- // TODO: this should be merged with other annotation update stuff - that
- // sits on AlignViewport
- boolean updateCalcs = false;
- boolean conv = av.isShowGroupConservation();
- boolean cons = av.isShowGroupConsensus();
- boolean showprf = av.isShowSequenceLogo();
- boolean showConsHist = av.isShowConsensusHistogram();
- boolean normLogo = av.isNormaliseSequenceLogo();
-
- 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();
- if (aan != null)
- {
- for (int an = 0; an < aan.length; an++)
- {
- if (aan[an].autoCalculated && aan[an].groupRef != null)
- {
- oldrfs.put(aan[an].groupRef, aan[an].groupRef);
- av.alignment.deleteAnnotation(aan[an]);
- aan[an] = null;
- }
- }
- }
- SequenceGroup sg;
- if (gr != null)
- {
- for (int g = 0; g < gr.size(); g++)
- {
- updateCalcs = false;
- sg = (SequenceGroup) gr.elementAt(g);
- if (applyGlobalSettings || !oldrfs.containsKey(sg))
- {
- // set defaults for this group's conservation/consensus
- sg.setshowSequenceLogo(showprf);
- sg.setShowConsensusHistogram(showConsHist);
- sg.setNormaliseSequenceLogo(normLogo);
- }
- if (conv)
- {
- updateCalcs = true;
- av.alignment.addAnnotation(sg.getConservationRow(), 0);
- }
- if (cons)
- {
- updateCalcs = true;
- av.alignment.addAnnotation(sg.getConsensus(), 0);
- }
- // refresh the annotation rows
- if (updateCalcs)
- {
- sg.recalcConservation();
- }
- }
- }
- oldrfs.clear();
+ updateAnnotation(applyGlobalSettings, false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings,
+ boolean preserveNewGroupSettings)
+ {
+ av.updateGroupAnnotationSettings(applyGlobalSettings,
+ preserveNewGroupSettings);