X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;fp=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=c4a40d8f445a926d478b06c2a31984d7d708d132;hb=078d3939810e3be7d0ed9452df7db6b29e7b8e70;hp=241e0a3776c94e9d497663f8512bb32f5856ec50;hpb=3a10cfaddf4f4a0949fbecca95f97ccf1d1ca1d6;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 241e0a3..c4a40d8 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -515,8 +515,10 @@ 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);
@@ -562,7 +564,10 @@ public class AnnotationLabels extends JPanel
                                 "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);
               }