src/orthology.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 ORTHOLOGY_H
#define ORTHOLOGY_H

#include "orthologyi.h"

namespace Sleipnir {

class COrthology : COrthologyImpl {
public:
    bool Open( std::istream& istm );
    void Save( std::ostream& ostm ) const;

    size_t GetClusters( ) const {

        return m_vecvecpGenes.size( ); }

    size_t GetGenes( size_t iCluster ) const {

        return m_vecvecpGenes[ iCluster ].size( ); }

    CGene& GetGene( size_t iCluster, size_t iGene ) const {

        return *m_vecvecpGenes[ iCluster ][ iGene ]; }

    size_t GetGenomes( ) const {

        return m_vecpGenomes.size( ); }

    CGenome* GetGenome( size_t iOrganism ) const {

        return m_vecpGenomes[ iOrganism ]; }

    const std::string& GetOrganism( size_t iOrganism ) const {

        return m_vecstrOrganisms[ iOrganism ]; }

    size_t GetOrganism( const CGene& Gene ) const {
        TMapGeneI::const_iterator   iterGenome;

        return ( ( ( iterGenome = m_mapGenes.find( (CGene*)&Gene ) ) == m_mapGenes.end( ) ) ? -1 :
            iterGenome->second ); }
};

}

#endif // ORTHOLOGY_H