+ @Override
+ public HiddenMarkovModel getHMM()
+ {
+ return hmm;
+ }
+
+ @Override
+ public void setHMM(HiddenMarkovModel hmm)
+ {
+ this.hmm = hmm;
+ }
+
+ @Override
+ public void updateHMMMapping()
+ {
+ int node = 1;
+ int column = 0;
+ for (char residue : sequence)
+ {
+ if (!Comparison.isGap(residue))
+ {
+ hmm.setAlignmentColumn(node, column);
+ hmm.getNodeLookup().put(column, node);
+ node++;
+ }
+ else
+ {
+ hmm.getNodeLookup().remove(column);
+ }
+ column++;
+ }
+
+ }
+
+ @Override
+ public boolean isHMMConsensusSequence()
+ {
+ return isHMMConsensusSequence;
+ }
+
+ @Override
+ public void setIsHMMConsensusSequence(boolean isHMMConsensusSequence)
+ {
+ this.isHMMConsensusSequence = isHMMConsensusSequence;
+ }
+
+ @Override
+ public boolean hasHMMAnnotation()
+ {
+ return hasInfo;
+ /*
+ if (annotation == null)
+ {
+ return false;
+ }
+
+ for (AlignmentAnnotation annot : annotation)
+ {
+ if (annot.label.contains("_HMM"))
+ {
+ return true;
+ }
+ }
+ return false;
+ */
+ }
+
+ @Override
+ public void setHasInfo(boolean status)
+ {
+ hasInfo = true;
+ }
+
+ @Override
+ public int getPreviousPosition()
+ {
+ return previousPosition;
+ }
+
+ @Override
+ public void setPreviousPosition(int previousPosition)
+ {
+ this.previousPosition = previousPosition;
+ }
+