sample information management class More...

#include <Sample.h>

Inheritance diagram for kome::objects::Sample:

Collaboration diagram for kome::objects::Sample:

Public Member Functions
	Sample (SampleSet *sampleSet)
	constructor

virtual	~Sample ()
	destructor

SampleSet *	getSampleSet ()
	gets sample set object More...

void	setSampleIndex (const int index)
	sets sample index More...

int	getSampleIndex ()
	gets sample index More...

void	setName (const char *name)
	sets sample name More...

const char *	getName ()
	gets sample name More...

void	setType (const char *type)
	sets sample type More...

const char *	getType ()
	gets sample type More...

void	setInstrument (const char *instrument)
	sets instrument name More...

const char *	getInstrument ()
	gets instrument name More...

void	setMsCompany (const char *company)
	sets MS company More...

const char *	getMsCompany ()
	gets MS company More...

void	setSoftwareName (const char *name)
	sets software name More...

const char *	getSoftwareName ()
	gets software name More...

void	setSoftwareVersion (const char *version)
	sets software version More...

const char *	getSoftwareVersion ()
	gets software version More...

void	setOpened (const bool opened)
	sets opened flag More...

bool	isOpened ()
	judges whther this sample is opened or not More...

void	setEdited (const bool edited)
	sets edited flag More...

bool	isEdited ()
	judges whther this sample is edited or not More...

DataGroupNode *	getRootDataGroupNode ()
	gets root spectrum group More...

DataSet *	getHiddenDataSet ()
	gets the hidden data set More...

unsigned int	getNumberOfGroups ()
	gets the number of spectrum groups More...

DataGroupNode *	getGroup (const unsigned int index)
	gets spectrum group More...

void	setParallelReadable (const bool readable)
	sets parallel readable or not More...

bool	isParallelReadable ()
	gets whether this sample is parallel readable or not More...

bool	openSample (kome::core::Progress *progress=NULL)
	opens sample [out] progress progressbar to display More...

bool	closeSample ()
	closes sample More...

void	detectPeaksByAPI (Spectrum spec, Peaks peaks)
	detect peaks using Application Progreamming Interface More...

void	setSampleId (int id)
	set sample id More...

int	getSampleId ()
	get sample id More...

int	issueSpecId ()
	to issue the spectrum id More...

Spectrum *	getSpectrumById (int id)
	A spectrum is acquired by id. More...

int	issueChromId (Sample *sample)
	to issue the chromatogram id More...

Chromatogram *	getChromatogramById (int id)
	A schromatogram is acquired by id. More...

int	issueGroupId (Sample *sample)
	to issue the group id More...

DataGroupNode *	getGroupById (int id)
	A DataGroupNode is qcquired by id. More...

bool	isSupportedAPIPeaks ()
	judges whether API peak detection is supported on this sample. More...

void	setSupportedAPIPeaks (const bool supported)
	sets API peak dtection is supported on this sample. More...

Static Public Member Functions
static void	resetId ()
	Reset the ID of the sample.

static bool	isCommonProperty (const char *key)
	check whther the specified property key is common property or not More...

static int	issueSampleId ()
	to issue the sample id More...

static Sample *	getSampleById (int id)
	A sample is acquired by id. More...

Protected Member Functions
void	getGroups (DataGroupNode *parentGroup=NULL)
	gets spectrum groups More...

virtual void	onDetectPeaksByAPI (Spectrum spec, Peaks peaks)
	This methos is called by detectPeakByAPI method.

virtual bool	onOpenSample (DataGroupNode rootGroup, kome::core::Progress progress)=0
	This method is called by openSample method. (abstract method) More...

virtual bool	onCloseSample ()=0
	This method is called by closeSample method. (abstract method) More...

Protected Attributes
SampleSet *	m_sampleSet

int	m_sampleIdx

int	m_specId

std::string	m_name

std::string	m_type

std::string	m_instrument

std::string	m_company

std::string	m_softwareName

std::string	m_softwareVersion

DataGroupNode *	m_root

bool	m_opened

bool	m_edited

std::vector< DataGroupNode * >	m_groups

bool	m_parallelReadable

DataSet	m_hiddenSet

bool	m_supportedApiPeaks

Static Protected Attributes
static int	m_optSampleId = 0

static std::vector< std::string >	m_commonProps

Detailed Description

sample information management class

Definition at line 34 of file Sample.h.

