kome::io::mzml::MzmlChromatogram Class Reference

mzml sample spectrum class More...

#include <MzmlChromatogram.h>

Inheritance diagram for kome::io::mzml::MzmlChromatogram:

Collaboration diagram for kome::io::mzml::MzmlChromatogram:

Public Member Functions
	MzmlChromatogram (MzmlSample *file)
	constructor More...
virtual	~MzmlChromatogram ()
	destructor
void	setOffset (const long long offset)
	sets data offset More...
long long	getOffset ()
	gets data offset More...

Protected Member Functions
void	parse (xercesc::SAX2XMLReader *parser)
	parse XML data More...
virtual void	onGetXYData (kome::core::XYData *const xyData)
	This method is called by getXYData method (override method) More...
virtual void	onGetSpectra (kome::objects::DataSet &dataSet, const double startRt, const double endRt, const kome::objects::SearchType startSearch, const kome::objects::SearchType endSearch)
	This method is called by searchSpectrum or getSpectra method (overriede method) More...
virtual double	onGetMass (const unsigned int index)
	This method is called by getMass method (override method) More...
virtual int	onGetMsStage (const unsigned int index)
	This method is called by getMsStage method (override method) More...
virtual double	onGetPrecursor (const unsigned int index)
	This method is called by getPrecursor method (override method) More...

Protected Attributes
MzmlSample *	m_mzmlSample
long long	m_offset

Detailed Description

mzml sample spectrum class

Definition at line 29 of file MzmlChromatogram.h.

Constructor & Destructor Documentation

kome::io::mzml::MzmlChromatogram::MzmlChromatogram

(

MzmlSample *

file

)

constructor

Parameters

file

sample

Definition at line 36 of file MzmlChromatogram.cpp.

        : kome::objects::Chromatogram( file ) {
    m_offset = -1;
    m_mzmlSample = file;
}

Member Function Documentation

long long kome::io::mzml::MzmlChromatogram::getOffset

(

)

gets data offset

Returns

data offset

Definition at line 52 of file MzmlChromatogram.cpp.

                                      {
    return m_offset;
}

double kome::io::mzml::MzmlChromatogram::onGetMass ( const unsigned int  index )

protectedvirtual

This method is called by getMass method (override method)

Parameters

index

data index

Returns

mass

Definition at line 172 of file MzmlChromatogram.cpp.

                                                             {
    return -1.0;
}

int kome::io::mzml::MzmlChromatogram::onGetMsStage ( const unsigned int  index )

protectedvirtual

This method is called by getMsStage method (override method)

Parameters

index

data index

Returns

MS stage.

Definition at line 177 of file MzmlChromatogram.cpp.

                                                             {
    return -1;
}

double kome::io::mzml::MzmlChromatogram::onGetPrecursor ( const unsigned int  index )

protectedvirtual

This method is called by getPrecursor method (override method)

Parameters

index

data index

Returns

precursor mass

Definition at line 182 of file MzmlChromatogram.cpp.

                                                                  {
    return -1.0;
}

void kome::io::mzml::MzmlChromatogram::onGetSpectra ( kome::objects::DataSet &  dataSet, const double  startRt, const double  endRt, const kome::objects::SearchType  startSearch, const kome::objects::SearchType  endSearc  )

protectedvirtual

This method is called by searchSpectrum or getSpectra method (overriede method)

Parameters

spectra	spectra object to store spectra
startRt	start RT
endRt	end RT
startSearch	start search type
endSearch	end search type

Definition at line 162 of file MzmlChromatogram.cpp.

  {
}

void kome::io::mzml::MzmlChromatogram::onGetXYData ( kome::core::XYData *const  xyData )

protectedvirtual

This method is called by getXYData method (override method)

Parameters

xyData

object to store data points

Definition at line 120 of file MzmlChromatogram.cpp.

