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 (executable)
--- 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 (file)
--- 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 (executable)
--- 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 (executable)
--- 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 (executable)
--- 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