Data.h

/*
 * data.h
 *
 *  Created on: Feb 10, 2016
 *      Author: Joey
 */

#ifndef DATA_H_
#define DATA_H_

#include <iostream>
#include <armadillo>
#include <map>
#include <set>
#include <iterator>
#include <bitset>
#include <functional>

#include "IndividualDataSet.h"
#include "Option.h"
#include "Scorer.h"

//!  A class to load all relevant data.  Responsible solely for loading data - not for reconciling missing individuals.
/*!
   Loads data into the userDataSet, trait, lambdaVec, and scorers fields.
*/
class Data
{
	public:
		Data(Option &option);
		void load(Option &option);
		void writeKinship(std::string outDir);

		IndividualDataSet individualDataSet;
		arma::mat trait;
		std::vector<double> lambdaVec;
		std::vector<Scorer> scorers;

	private:
		bool canLoadFam(const Option &option);
		void loadFam(const Option &option);
		bool canLoadPheno(const Option &option);
		void loadPheno(const Option &option);
		bool canLoadQCov(const Option &option);
		void loadQCov(const Option &option);
		bool canLoadCCov(const Option &option);
		void loadCCov(const Option &option);
		bool canLoadSNP(const Option &option);
		void loadSNP(const Option &option);
		bool canLoadTrait(const Option &option);
		void loadTrait(const Option &option);
		bool canLoadLambdaVecFile(const Option &option);
		void loadLambdaVecFile(const Option &option);
};


#endif /* DATA_H_ */