html
+++ b/help/html/calculations/conservation.html
@@ -65,11 +65,16 @@
     (e.g. !proline).
   </p>
   <p>
-    <em>Colouring an alignment by conservation</em><br>
+    <strong>Colouring an alignment by conservation</strong><br>
     Conservation scores can be used to colour an alignment. This is
     explained further in the help page for <a
       href="../colourSchemes/conservation.html"
     >conservation colouring</a>.
   </p>
+  <p>
+    <strong>Group conservation</strong><br>
+    If sequence groups have been defined, then selecting option 'Group Conservation' in the <a href="../menus/alwannotation.html">Annotations menu</a> will 
+    result in Conservation being calculated for each group, as well as the alignment as a whole.
+  </p>
 </body>
 </html>
diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index a645630..7e52c46 100755
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -48,6 +48,25 @@ alignment window or loaded from the alignment's file menu.
 			href="../webServices/proteinDisorder.html">disordered region</a>
 		prediction methods. 
 </p>
+<p><strong>Sequence Group Annotation</strong>
+</p>
+<p>
+	If sequence groups are defined, <a href="../calculations/conservation.html">Conservation</a>
+	 and <a href="../calculations/consensus.html">Consensus</a> annotation can be enabled
+	for each group from the <a href="../menus/alwannotation.html">Annotations menu</a>, or can
+	be imported from a Jalview <a href="annotationsFormat.html">Annotations file</a>.
+</p>
+<p><strong>Sequence Selection from Annotation</strong>
+</p>
+<p>
+    Sequences associated with sequence (or sequence group) annotations can be selected by
+    double-clicking the annotation label with these key combinations:
+    <ul>
+    <li>double-click - Select associated sequences (replaces current selection)</li>
+    <li>shift double-click - add  sequences to selection</li>
+    <li>Ctrl (Mac CMD) double-click - toggles inclusion of associated sequences in the current selection</li>
+    </ul>
+    Note this also works in combination with manual sequence selection in the alignment.
 <p><strong>Interactive Alignment Annotation</strong></p>
 <p>
 Annotation rows are added using the <strong>Annotation Label</strong>
-- 
1.7.10.2