kome::io::mzml::AccessionManager Class Reference

accession object management class More...

#include <AccessionManager.h>

Public Member Functions
unsigned int	getNumberOfAccessions ()
	gets the number of accessions More...
Accession *	getAccession (const unsigned int idx)
	gets accession More...
Accession *	getAccession (const char *id)
	gets accession More...

Static Public Member Functions
static AccessionManager &	getInstance ()
	gets accession manager object (This is the only object.) More...

Protected Member Functions
	AccessionManager ()
	constructor
virtual	~AccessionManager ()
	destructor
void	clearAccessions ()
	clears accessions
void	readOboFile (const char *path)
	reads obo file More...

Protected Attributes
std::vector< Accession * >	m_accessions

Detailed Description

accession object management class

Definition at line 26 of file AccessionManager.h.

Member Function Documentation

Accession * kome::io::mzml::AccessionManager::getAccession

(

const unsigned int

idx

)

gets accession

Parameters

idx	accession index

Returns

accession (If NULL, the index is illegal.)

Definition at line 58 of file AccessionManager.cpp.

                                                                  {
    if( idx >= m_accessions.size() ) {
        return NULL;
    }
    return m_accessions[ idx ];
}

Accession * kome::io::mzml::AccessionManager::getAccession

(

const char *

id

)

gets accession

Parameters

id	accession ID

Returns

accession (If NULL, the ID is illegal.)

Definition at line 66 of file AccessionManager.cpp.

                                                          {
    // 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;
}

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static AccessionManager & kome::io::mzml::AccessionManager::getInstance ( )

static

gets accession manager object (This is the only object.)

Returns

accession manager object

Definition at line 154 of file AccessionManager.cpp.

                                                {
    static AccessionManager mgr;
    return mgr;
}

unsigned int kome::io::mzml::AccessionManager::getNumberOfAccessions

(

)

gets the number of accessions

Returns

the number of accessions

Definition at line 53 of file AccessionManager.cpp.

                                                     {
    return m_accessions.size();
}

void kome::io::mzml::AccessionManager::readOboFile ( const char *  path )

protected

reads obo file

Parameters

path	obo file path

Definition at line 83 of file AccessionManager.cpp.

                                                     {
    // 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 );
            }
        }
    }
}

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Member Data Documentation

std::vector< Accession* > kome::io::mzml::AccessionManager::m_accessions

protected

accessions

Definition at line 42 of file AccessionManager.h.

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The documentation for this class was generated from the following files:

• MzmlIOPlugin/AccessionManager.h
• MzmlIOPlugin/AccessionManager.cpp