MzmlSample.cpp

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#include "stdafx.h"
#include "MzmlSample.h"

#include "MzmlSampleSet.h"
#include "MzmlHandler.h"


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
MzmlSample::MzmlSample( MzmlSampleSet* sampleSet ) : kome::objects::Sample( sampleSet ) {
    // initialize
    m_sampleSet = sampleSet;

    setParallelReadable( true );
}

// destructor
MzmlSample::~MzmlSample() {
}

// add parent file
void MzmlSample::addParentFile( const char* path ) {
    // string object
    std::string p = NVL( path, "" );

    // check
    for( unsigned int i = 0; i < m_parentFiles.size(); i++ ) {
        if( p.compare( m_parentFiles[ i ] ) == 0 ) {
            return;
        }
    }

    // property
    kome::core::Properties& props = getRootDataGroupNode()->getProperties();
   
    std::string key = FMT( "Parent File %d", m_parentFiles.size() );
    props.setValue( key.c_str(), p.c_str() );

    // add
    m_parentFiles.push_back( p );
}

// mzML sample set object
MzmlSampleSet* MzmlSample::getMzmlSampleSet() {
    return m_sampleSet;
}

// get the number of parent files
unsigned int MzmlSample::getNumberOfParentFiles() {
    return m_parentFiles.size();
}

// get parent file path
const char* MzmlSample::getParentFilePath( const unsigned int index ) {
    if( index >= m_parentFiles.size() ) {
        return NULL;
    }
    return m_parentFiles[ index ].c_str();
}

// add array information
void MzmlSample::addArrayInfo(
        const char* name,
        const int bits,
        const bool compressed,
        const double scale,
        const bool isY
) {
    // check the name
    if( name == NULL ) {
        return;
    }

    // get array information
    ArrayInfo* info = getArrayInfo( name );
    if( info == NULL ) {
        m_arrayInfo.resize( m_arrayInfo.size() + 1 );
        info = &( m_arrayInfo.back() );
    }

    // set values
    info->name = name;
    info->bits = bits;
    info->compressed = compressed;
    info->scale = scale;
    info->isY = isY;
}

// get array information
MzmlSample::ArrayInfo* MzmlSample::getArrayInfo( const char* name ) {
    // check the name
    if( name == NULL ) {
        return NULL;
    }

    // search
    ArrayInfo* info = NULL;
    for( unsigned int i = 0; i < m_arrayInfo.size() && info == NULL; i++ ) {
        ArrayInfo* tmp = &( m_arrayInfo[ i ] );
        if( tmp->name.compare( name ) == 0 ) {
            info = tmp;
        }
    }

    return info;
}

// on open
bool MzmlSample::onOpenSample( kome::objects::DataGroupNode* rootGroup, kome::core::Progress* progress ) {
    // handler
    MzmlHandler handler( *this );
    handler.parse( m_sampleSet->getFilePath() );

    return !handler.isError();
}

// on close sample
bool MzmlSample::onCloseSample() {
    return true;
}