- AlignmentAnnotation alan = alignmentAnnotation;
- cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true));
- ap.alignFrame.showContactMapTree(alan, cm);
+ final long progBar;
+ ap.alignFrame.setProgressBar(MessageManager.formatMessage("action.clustering_matrix_for",cm.getAnnotDescr(),5f), progBar = System.currentTimeMillis());
+ cm.setGroupSet(GroupSet.makeGroups(cm, true));
+ cm.randomlyReColourGroups();
+ cm.transferGroupColorsTo(alignmentAnnotation);
+ ap.alignmentChanged();
+ ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
+ ap.alignFrame.setProgressBar(null, progBar);