PEDIndividualsExtractor.h

#ifndef PEDIndividualsExtractor_H
#define PEDIndividualsExtractor_H

#include "BasicDefinitions.h"
#include "NucleotideMap.h"
#include "PolymorphicIndividualsExtractor.h"
#include <string>
using namespace std;

class PEDIndividualsExtractor : public PolymorphicIndividualsExtractor
{
public:

	// PEDIndividualsExtractor(): default constructor
	// Precondition: None.
	// Postcondition: three input files have been obtained from user
	PEDIndividualsExtractor();

	// getInput(): gets input from .haps file
	// Precondition: Input is a .ped file in a valid format
	// Postcondition: inds points to individuals from .ped file
    void getInput(string map, string ped);
	void loadInput();
	void getCompleteMarkerSet(Individual * p);
	void getCompleteMarkerSet(Individual * p0 , Individual * p1 );

	//////////////////////////////////////////////////////////////////////////////////
	void loadCompleteMarkerSet(Individual ** p);    
	void updateMarkerSet(Individual * p,unsigned int start,unsigned int end);
	void appendMarkerSet(Individual * p,unsigned int, int );

private:

	// getIndividuals(FamilyType ft): runs specific Individuals parser based on ft
	// Precondition: "ft" is set to a valid FamilyType (matches file input)
	// Postcondition: correct get method is run for family type
    
	//void getIndividuals();
	void stripWhitespace();
	void readMarkerSet( MarkerSet ** );

	// file name for input file
	string ped_file;
	// file name for info file
	string map_file;

	ifstream stream;

	// holds map of nucleotides to binary/quad values
	NucleotideMap inp;

	///////////////////////////////////////////////////////////////////////////////////
	void loadIndividuals();	
	void loadMarkerSet( MarkerSet ** );          
	

};

#endif

// end PEDIndividualsExtractor.h