src/orthologyi.h

/*****************************************************************************
* This file is provided under the Creative Commons Attribution 3.0 license.
*
* You are free to share, copy, distribute, transmit, or adapt this work
* PROVIDED THAT you attribute the work to the authors listed below.
* For more information, please see the following web page:
* http://creativecommons.org/licenses/by/3.0/
*
* This file is a component of the Sleipnir library for functional genomics,
* authored by:
* Curtis Huttenhower (chuttenh@princeton.edu)
* Mark Schroeder
* Maria D. Chikina
* Olga G. Troyanskaya (ogt@princeton.edu, primary contact)
*
* If you use this library, the included executable tools, or any related
* code in your work, please cite the following publication:
* Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, and
* Olga G. Troyanskaya.
* "The Sleipnir library for computational functional genomics"
*****************************************************************************/
#ifndef ORTHOLOGYI_H
#define ORTHOLOGYI_H

#include <map>

#include "file.h"

namespace Sleipnir {

class CGene;
class CGenome;

class COrthologyImpl : protected CFile {
protected:
    static const char   c_cOrgSep   = '|';

    typedef std::map<CGene*,size_t> TMapGeneI;

    ~COrthologyImpl( );

    void Reset( );

    std::vector<std::string>            m_vecstrOrganisms;
    std::vector<CGenome*>               m_vecpGenomes;
    TMapGeneI                           m_mapGenes;
    std::vector<std::vector<CGene*> >   m_vecvecpGenes;
};

}

#endif // ORTHOLOGYI_H