Member Function Documentation

bool kome::objects::Sample::closeSample ( )

closes sample

Returns: If true, it succeeded to close this sample.

Definition at line 357 of file Sample.cpp.

                          {
     if( !m_opened ) {
         return true;
     }
 
     // close
     bool ret = onCloseSample();
     DataManager::closeSample( this, false );
     m_opened = false;
 
     // delete spectra
     if( m_root != NULL ) {
         delete m_root;
         m_root = NULL;
         m_groups.clear();
     }
 
     // sample set
     if( m_sampleSet != NULL ) {
         m_sampleSet->onCloseSample( this );
     }
     m_specId = 0;   // @date 2013.09.05 <Add> M.Izumi
 
     return ret;
 }

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void kome::objects::Sample::detectPeaksByAPI	(	Spectrum *	spec,
		Peaks *	peaks
	)

detect peaks using Application Progreamming Interface

Parameters

[in]	spec	spectrum to detect peaks
[out]	peaks	peaks object to store peaks information

Definition at line 384 of file Sample.cpp.

                                                             {
     onDetectPeaksByAPI( spec, peaks );
 }

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Chromatogram * kome::objects::Sample::getChromatogramById ( int id )

A schromatogram is acquired by id.

Parameters

[in] id chromatogram id

Returns: chromatogram object

Definition at line 501 of file Sample.cpp.

                                                  {
     // @date 2013.09.03 <Mod> M.Izumi ->
     // gets all spectra
     kome::objects::DataSet chroms;
 
     kome::objects::DataGroupNode* root = getRootDataGroupNode();
     if( root == NULL ) {
         return NULL;
     }
     root->getDataSet( &chroms );
 
     // search spectrum
     kome::objects::Chromatogram* chrom = NULL;
     for( unsigned int i = 0; i < chroms.getNumberOfChromatograms() && chrom == NULL; i++ ) {
         kome::objects::Chromatogram* tmp = chroms.getChromatogram( i );
         if( tmp->getId() == id ) {
             chrom = tmp;
         }
     }
 
     return chrom;
     // @date 2013.09.03 <Mod> M.Izumi <-
 }

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DataGroupNode * kome::objects::Sample::getGroup ( const unsigned int index )

gets spectrum group

Parameters

[in] index spectrum group index

Returns: spectrum group (If NULL, the index is illegal.)

Definition at line 234 of file Sample.cpp.

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

DataGroupNode * kome::objects::Sample::getGroupById ( int id )

A DataGroupNode is qcquired by id.

Parameters

[in] id group id

Returns: DataGroupNode object

Definition at line 534 of file Sample.cpp.

                                            {
     int inum = getNumberOfGroups();
     for( int i=0; i < inum; i++ ){
         DataGroupNode* group = getGroup(i);
         if( group->getId() == id ){
             return group;
         }
     }
     return NULL;
 }

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void kome::objects::Sample::getGroups ( DataGroupNode * parentGroup = NULL )

protected

gets spectrum groups

Parameters

[in] parentGroup parent spectrum group

Definition at line 242 of file Sample.cpp.

                                                    {
     if( parentGroup == NULL ) {         // all groups
         // initialize
         m_groups.clear();
 
         if( m_root != NULL ) {
             getGroups( m_root );
         }
     }
     else {
         // add
         if( parentGroup->getNumberOfChildren() == 0 ) { // leaf
             // set index
             parentGroup->setGroupIndex( (int)m_groups.size() );
             m_groups.push_back( parentGroup );
         }
 
         // add children
         for( unsigned int i = 0; i < parentGroup->getNumberOfChildren(); i++ ) {
             // child
             DataGroupNode* child = parentGroup->getChild( i );
             if( child != NULL ) {
                 getGroups( child );
             }
         }
     }
 }

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DataSet * kome::objects::Sample::getHiddenDataSet ( )

gets the hidden data set

Returns: hidden data set

Definition at line 224 of file Sample.cpp.

