kome::io::mzml::MzmlSample Class Reference

mzML sample class More...

#include <MzmlSample.h>

Inheritance diagram for kome::io::mzml::MzmlSample:

Collaboration diagram for kome::io::mzml::MzmlSample:

Classes
struct	ArrayInfo

Public Member Functions
	MzmlSample (MzmlSampleSet *sampleSet)
	constructor More...
virtual	~MzmlSample ()
	destructor
MzmlSampleSet *	getMzmlSampleSet ()
	gets mzML sample set object More...
void	addParentFile (const char *path)
	adds parent files More...
unsigned int	getNumberOfParentFiles ()
	gets the number of parent files More...
const char *	getParentFilePath (const unsigned int index)
	gets parent file path More...
void	addArrayInfo (const char *name, const int bits, const bool compressed, const double scale, const bool isY)
	adds array information More...
ArrayInfo *	getArrayInfo (const char *name)
	gets array information More...

Public Attributes
MzmlSampleSet *	m_sampleSet
std::vector< std::string >	m_parentFiles

Protected Member Functions
virtual bool	onOpenSample (kome::objects::DataGroupNode *rootGroup, kome::core::Progress *progress=NULL)
	This method is called by openTreatment method. (override method) More...
virtual bool	onCloseSample ()
	This method is called by closeTreatment method. (override method) More...

Protected Attributes
std::vector< ArrayInfo >	m_arrayInfo

Detailed Description

mzML sample class

Definition at line 26 of file MzmlSample.h.

Constructor & Destructor Documentation

kome::io::mzml::MzmlSample::MzmlSample

(

MzmlSampleSet *

sampleSet

)

constructor

Parameters

sampleSet

sample set object

Definition at line 31 of file MzmlSample.cpp.

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

    setParallelReadable( true );
}

Member Function Documentation

void kome::io::mzml::MzmlSample::addArrayInfo	(	const char *	name,
		const int	bits,
		const bool	compressed,
		const double	scale,
		const bool	isY
	)

adds array information

Parameters

name	array information name
bits	data size of element
compressed	if true, the array data is compressed
scale	unit size scale
isY	if true, the array data is y coordinate values

Definition at line 83 of file MzmlSample.cpp.

  {
    // 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;
}

Here is the call graph for this function:

void kome::io::mzml::MzmlSample::addParentFile

(

const char *

path

)

adds parent files

Parameters

path	parent file path

Definition at line 43 of file MzmlSample.cpp.

                                                 {
    // 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 );
}

ArrayInfo * kome::io::mzml::MzmlSample::getArrayInfo

(

const char *

name

)

gets array information

Parameters

name	array information name

Returns

array information (If NULL, specified name is not found.)

Definition at line 111 of file MzmlSample.cpp.

                                                                {
    // 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;
}

MzmlSampleSet * kome::io::mzml::MzmlSample::getMzmlSampleSet

(

)

gets mzML sample set object

Returns

mzML sample set object

Definition at line 65 of file MzmlSample.cpp.

                                            {
    return m_sampleSet;
}

unsigned int kome::io::mzml::MzmlSample::getNumberOfParentFiles

(

)

gets the number of parent files

Returns

the number of parent files

Definition at line 70 of file MzmlSample.cpp.

                                                {
    return m_parentFiles.size();
}

const char * kome::io::mzml::MzmlSample::getParentFilePath

(

const unsigned int

index

)

gets parent file path

Parameters

index

parent file index

Returns

parent file path (If the index is illegal, this method returns NULL.)

Definition at line 75 of file MzmlSample.cpp.

                                                                    {
    if( index >= m_parentFiles.size() ) {
        return NULL;
    }
    return m_parentFiles[ index ].c_str();
}

bool kome::io::mzml::MzmlSample::onCloseSample ( )

protectedvirtual

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

Returns

If true, it succeeded to close this sample.

Definition at line 139 of file MzmlSample.cpp.

                               {
    return true;
}

bool kome::io::mzml::MzmlSample::onOpenSample ( kome::objects::DataGroupNode *  rootGroup, kome::core::Progress *  progress = NULL  )

protectedvirtual

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

Parameters

rootGroup

root spectrum group

Returns

If true, it succeeded to open this sample.

Definition at line 130 of file MzmlSample.cpp.

                                                                                               {
    // handler
    MzmlHandler handler( *this );
    handler.parse( m_sampleSet->getFilePath() );

    return !handler.isError();
}

Member Data Documentation

std::vector< ArrayInfo > kome::io::mzml::MzmlSample::m_arrayInfo

protected

array information

Definition at line 63 of file MzmlSample.h.

std::vector< std::string > kome::io::mzml::MzmlSample::m_parentFiles

parent files

Definition at line 46 of file MzmlSample.h.

MzmlSampleSet* kome::io::mzml::MzmlSample::m_sampleSet

sample set

Definition at line 43 of file MzmlSample.h.

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

• MzmlIOPlugin/MzmlSample.h
• MzmlIOPlugin/MzmlSample.cpp