Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629

[jalview.git] / src / jalview / gui / AnnotationLabels.java

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 6b82a37..28065c3 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -497,8 +497,10 @@ public class AnnotationLabels extends JPanel
           public void actionPerformed(ActionEvent e)
           {
             sel_row.setShowGroupsForContactMatrix(chitem.getState());
-            ap.getAnnotationPanel()
-            .paint(ap.getAnnotationPanel().getGraphics());
+            // so any annotation colour changes are propagated - though they
+            // probably won't be unless the annotation row colours are removed
+            // too!
+            ap.alignmentChanged();
           }
         });
         pop.add(chitem);
@@ -536,7 +538,10 @@ public class AnnotationLabels extends JPanel
               {
                 final long progBar;
                 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);
               }