JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 6b82a37..d26ba89 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);
               }
@@ -1232,7 +1237,7 @@ public class AnnotationLabels extends JPanel
             {
               if (debugRedraw)
               {
-                System.out.println("before vis: " + i);
+                jalview.bin.Console.outPrintln("before vis: " + i);
               }
               before = true;
             }
@@ -1246,7 +1251,7 @@ public class AnnotationLabels extends JPanel
             {
               if (debugRedraw)
               {
-                System.out.println(
+                jalview.bin.Console.outPrintln(
                         "Scroll offset: " + sOffset + " after vis: " + i);
               }
               after = true;