                                   {
     return &m_hiddenSet;
 }

const char * kome::objects::Sample::getInstrument ( )

gets instrument name

Returns: instrument name

Definition at line 152 of file Sample.cpp.

                                   {
     return m_instrument.c_str();
 }

const char * kome::objects::Sample::getMsCompany ( )

gets MS company

Returns: MS company

Definition at line 166 of file Sample.cpp.

                                  {
     return m_company.c_str();
 }

const char * kome::objects::Sample::getName ( )

gets sample name

Returns: sample name

Definition at line 102 of file Sample.cpp.

                             {
     return m_name.c_str();
 }

unsigned int kome::objects::Sample::getNumberOfGroups ( )

gets the number of spectrum groups

Returns: the number of spectrum groups

Definition at line 229 of file Sample.cpp.

                                        {
     return m_groups.size();
 }

DataGroupNode * kome::objects::Sample::getRootDataGroupNode ( )

gets root spectrum group

Returns: root spectrum group

Definition at line 219 of file Sample.cpp.

                                             {
     return m_root;
 }

static Sample * kome::objects::Sample::getSampleById ( int id )

static

A sample is acquired by id.

Parameters

[in] id sample id

Definition at line 447 of file Sample.cpp.

                                      {
     ActiveObjectsManager& aoMgr = ActiveObjectsManager::getInstance();
     
     int inum = aoMgr.getNumberOfOpenedSamples();
     for( int i=0; i < inum; i++ ){
         Sample* sample = aoMgr.getOpenedSample( i );
         if( m_optSampleId == id ){
             return sample;
         }
     }
     
     return NULL;
 }

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int kome::objects::Sample::getSampleId ( )

get sample id

Returns: sample id

Definition at line 442 of file Sample.cpp.

                        {
     return m_optSampleId;
 }

int kome::objects::Sample::getSampleIndex ( )

gets sample index

Returns: sample index

Definition at line 87 of file Sample.cpp.

                            {
     return m_sampleIdx;
 }

SampleSet * kome::objects::Sample::getSampleSet ( )

gets sample set object

Returns: sample set

Definition at line 77 of file Sample.cpp.

                                 {
     return m_sampleSet;
 }

const char * kome::objects::Sample::getSoftwareName ( )

gets software name

Returns: software name

Definition at line 180 of file Sample.cpp.

                                     {
     return m_softwareName.c_str();
 }

const char * kome::objects::Sample::getSoftwareVersion ( )

gets software version

Returns: software version

Definition at line 194 of file Sample.cpp.

                                        {
     return m_softwareVersion.c_str();
 }

Spectrum * kome::objects::Sample::getSpectrumById ( int id )

A spectrum is acquired by id.

Parameters

[in] id spectrum id

Returns: spectrum object

Definition at line 470 of file Sample.cpp.

                                          {
     // gets all spectra
     kome::objects::DataSet spectra;
 
     kome::objects::DataGroupNode* root = getRootDataGroupNode();
     if( root == NULL ) {
         return NULL;
     }
     root->getDataSet( &spectra );
 
     // search spectrum
     kome::objects::Spectrum* spec = NULL;
     for( unsigned int i = 0; i < spectra.getNumberOfSpectra() && spec == NULL; i++ ) {
         kome::objects::Spectrum* tmp = spectra.getSpectrum( i );
         if( tmp->getId() == id ) {
             spec = tmp;
         }
     }
 
     return spec;
 }

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const char * kome::objects::Sample::getType ( )

gets sample type

Returns: sample type

Definition at line 117 of file Sample.cpp.

                             {
     return m_type.c_str();
 }

static bool kome::objects::Sample::isCommonProperty ( const char * key )

static

check whther the specified property key is common property or not

Parameters

[in] key parameter key

Returns: If true, specified key is common property key

Definition at line 389 of file Sample.cpp.

