+ @Override
+ public HiddenMarkovModel getHMM()
+ {
+ return hmm;
+ }
+
+ @Override
+ public void setHMM(HiddenMarkovModel hmm)
+ {
+ this.hmm = hmm;
+ }
+
+ @Override
+ public boolean hasHMMAnnotation()
+ {
+ if (this.annotation == null) {
+ return false;
+ }
+ for (AlignmentAnnotation ann : annotation)
+ {
+ if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+ {
+ return true;
+ }
+ }
+ return false;
+ }