//ProbMatrix.cpp
//Coded by Vishakh (vishakh@uci.edu)
//ICS 175A, Winter 2004
//Project: Motif detection in yeast
//Purpose: Encapsulates the functionality of a probability matrix

#include "ProbMatrix.h"

/*
*FUNCTION:  ProbMatrix(int size)
*PURPOSE:	Creates an empty probability matrix of size 'n'.
*REMARKS:	
*/
ProbMatrix::ProbMatrix(int size)
{
	cols.resize(size);
}

/*
*FUNCTION:  ProbMatrix(DString seed)
*PURPOSE:	Creates a probability matrix based on the seed.
*REMARKS:	
*/
ProbMatrix::ProbMatrix(DString seed)
{
	cols.resize(seed.size());

	for(int i=0; i<cols.size(); i++)
	{
		setValue(i,'A', 0.1);
		setValue(i,'T', 0.1);
		setValue(i,'G', 0.1);
		setValue(i,'C', 0.1);

		if(seed[i]=='A') setValue(i,'A', 0.7);
		if(seed[i]=='T') setValue(i,'T', 0.7);
		if(seed[i]=='G') setValue(i,'G', 0.7);
		if(seed[i]=='C') setValue(i,'C', 0.7);
	}

}

/*
*FUNCTION:  int size()
*PURPOSE:	Returns the number of columns of the probability matrix
*REMARKS:	
*/
int ProbMatrix::size()
{
	return cols.size();
}

/*
*FUNCTION:  double getValue(int column, char letter);
*PURPOSE:	Returns the probability of a given letter in a given column
*REMARKS:	
*/
double ProbMatrix::getValue(int column, char letter)
{
	if(letter=='A') return cols[column].a;
	if(letter=='T') return cols[column].t;
	if(letter=='G') return cols[column].g;
	if(letter=='C') return cols[column].c;
	else return -1.0;
}

/*
*FUNCTION:  void setValue(int column, char letter, double val)
*PURPOSE:	Sets the probability of a given letter in a given column
*REMARKS:	
*/
void ProbMatrix::setValue(int column, char letter, double val)
{
	if(letter=='A') cols[column].a = val;
	if(letter=='T') cols[column].t = val;
	if(letter=='G') cols[column].g = val;
	if(letter=='C') cols[column].c = val;
}


/*
*FUNCTION:  void updateMatrix(vector<DString> substrings)
*PURPOSE:	Recreates the matrix with probabilities calculated using the given array of strings
*REMARKS:	
*/
void ProbMatrix::updateMatrix(vector<DString> substrings)
{
	ProbMatrix pm(cols.size());
	//Store number of occurances in matrix
	for(int i=0; i<substrings.size(); i++)
	{
		DString temp = substrings[i];
		for(int j=0; j<temp.size(); j++)
		{
			if(temp[j]=='A') pm.setValue(j, 'A', pm.getValue(j, 'A')+1.0);
			if(temp[j]=='T') pm.setValue(j, 'T', pm.getValue(j, 'T')+1.0);
			if(temp[j]=='G') pm.setValue(j, 'G', pm.getValue(j, 'G')+1.0);
			if(temp[j]=='C') pm.setValue(j, 'C', pm.getValue(j, 'C')+1.0);
		}
	}
	
	//Calcualate probabilities and copy them to probability matrix
	for(int i=0; i<pm.size(); i++)
	{
		setValue(i, 'A', pm.getValue(i, 'A')/substrings.size());
		setValue(i, 'T', pm.getValue(i, 'T')/substrings.size());
		setValue(i, 'G', pm.getValue(i, 'G')/substrings.size());
		setValue(i, 'C', pm.getValue(i, 'C')/substrings.size());
	}
}

/*
*FUNCTION:  void print()
*PURPOSE:	Prints the matrix
*REMARKS:	Careful, the rows and columns are switched on the display!
*/
void ProbMatrix::print()
{
	for(int i=0; i<size(); i++)
	{
		cout<<endl<<"Col "<<i<<"- A: "<<cols[i].a<< " \tT: "<<cols[i].t<<" \tC: "<<cols[i].c<<" \tG: "<<cols[i].g;
	}
}

/*
*FUNCTION:  vector<MatrixColumn> getMatrix()
*PURPOSE:	Returns matrix for the GUI
*REMARKS:	
*/
vector<MatrixColumn> ProbMatrix::getMatrix()
{
	return cols;
}