src/orthology.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 "orthology.h"
#include "genome.h"
#include "meta.h"

namespace Sleipnir {

COrthologyImpl::~COrthologyImpl( ) {

    Reset( ); }

void COrthologyImpl::Reset( ) {
    size_t  i;

    for( i = 0; i < m_vecpGenomes.size( ); ++i )
        delete m_vecpGenomes[ i ];
    m_vecpGenomes.clear( );
    m_vecstrOrganisms.clear( );
    m_mapGenes.clear( );
    m_vecvecpGenes.clear( ); }

bool COrthology::Open( std::istream& istm ) {
    vector<string>  vecstrLine;
    char*           acBuf;
    size_t          i, j;
    string          strOrganism, strGene;
    CGenome*        pGenome;
    CGene*          pGene;

    Reset( );
    acBuf = new char[ c_iBufferSize ];
    while( istm.peek( ) != EOF ) {
        istm.getline( acBuf, c_iBufferSize - 1 );
        vecstrLine.clear( );
        CMeta::Tokenize( acBuf, vecstrLine );
        if( vecstrLine.empty( ) )
            continue;

        m_vecvecpGenes.resize( m_vecvecpGenes.size( ) + 1 );
        {
            vector<CGene*>& vecpGenes   = m_vecvecpGenes[ m_vecvecpGenes.size( ) - 1 ];

            for( i = 0; i < vecstrLine.size( ); ++i ) {
                if( vecstrLine[ i ].length( ) == 0 )
                    continue;
                if( ( j = vecstrLine[ i ].find( c_cOrgSep ) ) == string::npos ) {
                    g_CatSleipnir( ).warn( "COrthology::Open( ) illegal gene token: %s",
                        vecstrLine[ i ].c_str( ) );
                    continue; }
                strOrganism = vecstrLine[ i ].substr( 0, j );
                strGene = vecstrLine[ i ].substr( j + 1 );
                for( j = 0; j < m_vecstrOrganisms.size( ); ++j )
                    if( strOrganism == m_vecstrOrganisms[ j ] )
                        break;
                if( j < m_vecpGenomes.size( ) )
                    pGenome = m_vecpGenomes[ j ];
                else {
                    m_vecpGenomes.push_back( pGenome = new CGenome( ) );
                    m_vecstrOrganisms.push_back( strOrganism ); }
                vecpGenes.push_back( pGene = &pGenome->AddGene( strGene ) );
                m_mapGenes[ pGene ] = j; }
        } }
    delete[] acBuf;

    return true; }

void COrthology::Save( std::ostream& ostm ) const {
    size_t  i, j;

    for( i = 0; i < m_vecvecpGenes.size( ); ++i ) {
        for( j = 0; j < m_vecvecpGenes[ i ].size( ); ++j )
            ostm << ( j ? "\t" : "" ) << m_vecstrOrganisms[ ((COrthology*)this)->m_mapGenes[
                m_vecvecpGenes[ i ][ j ] ] ] << c_cOrgSep << m_vecvecpGenes[ i ][ j ]->GetName( );

        ostm << endl; } }

}