src/pclset.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 PCLSET_H
#define PCLSET_H

#include "pclseti.h"
#include "meta.h"
#include "pcl.h"

namespace Sleipnir {

class CPCLSet : CPCLSetImpl {
public:
    bool Open( const std::vector<std::string>& vecstrFiles, size_t iSkip = 2,
        CPCL::ENormalize eNormalize = CPCL::ENormalizeNone );

    size_t GetGenes( ) const {

        return m_vecstrGenes.size( ); }

    size_t GetPCLs( ) const {

        return m_iPCLs; }

    float Get( size_t iPCL, size_t iGene, size_t iExperiment ) const {
        size_t  iMap;

        if( ( iMap = m_Genes.Get( iPCL, iGene ) ) == -1 )
            return CMeta::GetNaN( );

        return m_aPCLs[ iPCL ].Get( iMap, iExperiment ); }

    const float* Get( size_t iPCL, size_t iGene ) const {
        size_t  iMap;

        if( ( iMap = m_Genes.Get( iPCL, iGene ) ) == -1 )
            return NULL;

        return m_aPCLs[ iPCL ].Get( iMap ); }

    size_t GetGene( const std::string& strGene ) const {
        TMapStrI::const_iterator    iterGene;

        return ( ( ( iterGene = m_mapGenes.find( strGene ) ) == m_mapGenes.end( ) ) ? -1 :
            iterGene->second ); }

    const std::string& GetGene( size_t iGene ) const {

        return m_vecstrGenes[ iGene ]; }

    const std::vector<std::string>& GetGeneNames( ) const {

        return m_vecstrGenes; }

    const CPCL& Get( size_t iPCL ) const {

        return m_aPCLs[ iPCL ]; }
};

}

#endif // PCLSET_H