Merge branch 'develop' into feature/JAL-244_Automatically_adjust_left_margin_to_avoid...

diff --cc src/jalview/gui/AlignFrame.java
Simple merge

diff --cc src/jalview/gui/AnnotationLabels.java
index 241e0a3,28065c3..c4a40d8
--- 1/src/jalview/gui/AnnotationLabels.java
--- 2/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@@ -557,12 -537,11 +559,15 @@@ public class AnnotationLabels extends J
                public void run()
                {
                  final long progBar;
 -                ap.alignFrame.setProgressBar(MessageManager.formatMessage("action.clustering_matrix_for",cm.getAnnotDescr(),5f), progBar = System.currentTimeMillis());
 +                ap.alignFrame.setProgressBar(
 +                        MessageManager.formatMessage(
 +                                "action.clustering_matrix_for",
 +                                cm.getAnnotDescr(), 5f),
 +                        progBar = System.currentTimeMillis());
-                 cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true));
+                 cm.setGroupSet(GroupSet.makeGroups(cm, true));
+                 cm.randomlyReColourGroups();
+                 cm.transferGroupColorsTo(alignmentAnnotation);
+                 ap.alignmentChanged();
                  ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
                  ap.alignFrame.setProgressBar(null, progBar);
                }