                                                {
     // keys
     const char* keys[] = {
         "File Path",
         "File Name",
         "Instrument",
         "Manufacturer",
         "Sample Name",
         "Sample Type",
         "Software Name",
         "Software Version"
     };
 
     // create array
     if( m_commonProps.size() == 0 ) {
         const unsigned int num = sizeof( keys ) / sizeof( const char* );
 
         for( unsigned int i = 0; i < num; i++ ) {
             m_commonProps.push_back( keys[ i ] );
         }
     }
 
     // check the key
     if( key == NULL ) {
         return false;
     }
 
     for( unsigned int i = 0; i < m_commonProps.size(); i++ ) {
         if( m_commonProps[ i ].compare( key ) == 0 ) {
             return true;
         }
     }
 
     return false;
 }

bool kome::objects::Sample::isEdited ( )

judges whther this sample is edited or not

Returns: If true, this sample is edited.

Definition at line 214 of file Sample.cpp.

                       {
     return m_edited;
 }

bool kome::objects::Sample::isOpened ( )

judges whther this sample is opened or not

Returns: If true, this sample is opened.

Definition at line 204 of file Sample.cpp.

                       {
     return m_opened;
 }

bool kome::objects::Sample::isParallelReadable ( )

gets whether this sample is parallel readable or not

Returns: If true, this sample is parallel readable.

Definition at line 276 of file Sample.cpp.

                                 {
     return m_parallelReadable;
 }

int kome::objects::Sample::issueChromId ( Sample * sample )

to issue the chromatogram id

Parameters

[in] sample sample object

Returns: chromatogram id

Definition at line 493 of file Sample.cpp.

                                         {
     static int chromId = 0;
     chromId++;
 
     return chromId;
 }

int kome::objects::Sample::issueGroupId ( Sample * sample )

to issue the group id

Parameters

[in] sample sample object

Returns: group id

Definition at line 526 of file Sample.cpp.

                                         {
     static int groupId = 0;
 
     groupId++;
     return groupId;
 }

static int kome::objects::Sample::issueSampleId ( )

static

to issue the sample id

Returns: sample id

Definition at line 426 of file Sample.cpp.

                          {
     ActiveObjectsManager& aoMgr = ActiveObjectsManager::getInstance();
     int inum = aoMgr.getNumberOfOpenedSamples();
     int id = m_optSampleId;
     if( inum > 0 ){
         id++;
     }
     return id;
 }

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int kome::objects::Sample::issueSpecId ( )

to issue the spectrum id

Returns: new spectrum ID

Definition at line 462 of file Sample.cpp.

                         {
     int specId = m_specId;
     m_specId++;
 
     return specId;
 }

bool kome::objects::Sample::isSupportedAPIPeaks ( )

judges whether API peak detection is supported on this sample.

Returns: If true, API peak detection is supported.

Definition at line 546 of file Sample.cpp.

                                  {
     return m_supportedApiPeaks;
 }

bool kome::objects::Sample::onCloseSample ( )

protectedpure virtual

This method is called by closeSample method. (abstract method)

Returns: If true, it succeeded to close this sample.

Implemented in kome::operation::ManipulatedSample.

bool kome::objects::Sample::onOpenSample	(	DataGroupNode *	rootGroup,
		kome::core::Progress *	progress
	)

protectedpure virtual

This method is called by openSample method. (abstract method)

Parameters

[out] rootGroup root spectrum group [out] progress progressbar to display

Returns: If true, it succeeded to open this sample.

Implemented in kome::operation::ManipulatedSample.

bool kome::objects::Sample::openSample ( kome::core::Progress * progress = NULL )

opens sample [out] progress progressbar to display

Returns: If true, it succeeded to open this sample.

Definition at line 281 of file Sample.cpp.

