#ifndef ALIGNER_HH_
#define ALIGNER_HH_
/**
 * Project     : CASAVA
 * Module      : $RCSfile: Aligner.hh,v $
 * @author     : Tony Cox
 * Copyright   : Copyright (c) Illumina 2008, 2009. All rights reserved.
 *
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 *
 */

#include "common/SharedDataTypes.hh"

#include <string>

namespace ca {
namespace variance_detection {

using namespace casava::common;

/**
 * @class Aligner
 *
 * @brief Implementation of global alignment with affine gap costs.
 *
 * TODO: Integrate with Eland
 *
 */
struct Aligner {
public:
	Aligner(ScoreType w_match, ScoreType w_mismatch, ScoreType w_open,
			ScoreType w_extend) :
		w_match_(w_match), w_mismatch_(w_mismatch), w_open_(w_open),
				w_extend_(w_extend) {
	}

	ScoreType operator()(const char* x, const char* y, const unsigned x_size, const unsigned y_size);

	ScoreType operator()(const std::string& x, const std::string& y) {
		//(*this)(x.c_str(), y.c_str(), x.size(), y.size());
		return (*this)(x.c_str(),y.c_str(),x.size(),y.size());
	} // ~operator()

	//protected:

	// match score
	const ScoreType w_match_;
	// mismatch score
	const ScoreType w_mismatch_;
	// gap opening score
	const ScoreType w_open_;
	// gap extension score
	const ScoreType w_extend_;

	std::string xt_;
	std::string yt_;
	std::string at_;

	int x_start_;
	int y_start_;
	int x_end_;
	int y_end_;

	int score_;

};

}
} // end namespace casava{ namespace { applications

#endif /*ALIGNER_HH_*/