+ boolean centreColumnLabels;
+
+
+ public boolean getCentreColumnLabels()
+ {
+ return centreColumnLabels;
+ }
+
+ public void updateSequenceIdColours()
+ {
+ Vector groups = alignment.getGroups();
+ for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
+ if (sg.idColour != null)
+ {
+ Vector sqs = sg.getSequences(hiddenRepSequences);
+ for (int s = 0, sSize = sqs.size(); s < sSize; s++)
+ {
+ this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour);
+ }
+ }
+ }
+ }
+ public boolean followHighlight=false;
+ public boolean getFollowHighlight() {
+ return followHighlight;
+ }
+ /**
+ * show non-conserved residues only
+ */
+ public boolean showUnconserved=false;
+
+ /**
+ * when set, alignment should be reordered according to a newly opened tree
+ */
+ public boolean sortByTree=false;
+
+ /**
+ * @return the showUnconserved
+ */
+ public boolean getShowunconserved()
+ {
+ return showUnconserved;
+ }
+
+ /**
+ * @param showUnconserved the showUnconserved to set
+ */
+ public void setShowunconserved(boolean displayNonconserved)
+ {
+ this.showUnconserved = displayNonconserved;
+ }