AccessionManager.cpp

/*
 * @file AccessionManager.cpp
 * @brief implements of AccessionManager class
 *
 * @author S.Tanaka
 * @date 2009.04.14
 * 
 * Copyright(C) 2006-2014 Eisai Co., Ltd. All rights reserved.
 */


#include "stdafx.h"
#include "AccessionManager.h"
#include "Accession.h"

#include <fstream>

using namespace kome::io::mzml;


#include <crtdbg.h>
#ifdef _DEBUG
    #define new new( _NORMAL_BLOCK, __FILE__, __LINE__ )
    #define malloc( s ) _malloc_dbg( s, _NORMAL_BLOCK, __FILE__, __LINE__ )
#endif    // _DEBUG



// constructor
AccessionManager::AccessionManager() {
    // obo file path
    kome::core::ResourceBundle& rb = kome::core::ResourceBundle::getInstance();
    std::string path = rb.searchResource( "psi-ms", NULL, "obo" );
    
    readOboFile( path.c_str() );
}

// destructor
AccessionManager::~AccessionManager() {
    clearAccessions();
}

// clear accessions
void AccessionManager::clearAccessions() {
    for( unsigned int i = 0; i < m_accessions.size(); i++ ) {
        delete m_accessions[ i ];
    }

    m_accessions.clear();
}

// get the number of accessions
unsigned int AccessionManager::getNumberOfAccessions() {
    return m_accessions.size();
}

// get accession
Accession* AccessionManager::getAccession( const unsigned int idx ) {
    if( idx >= m_accessions.size() ) {
        return NULL;
    }
    return m_accessions[ idx ];
}

// get accession
Accession* AccessionManager::getAccession( const char* id ) {
    // string object
    std::string idStr = NVL( id, "" );

    // search
    Accession* acc = NULL;
    for( unsigned int i = 0; i < m_accessions.size() && acc == NULL; i++ ) {
        Accession* tmp = m_accessions[ i ];
        if( idStr.compare( tmp->getId() ) == 0 ) {
            acc = tmp;
        }
    }

    return acc;
}

// read obo file
void AccessionManager::readOboFile( const char* path ) {
    // open
    std::fstream fs;
    fs.open( path, std::ios::in );
    if( fs.fail() ) {
        return;
    }

    // read
    char line[ 0x1000 ];
    Accession* acc = NULL;
    std::map< std::string, Accession* > accMap;
    std::map< Accession*, std::string > parentMap;

    while( !fs.eof() ) {
        fs.getline( line, 0x1000 );
        line[ 0x1000 - 1 ] = '\0';

        char* colon = strstr( line, ":" );
        if( colon != NULL ) {
            // title
            std::string title( line, colon );
            title = trimstring( title.c_str() );

            // value
            char* v = colon + 1;
            while( *v == ' ' || *v == '\n' || *v == '\t' || *v == '\r' ) {
                v = v + 1;
            }
            std::string value = trimstring( v );

            // set accession
            if( title.compare( "id" ) == 0 ) {  // ID
                acc = new Accession( value.c_str() );
                m_accessions.push_back( acc );
                accMap[ value ] = acc;
            }
            else if( title.compare( "name" ) == 0 ) {   // name
                if( acc != NULL ) {
                    acc->setName( value.c_str() );
                }
            }
            else if( title.compare( "is_a" ) == 0 ) {   // parent
                unsigned int pos = value.find( "!" );
                if( pos != (unsigned int)value.npos ) {
                    value = value.substr( 0, pos );
                    value = trimstring( value.c_str() );

                    parentMap[ acc ] = value;
                }
            }
        }
    }

    // close
    fs.close();

    // set parents
    for( unsigned int i = 0; i < m_accessions.size(); i++ ) {
        acc = m_accessions[ i ];
        if( parentMap.find( acc ) != parentMap.end() ) {
            std::string parentName = parentMap[ acc ];
            if( accMap.find( parentName ) != accMap.end() ) {
                Accession* parent = accMap[ parentName ];
                acc->setParent( parent );
            }
        }
    }
}

// get accession manager object
AccessionManager& AccessionManager::getInstance() {
    static AccessionManager mgr;
    return mgr;
}