IndividualDataSet.h

/*
 * UserDataSet.h
 *
 *  Created on: March 22, 2017
 *      Author: Daniel
 */

#ifndef INDIVIDUAL_DATA_SET_H_
#define INDIVIDUAL_DATA_SET_H_

#include "GivenKinship.h"
#include <armadillo>
#include <list>
#include <functional>

#include "IndividualData.h"
#include "Option.h"
#include "SnpKinship.h"

//!  A class to keep track of and reconcile IndividualData objects.
class IndividualDataSet
{
	public:
		void addingPedData();
		void addPedData(std::string id, int pedId, std::vector<double>& pedData);
		void addingPhenData();
		void addPhenData(std::string id, std::vector<double>& phenData);
		void addingQCovData();
		void addQCovData(std::string id, std::vector<double>& qCovData);
		void addingCCovData();
		void addCCovData(std::string id, std::vector<double>& cCovData);
		void addingChrData();
		void setChrData(std::vector<int>& chrNew);
		void settingGenoData();
		void setGenoData(arma::mat& genoNew, std::vector<int> numMissingValues);
		void setOption(Option &optionNew);
		void reconcile();

		int getNumSubjects();
		bool getCovAdded();

		arma::mat& getGeno();
		std::vector<int>& getChr();
		arma::mat& getAN();
		arma::mat& getGrm(int idx);
		arma::mat& getCov(int idx);
		arma::mat& getPhen(int idx);
		arma::mat& getGrmWithoutSplit(int idx);
		arma::mat& getCovWithoutSplit(int idx);
		arma::mat& getPhenWithoutSplit(int idx);
		arma::mat& getPed();
		std::vector< std::vector<std::string> >& getSplitPartIds();
		std::list< std::reference_wrapper<IndividualData> >& getIndividualList();
		std::map<std::string, IndividualData>& getIndividualMap();

	private:
		bool pregivenGrmAdded = false;
		bool pedAdded = false;
		int numPedCols = -1;
		bool phenAdded = false;
		int numPhenCols = -1;
		bool qCovAdded = false;
		int numQCovCols = -1;
		bool cCovAdded = false;
		int numCCovCols = -1;
		bool chrAdded = false;
		int numChrCols = -1;
		bool genoAdded = false;

		Option option;

		SnpKinship snpKinship;
		arma::mat grmInit;
		arma::mat ped;

		std::vector<arma::mat> phenSplit;
		std::vector<arma::mat> phenWithoutSplit;
		std::vector<arma::mat> covSplit;
		std::vector<arma::mat> covWithoutSplit;
		std::vector<arma::mat> grmSplit;
		std::vector<arma::mat> grmWithoutSplit;

		arma::mat phenFull;
		arma::mat covFull;
		arma::mat grmFull;

		std::vector<int> chr;
		arma::mat genoInit;
		arma::mat geno;
		std::map<std::string, IndividualData> individualDataIdMap;
		std::list< std::reference_wrapper<IndividualData> > individualDataList;

		std::vector< std::vector<std::string> > splitPartIds;

		void addingPregivenGrm();
		void addPregivenGrm(arma::mat& newGrm, std::vector<std::string>& grmIds);

		void addIndividualIfNotAdded(std::string &id);

		void createGeno();
		void createMatrices(std::string type, std::vector<std::string>& idList, int splitId);
		void createPed();
};


#endif /* INDIVIDUAL_DATA_SET_H_ */