                                                     {
     if( m_opened ) {        // already opened
         return true;
     }
 
     // active objects manager
     ActiveObjectsManager& activeMgr = ActiveObjectsManager::getInstance();
 
     // create root group
     if( m_root != NULL ) {
         delete m_root;
         m_groups.clear();
     }
     std::string groupName = m_name;
 
     std::string fileName;
     if( m_sampleSet != NULL ) {
         fileName = m_sampleSet->getFileName();
     }
 
     if( !fileName.empty() ) {
         if( !groupName.empty() ) {
             groupName.append( " : " );
         }
         groupName.append( fileName );
     }
 
     if( m_sampleSet != NULL && m_sampleSet->getNumberOfSamples() > 1 ) {
         groupName.append( FMT( "(%d)", this->m_sampleIdx ) );
     }
 
     m_root = new DataGroupNode( this, groupName.c_str() );
     
     // sample set
     SampleSet::startLoadingTimer();
     if( m_sampleSet != NULL ) {
         m_sampleSet->onOpenSample( this, progress ); // add param @date 2014.07.08 <Mod> M.Izumi
     }
 
     // open
     LOG_INFO( FMT( "Open Sample [%s]", m_name.c_str() ) );
     bool ret = onOpenSample( m_root, progress );
     
     // add sort @date 2011.10.31 <Add> M.Izumi
     m_root->sortSpectra();
         
     SampleSet::stopLoadingTimer();
 
     // properties
     if( m_sampleSet != NULL ) {
         m_root->getProperties().setValue( "File Path", m_sampleSet->getFilePath() );
         m_root->getProperties().setValue( "File Name", m_sampleSet->getFileName() );
     }
     m_root->getProperties().setValue( "Instrument", m_instrument.c_str() );
     m_root->getProperties().setValue( "Manufacturer", m_instrument.c_str() );
     m_root->getProperties().setValue( "Sample Name", m_name.c_str() );
     m_root->getProperties().setValue( "Sample Type", m_type.c_str() );
     m_root->getProperties().setValue( "Software Name", m_softwareName.c_str() );
     m_root->getProperties().setValue( "Software Version", m_softwareVersion.c_str() );
          
     if( ret ) {     // success
         m_opened = true;
         getGroups( NULL );
 
         DataManager::openSample( this );
     }
     else {  // failed
         LOG_ERROR( FMT( "Failed to open the sample.[%s]", m_name.c_str() ) );
         closeSample();
     }
 
 
     return ret;
 }

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void kome::objects::Sample::setEdited ( const bool edited )

sets edited flag

Parameters

[in] edited edited flag value

Definition at line 209 of file Sample.cpp.

                                           {
     m_edited = edited;
 }

void kome::objects::Sample::setInstrument ( const char * instrument )

sets instrument name

Parameters

[in] instrument instrument name

Definition at line 122 of file Sample.cpp.

                                                    {
     // clear
     m_instrument.clear();
     if( instrument == NULL ) {
         return;
     }
 
     // instrument name
     std::string instStr = trimstring( instrument );
     bool prevSpace = false;
     for( unsigned int i = 0; i < instStr.size(); i++ ) {
         char c = instStr[ i ];
         if( isalpha( c ) || isdigit( c ) ) {
             prevSpace = false;
             c = (char)toupper( c );
             m_instrument.push_back( c );
         }
         else if( !prevSpace ) {
             prevSpace = true;
             m_instrument.push_back( '-' );
         }
     }
 
     // set property
     if( m_root != NULL ) {
         m_root->getProperties().setValue( "Instrument", m_instrument.c_str() );
     }
 }

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void kome::objects::Sample::setMsCompany ( const char * company )

sets MS company

Parameters

[in] company MS company

Definition at line 157 of file Sample.cpp.

                                                {
     m_company = NVL( company, "" );
 
     if( m_root != NULL ) {
         m_root->getProperties().setValue( "Manufacturer", m_company.c_str() );
     }
 }

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void kome::objects::Sample::setName ( const char * name )

sets sample name

Parameters

[in] name sample name

Definition at line 92 of file Sample.cpp.

                                        {
     m_name = NVL( name, "" );
 
     // property
     if( m_root != NULL ) {
         m_root->getProperties().setValue( "Sample Name", m_name.c_str() );
     }
 }

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void kome::objects::Sample::setOpened ( const bool opened )

sets opened flag

Parameters

[in] opened opened flag value

Definition at line 199 of file Sample.cpp.

                                           {
     m_opened = opened;
 }

void kome::objects::Sample::setParallelReadable ( const bool readable )

sets parallel readable or not

Parameters

[in] readable If true, this sample is parallel readabale.

