From 87fa9a883d14416ba0e7f778bad69de813048b9c Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Sun, 12 Oct 2014 18:32:48 +0100
Subject: [PATCH] JAL-1264 help updates for show/hide annotations on
 View/Annotations/Popup menus

---
 help/html/features/annotation.html  |   15 +++++++++++----
 help/html/menus/alignmentMenu.html  |    9 +++++++--
 help/html/menus/alwannotations.html |   13 ++++++++++---
 help/html/menus/alwview.html        |    7 ++++++-
 help/html/menus/popupMenu.html      |   20 ++++++++++++++------
 5 files changed, 48 insertions(+), 16 deletions(-)

diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index 8e9bcdf..49128c2 100755
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -46,16 +46,23 @@ 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 
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index f219269..a7cb733 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -112,7 +112,7 @@
 				</li>
 				<li><strong>Load Associated Tree<br> </strong><em>Jalview
 						can <a href="../calculations/treeviewer.html">view trees</a>
-						stored in the Newick file format, and associate them with the
+						 stored in the Newick file format, and associate them with the
 						alignment. Note: the ids of the tree file and your alignment MUST
 						be the same.</em></li>
 				<li><strong>Load Features / Annotations<br> </strong><em>Load
@@ -285,6 +285,11 @@
 						conservation calculation, quality calculation and consensus values
 						as bar charts. </em>
 				</li>
+			  <li><strong>Show All Annotations</strong><em><br>
+			    Show all available annotations on the alignment. You can selectively hide these from the <a href="./popupMenu.html">Popup</a> 
+			    or <a href="../features/annotation.html">Annotation</a> menus. (Since Jalview 2.8.2)</em></li>
+			  <li><strong>Hide All Annotations</strong><em><br>
+			    Hide all annotations on the alignment. (Since Jalview 2.8.2)</em></li>
 				<li><strong>Autocalculated Annotation<br> </strong><em>Settings
 					for the display of autocalculated annotation.</em>
 					<ul>
@@ -310,7 +315,7 @@
 				<li><strong>Show Sequence Features</strong><br> <em>Show
 						or hide sequence features on this alignment.</em>
 				</li>
-				<li><strong><a href="../features/featuresettings.html">Seqence
+				<li><strong><a href="../features/featuresettings.html">Sequence
 							Feature Settings...</a> </strong><em><br> <em>Opens the
 							Sequence Feature Settings dialog box to control the colour and
 							display of sequence features on the alignment, and configure and
diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html
index 4b89049..7375e63 100755
--- a/help/html/menus/alwannotations.html
+++ b/help/html/menus/alwannotations.html
@@ -32,9 +32,16 @@
       <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><strong>Hide Row</strong><br>
-        <em>Hides the annotation row whose label was clicked in order to bring 
-        up the menu.</em> </li>
+	  <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><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 Row</strong><br>
         <em>Deletes the annotation row whose label was clicked in order to bring 
         up the menu.</em> </li>
diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index 3d2d3be..cb38708 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -42,6 +42,11 @@
     </strong><em>If this is selected the &quot;Annotation Panel&quot; will be 
     displayed below the alignment. The default setting is to display the conservation 
     calculation, quality calculation and consensus values as bar charts. </em></li>
+  <li><strong>Show All Annotations</strong><em><br>
+    Show all available annotations on the alignment. You can selectively hide these from the <a href="./popupMenu.html">Popup</a> 
+    &nbsp;or <a href="../features/annotation.html">Annotation</a>&nbsp;menus. (Since Jalview 2.8.2)</em></li>
+  <li><strong>Hide All Annotations</strong><em><br>
+    Hide all annotations on the alignment. (Since Jalview 2.8.2)</em></li>
     <li><strong>Autocalculated Annotation<br></strong>Settings for the display of autocalculated annotation.
     <ul><li>
     	<strong>Apply to all groups<br></strong>
@@ -77,7 +82,7 @@
   </li>
   <li><strong>Show Sequence Features</strong><br>
     <em>Show or hide sequence features on this alignment.</em></li>
-  <li><strong><a href="../features/featuresettings.html">Seqence Feature Settings...</a></strong><em><br>
+  <li><strong><a href="../features/featuresettings.html">Sequence Feature Settings...</a></strong><em><br>
     Opens the Sequence Feature Settings dialog box to control the colour and display 
     of sequence features on the alignment, and configure and retrieve features 
     from DAS annotation servers.</em></li>
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index e28c7e1..511b85f 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -31,14 +31,24 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
 <ul>
   <li><strong>Selection</strong> 
     <ul>
-      <li><a name="sqreport"><strong>Sequence Details ...<br>
+      <li><a name="sqreport"><strong>Sequence Details...<br>
           </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
-            and database cross references</a> normally shown in the sequence's
+            and database cross references</a>&nbsp;normally shown in the sequence's
             tooltip.</em></li>
+      <li><strong>Show Annotations...<br>
+          </strong><em>Choose to show (unhide) either All or 
+          a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+      <li><strong>Hide Annotations...<br>
+          </strong><em>Choose to hide either All or 
+          a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+      <li><strong>Add Reference Annotations...<br>
+          </strong><em>Add to the alignment window any annotations on the selected sequences
+          which have been read from reference sources or calculated (for example, 
+          secondary structure derived from 3D structure). (Since Jalview 2.8.2)</em></li>
       <li><strong>Edit </strong> 
         <ul>
           <li><strong>Copy</strong><br>
-            <em>Copys the selected region. In the applet version, the copied sequences 
+            <em>Copies the selected region. In the applet version, the copied sequences 
             are not available to the system clipboard.</em></li>
           <li><strong>Cut<br>
             </strong><em>Cuts the selected region from the alignment. In the applet 
@@ -186,9 +196,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
     (The View representative structures option was introduced in
         Jalview 2.8.1)</em></li>
   </ul>
-  <br> <li>
-      
-      </li>
+  <br> 
     </ul>
   </li>
   <li><strong>Hide Sequences</strong><br>
-- 
1.7.10.2