XML data handler to get spectrum data points. More...

#include <MzmlDataHandler.h>

Inheritance diagram for kome::io::mzml::MzmlDataHandler:

Collaboration diagram for kome::io::mzml::MzmlDataHandler:

Public Member Functions
	MzmlDataHandler (MzmlSample &sample, const char *id, kome::core::XYData &xyData)
	constructor More...

virtual	~MzmlDataHandler ()
	destructor

Protected Member Functions
void	setPoints ()
	set data points

virtual void	onStartDocument ()
	This method is called by startDocument method. (override method)

virtual void	onEndDocument ()
	This method is called by endDocument method. (override method)

virtual void	onStartElement (const char *name, kome::core::Properties &attrs)
	This method is called by startElement method. (override method) More...

virtual void	onEndElement (const char name, const char text)
	This method is called by end element method. (override method) More...

Protected Attributes
MzmlSample &	m_sample

std::string	m_id

kome::core::XYData &	m_xyData

int	m_dataLength

bool	m_reverseFlg

MzmlSample::ArrayInfo	m_arrayInfo

bool	m_available

double *	m_xArray

double *	m_yArray

bool	m_reading

Detailed Description

XML data handler to get spectrum data points.

Definition at line 29 of file MzmlDataHandler.h.

Constructor & Destructor Documentation

kome::io::mzml::MzmlDataHandler::MzmlDataHandler	(	MzmlSample &	sample,
		const char *	id,
		kome::core::XYData &	xyData
	)

constructor

Parameters

sample	sample
id	data ID
xyData	xy data object to store data points

Definition at line 48 of file MzmlDataHandler.cpp.

         : m_sample( sample ), m_id( NVL( id, "" ) ), m_xyData( xyData ) {
     m_reverseFlg = isbigendian();
     onStartDocument();
 }

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Member Function Documentation

void kome::io::mzml::MzmlDataHandler::onEndElement	(	const char *	name,
		const char *	text
	)

protectedvirtual

This method is called by end element method. (override method)

Parameters

name	tag name
text	body text

Definition at line 194 of file MzmlDataHandler.cpp.

                                                                        {
     // each tags
     if( strcmp( name, SPEC_TAG_NAME ) == 0 ) {  // </spectrum>
         if( m_reading ) {
             setPoints();
         }
     }
     else if( strcmp( name, CHROM_TAG_NAME ) == 0 ) {    // </chromatogram>
         if( m_reading ) {
             setPoints();
         }
     }
     else if( strcmp( name, BINARY_TAG_NAME ) == 0 ) {   // </binary>
         if( m_reading && m_available && m_dataLength > 0 ) {
             // create array
             double* arr = NULL;
             if( m_arrayInfo.isY ) {
                 if( m_yArray == NULL ) {
                     m_yArray = new double[ m_dataLength ];
                 }
                 arr = m_yArray;
             }
             else {
                 if( m_xArray == NULL ) {
                     m_xArray = new double[ m_dataLength ];
                 }
                 arr = m_xArray;
             }
 
             // get data
             char* data0 = new char[ strlen( text ) ];
             unsigned long size0 = kome::core::Base64::decode( (char*)text, strlen( text ), data0, strlen( text ) );
 
             unsigned long size1 = m_dataLength * m_arrayInfo.bits / 8;
             char* data1 = new char[ size1 ];
 
             if( m_arrayInfo.compressed ) {
                 uncompress( (Bytef*)data1, &size1, (Bytef*)data0, size0 );
             }
             else {
                 memcpy( data1, data0, size1 );
             }
 
             // add to array
             if( m_arrayInfo.bits == 64 ) {  // double
                 double* dArr = (double*)data1;
                 for( int i = 0; i < m_dataLength; i++ ) {
                     arr[ i ] = dArr[ i ] * m_arrayInfo.scale;
                     if( m_reverseFlg ) {
                         memreverse( arr + i, sizeof( double ) );
                     }
                 }
             }
             else {  // float
                 float* fArr = (float*)data1;
                 for( int i = 0; i < m_dataLength; i++ ) {
                     arr[ i ] = (double)fArr[ i ] * m_arrayInfo.scale;
                     if( m_reverseFlg ) {
                         memreverse( arr + i, sizeof( double ) );
                     }
                 }
             }
 
             // delete
             delete[] data0;
             delete[] data1;
         }
         m_available = false;
     }
 }

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void kome::io::mzml::MzmlDataHandler::onStartElement	(	const char *	name,
		kome::core::Properties &	attrs
	)

protectedvirtual

This method is called by startElement method. (override method)

Parameters

name	tag name
attrs	attributes

Definition at line 109 of file MzmlDataHandler.cpp.

