X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=7e52c46b822e2320f090d4477bfcf8a8d5bf41be;hb=0ac97c219bf88278f77306a5695e8bd9d9ca9179;hp=8e9bcdf52021349ce994c297eabcd8273903dc1f;hpb=e5cbd35e13f46ae1d59a08b0af1086677418141d;p=jalview.git

diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index 8e9bcdf..7e52c46 100755
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -39,6 +39,34 @@ and symbolic annotations can be added to an alignment via an <a
 href="annotationsFormat.html">Annotations File</a> dragged into the
 alignment window or loaded from the alignment's file menu.
 </p>
+<p><a name="seqannots"/><strong>Sequence Reference Annotation</strong>
+</p>
+<p>
+		Sequence reference annotation is created from 3D structure
+		data, and from the results of sequence based prediction of
+		<a href="../webServices/jnet.html">secondary structure</a> and <a
+			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>
@@ -46,16 +74,23 @@ menu, which is obtained by clicking anywhere on the annotation row labels
 area (below the sequence ID area).
 </p>
 <ul>
-  <li>Add New Row<br>
+  <li><strong>Add New Row</strong><br>
     <em>Adds a new, named annotation row (a dialog box will pop up for you to 
     enter the label for the new row). </em> </li>
-  <li>Hide Row<br>
+  <li><strong>Edit Label/Description</strong><br>
+    <em>This opens a dialog where you can change the name (displayed label), or the description
+    (as shown on the label tooltip) of the clicked annotation. </em> </li>
+  <li><strong>Hide This Row</strong><br>
     <em>Hides the annotation row whose label was clicked in order to bring up 
     the menu.</em> </li>
-  <li>Delete Row<br>
+  <li><strong>Hide All <em>&lt;label&gt;</em></strong><br>
+    <em>Hides all annotation rows whose label matches the one clicked. 
+    (This option is only shown for annotations that relate to individual sequences, 
+    not for whole alignment annotations. Since Jalview 2.8.2.)</em> </li>
+  <li><strong>Delete This Row</strong><br>
     <em>Deletes the annotation row whose label was clicked in order to bring up 
     the menu.</em> </li>
-  <li>Show All Hidden Rows<br>
+  <li><strong>Show All Hidden Rows</strong><br>
     <em>Shows all hidden annotation rows.</em> </li>
           <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
        <em>Annotations can be saved to file or output to a text window in either the 
@@ -101,7 +136,7 @@ found not to match.
 </li>
 <li>Label<br><em>Set the text label at the selected positions. A
 dialog box will open for you to enter the text.  If
-more that one consecutive position is marked with the same label, only
+more than one consecutive position is marked with the same label, only
 the first position's label will be rendered.</em>
 </li>
 <li>Colour<br><em>Changes the colour of the annotation text label.</em>
@@ -116,7 +151,7 @@ href="../features/jalarchive.html">Jalview Archives</a>.
 </p>
 <p><em>Current Limitations</em></p>
 <p>As of version 2.5, the Jalview user interface does not support the 
-creation and editing quantitative annotation (histograms and line graphs), or 
+creation and editing of quantitative annotation (histograms and line graphs), or 
 to create annotation associated with a specific sequence. It is also incapable of
 annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an 
 <a href="annotationsFormat.html">Annotation file</a>.<br>
