//select() method returns the index of n-th occurence of given character in input nucleotide string.
//It doesn't use RRR data structure, it uses regular bitmap.
public int select(int nthOccurrence, char character)
{
Interval alphabeticInterval = new Interval(0, alphabet.Count - 1);
WaveletNode currentNode = rootNode;
int indexOfCharInAlph = getIndex(character, alphabet);
bool characterRepresentedWithZero = true;
while (alphabeticInterval.isGreaterThanTwo())
{
if (alphabeticInterval.getSize() == 3)
{
if (alphabeticInterval.getRightIndex() == indexOfCharInAlph)
{
characterRepresentedWithZero = false;
break;
}
}
if (indexOfCharInAlph <= alphabeticInterval.getMiddleIndex())
{
currentNode = currentNode.getLeftChild();
alphabeticInterval.setRightIndex();
}
else
{
currentNode = currentNode.getRightChild();
alphabeticInterval.setLeftIndex();
}
}
if (characterRepresentedWithZero)
{
if (alphabeticInterval.getLeftIndex() == indexOfCharInAlph)
{
characterRepresentedWithZero = true;
}
else
{
characterRepresentedWithZero = false;
}
}
int position = getPositionOfNthOccurrence(currentNode.getBitmap(), nthOccurrence, characterRepresentedWithZero);
if (position == 0)
{
return(-1);
}
WaveletNode child = currentNode;
currentNode = currentNode.getParent();
while (currentNode != null)
{
if (currentNode.getLeftChild().Equals(child))
{
position = getPositionOfNthOccurrence(currentNode.getBitmap(), position, true);
}
else
{
position = getPositionOfNthOccurrence(currentNode.getBitmap(), position, false);
}
currentNode = currentNode.getParent();
child = child.getParent();
}
return(position - 1);
}
//selectRRR() method returns index of n-th occurence of given character in input nucleotide string
public int selectRRR(int nthOccurrence, char character)
{
Interval alphabeticInterval = new Interval(0, alphabet.Count - 1);
WaveletNode currentNode = rootNode;
int indexOfCharInAlph = getIndex(character, alphabet);
bool characterRepresentedWithZero = true;
while (alphabeticInterval.isGreaterThanTwo())
{
if (alphabeticInterval.getSize() == 3)
{
if (alphabeticInterval.getRightIndex() == indexOfCharInAlph)
{
characterRepresentedWithZero = false;
break;
}
}
if (indexOfCharInAlph <= alphabeticInterval.getMiddleIndex())
{
currentNode = currentNode.getLeftChild();
alphabeticInterval.setRightIndex();
}
else
{
currentNode = currentNode.getRightChild();
alphabeticInterval.setLeftIndex();
}
}
if (characterRepresentedWithZero)
{
if (alphabeticInterval.getLeftIndex() == indexOfCharInAlph)
{
characterRepresentedWithZero = true;
}
else
{
characterRepresentedWithZero = false;
}
}
// bottom-up tree traversal once we have node representing given character
int position = selectOnBitmap(currentNode, nthOccurrence, characterRepresentedWithZero);
if (position == 0)
{
return(-1); // no n occurrences of character
}
WaveletNode child = currentNode;
currentNode = currentNode.getParent();
while (currentNode != null)
{
if (currentNode.getLeftChild().Equals(child))
{
position = selectOnBitmap(currentNode, position, true);
}
else
{
position = selectOnBitmap(currentNode, position, false);
}
currentNode = currentNode.getParent();
child = child.getParent();
}
return(position - 1);
}
