src/genomei.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 GENOMEI_H
#define GENOMEI_H

#include <map>
#include <vector>

#include "filei.h"

namespace Sleipnir {

class CGene;
class CGenome;
class IOntology;

class CGeneImpl {
protected:
    CGeneImpl( const std::string& );
    ~CGeneImpl( );

    CGeneImpl& operator=( const CGeneImpl& );
    void IncrementOntologies( const IOntology* );

    std::string             m_strName;
    size_t                  m_iOntologies;
    const IOntology**       m_apOntologies;
    std::vector<size_t>**   m_apveciAnnotations;
    size_t                  m_iSynonyms;
    std::string*            m_astrSynonyms;
    bool                    m_fRNA;
    bool                    m_fDubious;
    std::string             m_strGloss;
    float                   m_weight;
};

class CGenomeImpl : protected CFileImpl {
protected:
    typedef std::map<std::string,size_t>    TMapStrI;

    static const char   c_szDubious[];
    static const char   c_szORF[];
    static const char*  c_aszRNA[];

    ~CGenomeImpl( );

    std::vector<CGene*> m_vecpGenes;
    TMapStrI            m_mapGenes;
};

class CGenesImpl {
protected:
    static const char   c_cComment  = '#';

    typedef std::map<std::string,size_t>    TMapStrI;

    CGenesImpl( CGenome& );

    CGenome&            m_Genome;
    std::vector<CGene*> m_vecpGenes;
    TMapStrI            m_mapGenes;
    bool                isWeighted;
};
}

#endif // GENOMEI_H