                                                                 {
    // check the parameter
    if( xyData == NULL ) {
        return;
    }

    // data points
    kome::core::DataPoints dps;

    // parser
    xercesc::SAX2XMLReader* parser = kome::xml::XercesTool::getParser( NULL );
    parser->setFeature( xercesc::XMLUni::fgXercesSchema, false );
    parser->setFeature( xercesc::XMLUni::fgXercesSchemaFullChecking, false );

    // create handler
    MzmlDataHandler handler( *m_mzmlSample, getName(), dps );

    parser->setContentHandler( &handler );
    parser->setErrorHandler( &handler );

    // parse
    try {
        parse( parser );
        for( unsigned int i = 0; i < dps.getLength(); i++ ) {
            xyData->addPoint( dps.getX( i ), dps.getY( i ) );
        }
    }
    catch( const xercesc::XMLException& e ) {
        LOG_ERROR( FMT( "XML Exception: %s", kome::xml::XercesTool::transcode( e.getMessage() ).c_str() ) );
        handler.setError( true );
    }
    catch( const xercesc::SAXParseException& e ) {
        LOG_ERROR( FMT( "SAX Parse Exception: %s", kome::xml::XercesTool::transcode( e.getMessage() ).c_str() ) );
        handler.setError( true );
    }
    catch( ... ) {
        LOG_ERROR( FMT( "Unexpected Exception" ) );
        handler.setError( true );
    }
}

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void kome::io::mzml::MzmlChromatogram::parse ( xercesc::SAX2XMLReader *  parser )

protected

parse XML data

Parameters

parser

parser

Definition at line 57 of file MzmlChromatogram.cpp.

                                                           {
    // get file
    MzmlSample* sample = (MzmlSample*)getSample();
    MzmlSampleSet* sampleSet = sample->getMzmlSampleSet();

    // parse
    if( m_offset > 0 ) {
        // seek
        FILE* fp = sampleSet->getFile();
        fileseek( fp, m_offset, SEEK_SET );

        // read file
        std::string tag;
        char buff[ 1024 ];
        bool loop = true;
        bool endTag = false;
        while( loop ) {
            // read
            int readSize = fread( buff, 1, 1023, fp );

            // add to tag
            if( readSize > 0 ) {
                buff[ readSize ] = '\0';
                tag.append( buff );
            }

            // check the tag
            unsigned int pos = tag.find( "</chromatogram>" );
            if( pos != (unsigned int)tag.npos ) {
                endTag = true;
                loop = false;

                tag = tag.substr( 0, pos );
                tag.append( "</chromatogram>" );
            }

            // check the size
            if( readSize < 1023 ) {
                loop = false;
            }
        }

        unsigned int pos = tag.find( "<chromatogram" );
        if( pos != (unsigned int)tag.npos ) {
            tag = tag.substr( pos );
        }

        // parse
        if( endTag ) {
            xercesc::MemBufInputSource source( (const XMLByte*)tag.c_str(), tag.size(), "memory_buffer", false );
            parser->parse( source );
        }
        else {
            LOG_WARN( FMT( "Failed to get the chromatogram tag." ) );
        }
    }
    else {
        // parse file
        parser->parse( sampleSet->getFilePath() );
    }
}

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void kome::io::mzml::MzmlChromatogram::setOffset

(

const long long

offset

)

sets data offset

Parameters

offset

data offset

Definition at line 47 of file MzmlChromatogram.cpp.

                                                         {
    m_offset = offset;
}

Member Data Documentation

MzmlSample* kome::io::mzml::MzmlChromatogram::m_mzmlSample

protected

sample

Definition at line 46 of file MzmlChromatogram.h.

long long kome::io::mzml::MzmlChromatogram::m_offset

protected

data offset

Definition at line 50 of file MzmlChromatogram.h.

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

• MzmlIOPlugin/MzmlChromatogram.h
• MzmlIOPlugin/MzmlChromatogram.cpp