From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 6 Mar 2015 15:13:51 +0000 (+0000)
Subject: reassign features already created/documented for 2.9 to 2.8.3 JAL-1682
X-Git-Tag: Jalview_2_9~78
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=895fba3bf4b40617d3547daf20d676b624286f42;hp=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git

reassign features already created/documented for 2.9 to 2.8.3 JAL-1682
---

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index e5e1fdb..06477df 100755
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -207,7 +207,7 @@ Group association is turned off for subsequent annotation rows by:
 </p>
 <hr/>
 <p><strong><a name="refsandviews">VIEW_SETREF, VIEW_HIDECOL and HIDE_INSERTIONS</a></strong><br/>
-Since Jalview 2.9, the Annotations file has also supported the definition of views on the alignment, and definition of hidden regions.</p>
+Since Jalview 2.8.3, the Annotations file has also supported the definition of views on the alignment, and definition of hidden regions.</p>
 <!-- 	<p>
 		<em>VIEW_DEF</em> allows the current view to be named according to the
 		first argument after the tab character. If a second argument is
diff --git a/help/html/menus/alwselect.html b/help/html/menus/alwselect.html
index a804a4c..d400972 100644
--- a/help/html/menus/alwselect.html
+++ b/help/html/menus/alwselect.html
@@ -49,7 +49,7 @@
 				currently selected groups of the alignment will be subdivided
 				according to the contents of the currently selected region. <br />Use
 				this to subdivide an alignment based on the different combinations
-				of residues at marked columns. (since Jalview 2.9)
+				of residues at marked columns. (since Jalview 2.8.3)
 		</em></li>
 		<li><strong>Undefine Groups (Control U)<br>
   </strong><em>The alignment will be reset with no defined groups.<br>
diff --git a/help/html/releases.html b/help/html/releases.html
index 8b9db7a..2bfa4bc 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -62,7 +62,7 @@
 		</tr>
 		<tr>
 			<td><div align="center">
-					<strong><a name="Jalview.2.9">2.9</a><br /> <em>23/2/2015</em></strong>
+					<strong><a name="Jalview.2.8.3">2.8.3</a><br /> <em>13/4/2015</em></strong>
 				</div></td>
 			<td><em>General</em>
 				<ul>
diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index 7bba590..c90f499 100755
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -110,11 +110,15 @@ The annotation bars below the alignment are as follows:
 	invoked to rationalise significantly different primary predictions.</em></li>
 </ul>
 </p>
-<em>JNet annotation created in Jalview 2.8.2 and later versions can be displayed on other alignments via the <a href="">Add reference annotation</a></em>
-<em>As of Jalview 2.6, the Jnet service accessed accessed via the
+	<em>JNet annotation created in Jalview 2.8.2 and later versions
+		can be displayed on other alignments via the <a
+		href="../features/annotation.html#seqannots">Add reference
+			annotation</a> Sequence ID popup menu option.
+	</em>
+	<em>As of Jalview 2.6, the Jnet service accessed accessed via the
 'Secondary structure prediction' submenu should be considered a legacy
 Jalview SOAP service, and will be replaced in the near future by a
-JABAWS Jnet service (now available in the Jalview 2.9 development version).</em>
+JPred4 Rest service.</em>
 
 </body>
 </html>
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 62503a0..c9e87e3 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -88,8 +88,8 @@ public class AnnotationFile
   }
 
   /**
-   * convenience method for pre-2.9 annotation files which have no view, hidden
-   * columns or hidden row keywords.
+   * convenience method for pre-2.8.3 annotation files which have no view,
+   * hidden columns or hidden row keywords.
    * 
    * @param annotations
    * @param list