src/pclset.cpp

/*****************************************************************************
* 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"
*****************************************************************************/
#include "stdafx.h"
#include "pclset.h"

namespace Sleipnir {

CPCLSetImpl::CPCLSetImpl( ) : m_aPCLs(NULL), m_iPCLs(0) { }

CPCLSetImpl::~CPCLSetImpl( ) {

    Reset( ); }

void CPCLSetImpl::Reset( ) {

    if( m_aPCLs ) {
        delete[] m_aPCLs;
        m_aPCLs = NULL; }
    m_iPCLs = 0;
    m_vecstrGenes.clear( );
    m_Genes.Reset( ); }

bool CPCLSet::Open( const std::vector<std::string>& vecstrFiles, size_t iSkip, CPCL::ENormalize eNormalize ) {
    size_t                      i, j;
    ifstream                    ifsm;
    set<string>                 setstrGenes;
    set<string>::const_iterator iterGene;

    Reset( );
    m_aPCLs = new CPCL[ m_iPCLs = vecstrFiles.size( ) ];
    for( i = 0; i < m_iPCLs; ++i ) {
        ifsm.clear( );
        ifsm.open( vecstrFiles[ i ].c_str( ) );
        if( !m_aPCLs[ i ].Open( ifsm, iSkip ) )
            return false;
        ifsm.close( );
        m_aPCLs[ i ].Normalize( eNormalize );
        for( j = 0; j < m_aPCLs[ i ].GetGenes( ); ++j )
            setstrGenes.insert( m_aPCLs[ i ].GetGene( j ) ); }
    m_vecstrGenes.resize( setstrGenes.size( ) );
    for( iterGene = setstrGenes.begin( ),i = 0; iterGene != setstrGenes.end( );
        ++iterGene,++i ) {
        m_vecstrGenes[ i ] = *iterGene;
        m_mapGenes[ *iterGene ] = i; }

    m_Genes.Initialize( m_iPCLs, m_vecstrGenes.size( ) );
    for( i = 0; i < m_iPCLs; ++i )
        for( j = 0; j < m_vecstrGenes.size( ); ++j )
            m_Genes.Set( i, j, m_aPCLs[ i ].GetGene( m_vecstrGenes[ j ] ) );

    return true; }

}