JAL-1682 JAL-1645 remove references to 2.8.3

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 95a4511..c880a84 100644 (file)
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -190,7 +190,7 @@ the applet can be interacted with <em>via</em> its
             <td>file2</td>
             <td>fileName</td>
             <td>A second file to open. If one file is nucleotide and the other peptide, and at least one peptide sequence
-            is the translation of one of the nucleotide sequences, then alignments will be displayed linked in a split frame (<em>since 2.8.3</em>).</td>
+            is the translation of one of the nucleotide sequences, then alignments will be displayed linked in a split frame (<em>since 2.9</em>).</td>
           </tr>
           <tr> 
             <td>sequence1,<br>
@@ -401,7 +401,7 @@ the applet can be interacted with <em>via</em> its
           </tr>
           <tr><td>scaleProteinAsCdna</td><td>true or false (default is false)</td>
           <td>Set true to shown protein residues the same width as their encoding codons. 
-          For use with parameter file2 when showing a split frame of cDNA and protein. (<em>since 2.8.3</em>)</td></tr>
+          For use with parameter file2 when showing a split frame of cDNA and protein. (<em>since 2.9</em>)</td></tr>
           <tr><td>centrecolumnlabels</td>
           <td>true or false (default is false)</td>
           <td>When true, text labels associated with a column in the alignment will be shown centered with respect to the column. (<em>since 2.4</em>)</td>

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index eeee788..2f030fc 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 2.8.3, the Annotations file has also supported the definition of views on the alignment, and definition of hidden regions.</p>
+Since Jalview 2.9, the Annotations file has also supported the definition of reference sequences and  hidden regions for an alignment view.</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 9680235..dc2b8a1 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 2.8.3)
+                               of residues at marked columns. (since Jalview 2.9)
                </em></li>
                <li><strong>Undefine Groups (Control U)<br>
   </strong><em>The alignment will be reset with no defined groups.<br>

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 88cb46e..12fa59f 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-2.8.3 annotation files which have no view,
-   * hidden columns or hidden row keywords.
+   * convenience method for pre-2.9 annotation files which have no view, hidden
+   * columns or hidden row keywords.
    * 
    * @param annotations
    * @param list