Merge branch 'releases/Release_2_10_2b1_Branch'

diff --git a/help/html/releases.html b/help/html/releases.html
index 5a1e324..e72c8a3 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -136,6 +136,10 @@ li:before {
               dragging a selected region off the visible region of the
               alignment
             </li>
+            <li>
+              <!-- JAL-2724 -->Cannot apply annotation based
+              colourscheme to all groups in a view
+            </li>
           </ul>
         </div></td>
     

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index f088791..8d123bb 100644 (file)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -456,22 +456,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter
         {
           continue;
         }
-
-        if (useOriginalColours.isSelected())
-        {
-          sg.setColourScheme(new AnnotationColourGradient(currentAnn,
-                  sg.getColourScheme(), selectedThresholdOption));
-          ((AnnotationColourGradient) sg.cs)
-                  .setSeqAssociated(seqAssociated.isSelected());
-        }
-        else
-        {
-          sg.setColourScheme(new AnnotationColourGradient(currentAnn,
-                  minColour.getBackground(), maxColour.getBackground(),
-                  selectedThresholdOption));
-          ((AnnotationColourGradient) sg.cs)
-                  .setSeqAssociated(seqAssociated.isSelected());
-        }
+        sg.setColourScheme(
+                acg.getInstance(sg, ap.av.getHiddenRepSequences()));
       }
     }
     return false;