- boolean updateCalcs = false;
- boolean conv = av.isShowGroupConservation();
- boolean cons = av.isShowGroupConsensus();
- boolean showprf = av.isShowConsensusProfile();
- boolean showConsHist = av.isShowConsensusHistogram();
-
- boolean sortg = true;
-
- // remove old automatic annotation
- // add any new annotation
-
- Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
- // intersect alignment annotation with alignment groups
-
- AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
- Hashtable oldrfs = new Hashtable();
- for (int an = 0; an < aan.length; an++)
+ updateAnnotation(applyGlobalSettings, false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings,
+ boolean preserveNewGroupSettings)
+ {
+ av.updateGroupAnnotationSettings(applyGlobalSettings,
+ preserveNewGroupSettings);
+ adjustAnnotationHeight();
+ }
+
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return av.getAlignment();
+ }
+
+ /**
+ * get the name for this view
+ *
+ * @return
+ */
+ public String getViewName()
+ {
+ return av.viewName;
+ }
+
+ /**
+ * Make/Unmake this alignment panel the current input focus
+ *
+ * @param b
+ */
+ public void setSelected(boolean b)
+ {
+ try
+ {
+ alignFrame.setSelected(b);
+ } catch (Exception ex)