//genomicPair.cpp
//Coded by Jeff Weiss (jmweiss@uci.edu)
//ICS 175A, Winter 2004
//Project: Motif detection in yeast
//Purpose: provides a data structure to store genetic squences along with the statistical
//information we for each sequence


#include "genomicPair.h"


/*
*FUNCTION:	genomicPair
*PURPOSE:	constructor
*REMARKS:	note that count starts at 0 and scores start at -1
*/
GenomicPair::GenomicPair()
{
	count=0;
	sequence=DString();
	score1=-1;
	score2=-1;
	score3=-1;
}

/*GenomicPair::GenomicPair(DString newSequence,int newCount)
{
	count = newCount;
	sequence = newSequence;
}*/


/*
*FUNCTION:	constructor
*PURPOSE:	constructor that takes in the sequence and the count
*REMARKS:
*/
GenomicPair::GenomicPair(const DString newSequence, const int newCount)
{
	count = newCount;
	sequence = newSequence;
	score1=-1;
	score2=-1;
	score3=-1;
}


/*
*FUNCTION:	Constructor
*PURPOSE:	takes in a sqeuence name
*REMARKS:	note that count is initialized to 1, not 0
*/
GenomicPair::GenomicPair(DString newSequence)
{
	sequence=newSequence;
	count=1;
	score1=-1;
	score2=-1;
	score3=-1;
}


/*
*FUNCTION:	constructor
*PURPOSE:	takes in call values needed for a new genomic pair
*REMARKS:	used when loading from a file	
*/
GenomicPair::GenomicPair(DString newSequence,int newCount,int newScore1,int newScore2,int newScore3)
{
	sequence=newSequence;
	count=newCount;
	score1=newScore1;
	score2=newScore2;
	score3=newScore3;
}


/*
*FUNCTION:	constructor
*PURPOSE:	this is a copy constructor
*REMARKS:	
*/
GenomicPair::GenomicPair(const GenomicPair& newGenomicPair)
{

	count=newGenomicPair.count;
	sequence=newGenomicPair.sequence;
	score1=newGenomicPair.score1;
	score2=newGenomicPair.score2;
	score3=newGenomicPair.score3;
}


/*
*FUNCTION:	operator =
*PURPOSE:	this is an assignment operator overload
*REMARKS:	
*/
void GenomicPair::operator=(GenomicPair rhs)
{
	sequence=rhs.sequence;
	count=rhs.count;
	score1=rhs.score1;
	score2=rhs.score2;
	score3=rhs.score3;
	
	//return GenomicPair(rhs.sequence,rhs.count,rhs.score1,rhs.score2,rhs.score3);	
}
/*
*FUNCTION:	< overload comparison operator
*PURPOSE:	compares score1 for sorting purposes
*REMARKS:	this is fixed comparison on one of 3 calues
*/
bool GenomicPair::operator<(GenomicPair rhs)
{
    return score1 < rhs.score1;
}







/*
*FUNCTION:	getCount
*PURPOSE:	get the count associated with the sequence
*REMARKS:	
*/
int GenomicPair::getCount()
{
	return count;
}

/*
*FUNCTION:	setCount
*PURPOSE:	set the count for the sequence
*REMARKS:	
*/
void GenomicPair::setCount(int newCount)
{
	count=newCount;
}

/*
*FUNCTION:	~GenomicPair
*PURPOSE:	destructor
*REMARKS:	note there is no explicit declaraiton of dynamic memory structors in GenomicPair
*/

GenomicPair::~GenomicPair()
{	
}


/*
*FUNCTION:	getSequence
*PURPOSE:	returns the sequence DString
*REMARKS:	
*/
DString GenomicPair::getSequence()
{
	return sequence;
}


/*
*FUNCTION:	set sequence
*PURPOSE:	sets the sequence
*REMARKS:	note there is no checking of the passed in value
*/
void GenomicPair::setSequence(DString newString)
{
	sequence=newString;
}

/*
*FUNCTION:	incrementCount
*PURPOSE:	increments the count by 1
*REMARKS:	no error reporting (i.e. if maxint is exceded)
*/
void GenomicPair::incrementCount()
{
	count++;
}


/*
*FUNCTION:	print
*PURPOSE:	print pair data to stdout
*REMARKS:	for testing/development purposes only, do not use in production code
*/
void GenomicPair::print()
{	
	cout<<" Count:"<<getCount()<<endl;
	cout<<"Pair:";
	sequence.print();

}