From 3c9a109fe89504b4713bfaf612275edc8c07e433 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 23 May 2014 12:10:57 +0100
Subject: [PATCH] JAL-1445 updated documentation and added link in whatsNew

---
 help/html/features/featuresettings.html |   33 ++++++++++++++++++++++---------
 help/html/releases.html                 |   33 +++++++++++++++++++++++++++++--
 help/html/whatsNew.html                 |    2 +-
 3 files changed, 56 insertions(+), 12 deletions(-)

diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html
index 9335d93..9526ed5 100755
--- a/help/html/features/featuresettings.html
+++ b/help/html/features/featuresettings.html
@@ -37,15 +37,30 @@ they are currently being displayed (only the ticked features and groups
 are displayed). <strong><em>You can change the colour or
 shading style used for a feature in the associated alignment by clicking
 on its colour box.</em></strong></p>
-  <p>
-    <strong><em>Selecting alignment columns by feature</em></strong><br>
-    <strong>Double-click</strong> a feature to add all the columns where
-    that feature is found to the current column selection. <strong>Shift+Double-click</strong>
-    will add all the columns where that feature is <strong>not</strong>
-    found. You can also find these options in the feature's pop-up menu
-    (see below). <br />
-    <em>Select columns by feature was added in Jalview 2.8.1</em>
-  </p>
+	<p>
+		<a name="selectbyfeature"><strong><em>Selecting
+					alignment columns by feature</em></strong></a><br> <strong>Double-clicking
+			a feature type</strong> allows you to select columns in the alignment that
+		contain (or do not contain) features of that type. If a region of the
+		alignment is currently selected, then only features in the current
+		selection will be searched. The following keys affect the way in which
+		selections are made:
+	
+	<ul>
+		<li>Hold down <strong>Alt</strong> to select columns not
+			containing features of a particular type.
+		</li>
+		<li>Hold down <strong>Shift</strong> to add columns to the
+			current selection.
+		</li>
+		<li>Press <strong>Command/Windows key</strong> to toggle column
+			selection state (XOR)
+		</li>
+	</ul>
+	Options are also provided in the feature's pop-up menu (see below).
+	<br />
+	<em>Select columns by feature was added in Jalview 2.8.1</em>
+	</p>
   <p><strong><em>Feature settings pop-up menu</em></strong><br>
 <strong>Right-click</strong> on a feature to open a pop-up menu that
 allows you to sort the alignment or current selection using that feature
diff --git a/help/html/releases.html b/help/html/releases.html
index c709a5f..b6fb83c 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -41,13 +41,42 @@
   </td>
       <td> <!--  New features -->
       <!--  For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
-        <ul>
+      <ul>
+      <li>i18n Internationalisation of user interface and translation for Spanish locale</li>
+      </ul>
+      <em>Application</em><ul>
+        <li>Define/Undefine group on current selection with Ctrl-G</li>
+ <li>Select columns containing particular features from Feature Settings dialog</li>
+<li>View all 'representative' PDB structures for selected sequences</li>
+<li>Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service</li>
+<li></li>
+      <li>Jalview v2.8.1 project preserves sequence dataset and dataset annotation (e.g. hidden secondary structure annotation rows) </li>
+        </ul>
+      <em>Applet</em><ul>
+      
         </ul> <em>Other improvements</em>
         <ul>
         </ul>
       </td>
       <td><!--  issues resolved -->
-        <ul>
+        <em>Application</em><ul>
+					<li>Newly created RNA secondary structure line doesn't have
+						'display all symbols' flag set</li>
+				  <li>T-COFFEE alignment score shading scheme not saved in
+						jalview project</li>
+					<li>Local file cannot be loaded in freshly downloaded Jalview</li>
+					<li>??? unresolved ??? Jalview icon not shown on dock in
+						Mountain Lion/Webstart</li>
+					<li>Load file from desktop file browser fails</li>
+					<li>Occasional NPE thrown when calculating large trees</li>
+				</ul>
+        <em>Applet</em>
+			<ul>
+					<li>Apply to all groups ticked but colourscheme changes don't
+						affect groups</li>
+				</ul> 
+				<em>Other</em><ul>
+        <li></li>
         </ul>
       </td>
     </tr>
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 7a786d5..a016a35 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -43,7 +43,7 @@
 	<strong>Enhancements and new features</strong>
 	<ul>
 	<li>
-  <li>Extended the <a href="features/featuresettings.html">feature settings dialog</a> to allow columns to be selected containing particular sequence features.</li>
+  <li>Extended the feature settings dialog to <a href="features/featuresettings.html#selectbyfeature">select columns containing particular sequence features.</a></li>
 	</ul>
 	<strong>Bug fixes</strong>
 	<ul>
-- 
1.7.10.2