Definition at line 271 of file Sample.cpp.

                                                       {
     m_parallelReadable = readable;
 }

void kome::objects::Sample::setSampleId ( int id )

set sample id

Parameters

[in] id sample id

Definition at line 437 of file Sample.cpp.

                                 {
     m_optSampleId = id;
 }

void kome::objects::Sample::setSampleIndex ( const int index )

sets sample index

Parameters

[in] index sample index

Definition at line 82 of file Sample.cpp.

                                              {
     m_sampleIdx = index;
 }

void kome::objects::Sample::setSoftwareName ( const char * name )

sets software name

Parameters

[in] name software name

Definition at line 171 of file Sample.cpp.

                                                {
     m_softwareName = NVL( name, "" );
 
     if( m_root != NULL ) {
         m_root->getProperties().setValue( "Software Name", m_softwareName.c_str() );
     }
 }

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void kome::objects::Sample::setSoftwareVersion ( const char * version )

sets software version

Parameters

[in] version software version

Definition at line 185 of file Sample.cpp.

                                                      {
     m_softwareVersion = NVL( version, "" );
 
     if( m_root != NULL ) {
         m_root->getProperties().setValue( "Software Version", m_softwareVersion.c_str() );
     }
 }

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void kome::objects::Sample::setSupportedAPIPeaks ( const bool supported )

sets API peak dtection is supported on this sample.

Parameters

[in] supported If true, API peak detection is supported.

Definition at line 551 of file Sample.cpp.

                                                         {
     m_supportedApiPeaks = supported;
 }

void kome::objects::Sample::setType ( const char * type )

sets sample type

Parameters

[in] type sample type

Definition at line 107 of file Sample.cpp.

                                        {
     m_type = NVL( type, "" );
 
     // property
     if( m_root != NULL ) {
         m_root->getProperties().setValue( "Sample Type", m_type.c_str() );
     }
 }

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Member Data Documentation

std::vector< std::string > Sample::m_commonProps

staticprotected

common properties

Definition at line 102 of file Sample.h.

std::string kome::objects::Sample::m_company

protected

company name

Definition at line 68 of file Sample.h.

bool kome::objects::Sample::m_edited

protected

edited flag

Definition at line 83 of file Sample.h.

std::vector< DataGroupNode* > kome::objects::Sample::m_groups

protected

groups

Definition at line 86 of file Sample.h.

DataSet kome::objects::Sample::m_hiddenSet

protected

data set

Definition at line 92 of file Sample.h.

std::string kome::objects::Sample::m_instrument

protected

instrument name

Definition at line 65 of file Sample.h.

std::string kome::objects::Sample::m_name

protected

name

Definition at line 59 of file Sample.h.

bool kome::objects::Sample::m_opened

protected

opened flag

Definition at line 80 of file Sample.h.

int Sample::m_optSampleId = 0

staticprotected

sample id

Definition at line 98 of file Sample.h.

bool kome::objects::Sample::m_parallelReadable

protected

parallel readable

Definition at line 89 of file Sample.h.

DataGroupNode* kome::objects::Sample::m_root

protected

root spectrum group

Definition at line 77 of file Sample.h.

int kome::objects::Sample::m_sampleIdx

protected

sample index

Definition at line 53 of file Sample.h.

SampleSet* kome::objects::Sample::m_sampleSet

protected

sample set

Definition at line 50 of file Sample.h.

std::string kome::objects::Sample::m_softwareName

protected

software name

Definition at line 71 of file Sample.h.

std::string kome::objects::Sample::m_softwareVersion

protected

software version

Definition at line 74 of file Sample.h.

int kome::objects::Sample::m_specId

protected

spectrum ID

Definition at line 56 of file Sample.h.

bool kome::objects::Sample::m_supportedApiPeaks

protected

api peaks support

Definition at line 95 of file Sample.h.

std::string kome::objects::Sample::m_type

protected

type

Definition at line 62 of file Sample.h.

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

DataObjects/Sample.h
DataObjects/Sample.cpp

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Function Documentation

Member Data Documentation