Alignment.h

/* 
 * DPPDiv version 1.0b source code (git: 9c0ac3d2258f89827cfe9ba2b5038f0f656b82c1)
 * Copyright 2009-2011
 * Tracy Heath(1,2,3) (NSF postdoctoral fellowship in biological informatics DBI-0805631)
 * Mark Holder(1)
 * John Huelsenbeck(2)
 *
 * (1) Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045
 * (2) Integrative Biology, University of California, Berkeley, CA 94720-3140
 * (3) email: tracyh@berkeley.edu
 *
 * DPPDiv is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * General Public License (the file gpl.txt included with this
 * distribution or http://www.gnu.org/licenses/gpl.txt for more
 * details.
 *
 * Some of this code is from publicly available source by John Huelsenbeck
 */

#ifndef AlIGNMENT_H
#define AlIGNMENT_H

#include <string>
#include <vector>
#include <iostream>


class Alignment {

	public:
									Alignment(std::string fn); 
									~Alignment(void);
		void						compress(void);
		int							getNumTaxa(void) { return numTaxa; }
		int							getNumChar(void);
		std::string					getTaxonName(int i) { return taxonNames[i]; }
		int							getIndexForTaxonNamed(std::string nm);
		int							getNucleotide(int i, int j);
		int							getNumSitesOfPattern(int i);
		void						getPossibleNucs (int nucCode, int *nuc);
		bool						isTaxonPresent(std::string nm);
		void						print(std::ostream &) const;
		int							getNumPatterns(void) { return numPatterns; }

	private:
		int							nucID(char nuc);
		int							numTaxa;
		int							numChar;
		int							**matrix;
		int							**compressedMatrix;
		int							*patternCount;
		int							numPatterns;
		bool						isCompressed;
		std::vector<std::string>	taxonNames;
};

#endif