                                                                                   {
     // each tags
     if( strcmp( name, SPEC_TAG_NAME ) == 0 ) {  // <spectrum>
         // ID
         const char* id = attrs.getStringValue( SPEC_ID_ATTR_NAME, "" );
         if( m_id.compare( id ) == 0 ) {
             m_reading = true;
             m_dataLength = attrs.getIntValue( SPEC_LENGTH_ATTR_NAME, 0 );
         }
     }
     else if( strcmp( name, CHROM_TAG_NAME ) == 0 ) {    // <chromatogram>
         // ID
         const char* id = attrs.getStringValue( CHROM_ID_ATTR_NAME, "" );
         if( m_id.compare( id ) == 0 ) {
             m_reading = true;
             m_dataLength = attrs.getIntValue( CHROM_LENGTH_ATTR_NAME, 0 );
         }
     }
     else if( strcmp( name, ARRAY_TAG_NAME ) == 0 ) {    // <binaryDataArray>
         if( m_reading ) {
             m_dataLength = attrs.getIntValue( ARRAY_LENGTH_ATTR_NAME, m_dataLength );
 
             m_arrayInfo.name.clear();
             m_arrayInfo.bits = 32;
             m_arrayInfo.compressed = false;
             m_arrayInfo.scale = 1.0;
             m_arrayInfo.isY = false;
 
             m_available = false;
         }
     }
     else if( strcmp( name, PARAM_GROUP_TAG_NAME ) == 0 ) {  // <referenceableParamGroupRef>
         if( m_reading ) {
             const char* id = attrs.getStringValue( PARAM_GROUP_ID_ATTR_NAME, "" );
             MzmlSample::ArrayInfo* info = m_sample.getArrayInfo( id );
             if( info != NULL ) {
                 m_arrayInfo = *info;
                 m_available = true;
             }
         }
     }
     else if( strcmp( name, CV_TAG_NAME ) == 0 ) {   // <cvParam>
         if( m_reading ) {
             // accession
             const char* accession = attrs.getStringValue( CV_ACCESSION_ATTR_NAME, "" );
 
             // each accessions
             if( strcmp( accession, "MS:1000514" ) == 0 ) {  // m/z array
                 m_arrayInfo.isY = false;
                 m_arrayInfo.scale = 1.0;
 
                 m_available = true;
             }
             else if( strcmp( accession, "MS:1000595" ) == 0 ) { // RT array
                 m_arrayInfo.isY = false;
                 m_arrayInfo.scale = 1.0;
 
                 m_available = true;
 
                 const char* unit = attrs.getStringValue( CV_UNIT_ATTR_NAME, "" );
                 if( strcmp( unit, "UO:0000031" ) != 0 ) {   // second
                     m_arrayInfo.scale = 1.0 / 60.0;
                 }
             }
             else if( strcmp( accession, "MS:1000515" ) == 0 ) { // intensity array
                 m_arrayInfo.isY = true;
                 m_available = true;
             }
             else if( strcmp( accession, "MS:1000521" ) == 0 ) { // 32-bit float
                 m_arrayInfo.bits = 32;
             }
             else if( strcmp( accession, "MS:1000523" ) == 0 ) { // 64-bit float
                 m_arrayInfo.bits = 64;
             }
             else if( strcmp( accession, "MS:1000576" ) == 0 ) { // no compression
                 m_arrayInfo.compressed = false;
             }
             else if( strcmp( accession, "MS:1000574" ) == 0 ) { // zlib compression
                 m_arrayInfo.compressed = true;
             }
         }
     }
 }

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Member Data Documentation

MzmlSample::ArrayInfo kome::io::mzml::MzmlDataHandler::m_arrayInfo

protected

array information

Definition at line 64 of file MzmlDataHandler.h.

bool kome::io::mzml::MzmlDataHandler::m_available

protected

available array flag

Definition at line 67 of file MzmlDataHandler.h.

int kome::io::mzml::MzmlDataHandler::m_dataLength

protected

data length

Definition at line 57 of file MzmlDataHandler.h.

std::string kome::io::mzml::MzmlDataHandler::m_id

protected

ID

Definition at line 51 of file MzmlDataHandler.h.

bool kome::io::mzml::MzmlDataHandler::m_reading

protected

reading flag

Definition at line 77 of file MzmlDataHandler.h.

bool kome::io::mzml::MzmlDataHandler::m_reverseFlg

protected

reverse flag

Definition at line 60 of file MzmlDataHandler.h.

MzmlSample& kome::io::mzml::MzmlDataHandler::m_sample

protected

sample

Definition at line 48 of file MzmlDataHandler.h.

double* kome::io::mzml::MzmlDataHandler::m_xArray

protected

x array

Definition at line 70 of file MzmlDataHandler.h.

kome::core::XYData& kome::io::mzml::MzmlDataHandler::m_xyData

protected

xy data

Definition at line 54 of file MzmlDataHandler.h.

double* kome::io::mzml::MzmlDataHandler::m_yArray

protected

y array

Definition at line 73 of file MzmlDataHandler.h.

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

MzmlIOPlugin/MzmlDataHandler.h
MzmlIOPlugin/MzmlDataHandler.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation