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MzMLHandler< MapType > Class Template Reference

XML handler for MzMLFile. More...

#include <OpenMS/FORMAT/HANDLERS/MzMLHandler.h>

Inheritance diagram for MzMLHandler< MapType >:
XMLHandler DefaultHandler

List of all members.

Classes

struct  BinaryData
 Spectrum representation. More...

Public Member Functions

virtual void endElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname)
 Parsing method for closing tags.
virtual void startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes)
 Parsing method for opening tags.
virtual void characters (const XMLCh *const chars, const XMLSize_t length)
 Parsing method for character data.
virtual void writeTo (std::ostream &os)
 Writes the contents to a stream.
void setOptions (const PeakFileOptions &opt)
Constructors and destructor

 MzMLHandler (MapType &exp, const String &filename, const String &version, ProgressLogger &logger)
 Constructor for a read-only handler.
 MzMLHandler (const MapType &exp, const String &filename, const String &version, const ProgressLogger &logger)
 Constructor for a write-only handler.
virtual ~MzMLHandler ()
 Destructor.

Protected Types

typedef MapType::PeakType PeakType
 Peak type.
typedef
MapType::ChromatogramPeakType 		ChromatogramPeakType
 Chromatogram peak type.
typedef MSSpectrum< PeakType > SpectrumType
 Spectrum type.
typedef MSChromatogram
< ChromatogramPeakType > 		ChromatogramType
 Spectrum type.

Protected Member Functions

void fillData_ ()
 Fills the current spectrum with peaks and meta data.
void fillChromatogramData_ ()
 Fills the current chromatogram with data points and meta data.
void handleCVParam_ (const String &parent_parent_tag, const String &parent_tag, const String &accession, const String &name, const String &value, const String &unit_accession="")
 Handles CV terms.
void handleUserParam_ (const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value)
 Handles user terms.
void writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent, String path, Internal::MzMLValidator &validator) const
 Writes user terms.
ControlledVocabulary::CVTerm getChildWithName_ (const String &parent_accession, const String &name) const
 Looks up a child CV term of parent_accession with the name name. If no such term is found, an empty term is returned.
void writeSoftware_ (std::ostream &os, const String &id, const Software &software, Internal::MzMLValidator &validator)
 Helper method that writes a software.
void writeSourceFile_ (std::ostream &os, const String &id, const SourceFile &software, Internal::MzMLValidator &validator)
 Helper method that writes a source file.
void writeDataProcessing_ (std::ostream &os, const String &id, const std::vector< DataProcessing > &dps, Internal::MzMLValidator &validator)
 Helper method that writes a data processing list.
void writePrecursor_ (std::ostream &os, const Precursor &precursor, Internal::MzMLValidator &validator)
 Helper method that write precursor information from spectra and chromatograms.
void writeProduct_ (std::ostream &os, const Product &product, Internal::MzMLValidator &validator)
 Helper method that write precursor information from spectra and chromatograms.
String writeCV_ (const ControlledVocabulary::CVTerm &c, const DataValue &metaValue) const
 Helper method to write an CV based on a meta value.
bool validateCV_ (const ControlledVocabulary::CVTerm &c, const String &path, const Internal::MzMLValidator &validator) const
 Helper method to validate if the given CV is allowed in the current location (path).

Protected Attributes

MapType * exp_
 map pointer for reading
const MapType * cexp_
 map pointer for writing
PeakFileOptions options_
 Options that can be set for loading/storing.
Base64 decoder_
 Decoder/Encoder for Base64-data in MzML.
const ProgressLogger & logger_
 Progress logger.
bool skip_spectrum_
 Flag that indicates whether this spectrum should be skipped (due to options).
ControlledVocabulary cv_
 Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo).
CVMappings mapping_
UInt selected_ion_count_
 Count of selected ions.
temporary data structures to hold parsed data

SpectrumType spec_
 The current spectrum.
ChromatogramType chromatogram_
 The current chromatogram.
std::vector< BinaryData > data_
 The spectrum data (or chromatogram data).
Size default_array_length_
 The default number of peaks in the current spectrum.
bool in_spectrum_list_
 Flag that indicates that we're inside a spectrum (in contrast to a chromatogram).
String current_id_
 Id of the current list. Used for referencing param group, source file, sample, software, ...
Map< String, std::vector
< SemanticValidator::CVTerm > > 		ref_param_
 The referencing param groups: id => array (accession, value).
Map< String, SourceFile > source_files_
 The source files: id => SourceFile.
Map< String, Sample > samples_
 The sample list: id => Sample.
Map< String, Software > software_
 The software list: id => Software.
Map< String, Instrument > instruments_
 The data processing list: id => Instrument.
Map< String, std::vector
< DataProcessing > > 		processing_
 The data processing list: id => Instrument.
String default_processing_
 id of the default data processing (used when no processing is defined)

Detailed Description

template<typename MapType>
class OpenMS::Internal::MzMLHandler< MapType >

XML handler for MzMLFile.

MapType has to be an MSExperiment or have the same interface.

Note:
Do not use this class. It is only needed in MzMLFile.

Member Typedef Documentation

typedef MapType::ChromatogramPeakType ChromatogramPeakType [protected]

Chromatogram peak type.

typedef MSChromatogram<ChromatogramPeakType> ChromatogramType [protected]

Spectrum type.

typedef MapType::PeakType PeakType [protected]

Peak type.

typedef MSSpectrum<PeakType> SpectrumType [protected]

Spectrum type.

Constructor & Destructor Documentation

MzMLHandler ( MapType &  exp,
const String &  filename,
const String &  version,
ProgressLogger &  logger 
) [inline]

Constructor for a read-only handler.

References MzMLHandler< MapType >::cv_, File::find(), ControlledVocabulary::loadFromOBO(), and MzMLHandler< MapType >::mapping_.

MzMLHandler ( const MapType &  exp,
const String &  filename,
const String &  version,
const ProgressLogger &  logger 
) [inline]

Constructor for a write-only handler.

References MzMLHandler< MapType >::cv_, File::find(), ControlledVocabulary::loadFromOBO(), and MzMLHandler< MapType >::mapping_.

virtual ~MzMLHandler (  )  [inline, virtual]

Destructor.

Member Function Documentation

void characters ( const XMLCh *const   chars,
const XMLSize_t  length 
) [virtual]

Parsing method for character data.

Reimplemented from XMLHandler.

References StringManager::convert(), MzMLHandler< MapType >::data_, XMLHandler::LOAD, XMLHandler::open_tags_, MzMLHandler< MapType >::skip_spectrum_, XMLHandler::sm_, String::trim(), and XMLHandler::warning().

void endElement ( const XMLCh *  uri,
const XMLCh *  localname,
const XMLCh *const   qname 
) [virtual]

Parsing method for closing tags.

Reimplemented from XMLHandler.

References MzMLHandler< MapType >::chromatogram_, StringManager::clear(), MzMLHandler< MapType >::current_id_, MzMLHandler< MapType >::data_, MzMLHandler< MapType >::default_array_length_, ProgressLogger::endProgress(), XMLHandler::equal_(), MzMLHandler< MapType >::exp_, MzMLHandler< MapType >::fillChromatogramData_(), MzMLHandler< MapType >::fillData_(), MzMLHandler< MapType >::in_spectrum_list_, MzMLHandler< MapType >::instruments_, MzMLHandler< MapType >::logger_, XMLHandler::open_tags_, MzMLHandler< MapType >::processing_, MzMLHandler< MapType >::ref_param_, MzMLHandler< MapType >::samples_, ProgressLogger::setProgress(), MzMLHandler< MapType >::skip_spectrum_, XMLHandler::sm_, MzMLHandler< MapType >::software_, MzMLHandler< MapType >::source_files_, and MzMLHandler< MapType >::spec_.

void fillChromatogramData_ (  )  [protected]

Fills the current chromatogram with data points and meta data.

References Base64::BYTEORDER_LITTLEENDIAN, MzMLHandler< MapType >::chromatogram_, MzMLHandler< MapType >::data_, Base64::decode(), Base64::decodeIntegers(), MzMLHandler< MapType >::decoder_, Base64::decodeStrings(), MzMLHandler< MapType >::default_array_length_, MzMLHandler< MapType >::BinaryData::DT_FLOAT, MzMLHandler< MapType >::BinaryData::DT_INT, MzMLHandler< MapType >::BinaryData::DT_STRING, DRange< D >::encloses(), MSChromatogram< PeakT >::getFloatDataArrays(), MSChromatogram< PeakT >::getIntegerDataArrays(), PeakFileOptions::getIntensityRange(), ChromatogramSettings::getNativeID(), PeakFileOptions::getRTRange(), MSChromatogram< PeakT >::getStringDataArrays(), PeakFileOptions::hasIntensityRange(), PeakFileOptions::hasRTRange(), OpenMS::Constants::k, XMLHandler::LOAD, MzMLHandler< MapType >::options_, MzMLHandler< MapType >::BinaryData::PRE_32, MzMLHandler< MapType >::BinaryData::PRE_64, MetaInfoInterface::setMetaValue(), and XMLHandler::warning().

Referenced by MzMLHandler< MapType >::endElement().

void fillData_ (  )  [protected]

Fills the current spectrum with peaks and meta data.

References Base64::BYTEORDER_LITTLEENDIAN, MzMLHandler< MapType >::data_, Base64::decode(), Base64::decodeIntegers(), MzMLHandler< MapType >::decoder_, Base64::decodeStrings(), MzMLHandler< MapType >::default_array_length_, MzMLHandler< MapType >::BinaryData::DT_FLOAT, MzMLHandler< MapType >::BinaryData::DT_INT, MzMLHandler< MapType >::BinaryData::DT_STRING, DRange< D >::encloses(), XMLHandler::fatalError(), MSSpectrum< PeakT >::getFloatDataArrays(), MSSpectrum< PeakT >::getIntegerDataArrays(), PeakFileOptions::getIntensityRange(), PeakFileOptions::getMZRange(), SpectrumSettings::getNativeID(), MSSpectrum< PeakT >::getStringDataArrays(), PeakFileOptions::hasIntensityRange(), PeakFileOptions::hasMZRange(), OpenMS::Constants::k, XMLHandler::LOAD, MzMLHandler< MapType >::options_, MzMLHandler< MapType >::BinaryData::PRE_32, MzMLHandler< MapType >::BinaryData::PRE_64, MetaInfoInterface::setMetaValue(), MzMLHandler< MapType >::spec_, and XMLHandler::warning().

Referenced by MzMLHandler< MapType >::endElement().

ControlledVocabulary::CVTerm getChildWithName_ ( const String &  parent_accession,
const String &  name 
) const [protected]

Looks up a child CV term of parent_accession with the name name. If no such term is found, an empty term is returned.

References MzMLHandler< MapType >::cv_, ControlledVocabulary::getAllChildTerms(), and ControlledVocabulary::getTerm().

Referenced by MzMLHandler< MapType >::writeSoftware_(), MzMLHandler< MapType >::writeSourceFile_(), and MzMLHandler< MapType >::writeTo().

void handleCVParam_ ( const String &  parent_parent_tag,
const String &  parent_tag,
const String &  accession,
const String &  name,
const String &  value,
const String &  unit_accession = "" 
) [protected]

Handles CV terms.

References InstrumentSettings::ABSORBTION, ChromatogramSettings::ABSORPTION_CHROMATOGRAM, SemanticValidator::CVTerm::accession, IonSource::AD, IonDetector::ADC, IonSource::AI, DataProcessing::ALIGNMENT, MassAnalyzer::ANALYZERNULL, IonSource::AP_MALDI, IonSource::APCI, IonSource::API, IonSource::APPI, IonDetector::ARRAYDETECTOR, XMLHandler::asDateTime_(), IonSource::ASI, IonSource::AUI, MassAnalyzer::AXIALEJECTIONLINEARIONTRAP, DataProcessing::BASELINE_REDUCTION, ChromatogramSettings::BASEPEAK_CHROMATOGRAM, IonSource::BATCH, Precursor::BIRD, DataProcessing::CALIBRATION, IonSource::CEI, IonDetector::CHANNELTRON, DataProcessing::CHARGE_CALCULATION, DataProcessing::CHARGE_DECONVOLUTION, IonSource::CHEMI, MzMLHandler< MapType >::chromatogram_, IonSource::CHROMATOGRAPHY, IonSource::CI, Precursor::CID, InstrumentSettings::CNG, InstrumentSettings::CNL, Instrument::COLLISION_QUADRUPOLE, PeakFileOptions::containsMSLevel(), IonSource::CONTINUOUSFLOWFASTATOMBOMBARDMENT, DataProcessing::CONVERSION_DTA, DataProcessing::CONVERSION_MZDATA, DataProcessing::CONVERSION_MZML, DataProcessing::CONVERSION_MZXML, IonDetector::CONVERSIONDYNODE, IonDetector::CONVERSIONDYNODEELECTRONMULTIPLIER, IonDetector::CONVERSIONDYNODEPHOTOMULTIPLIER, InstrumentSettings::CRM, MzMLHandler< MapType >::current_id_, MzMLHandler< MapType >::cv_, MassAnalyzer::CYCLOTRON, IonDetector::DALYDETECTOR, MzMLHandler< MapType >::data_, DataProcessing::DATA_PROCESSING, DataProcessing::DEISOTOPING, Instrument::DELAYED_EXTRACTION, IonSource::DI, IonSource::DIRECT, IonSource::DISSI, IonDetector::DYNODE, Precursor::ECD, IonSource::EI, Instrument::EINZEL_LENS, ChromatogramSettings::ELECTROMAGNETIC_RADIATION_CHROMATOGRAM, IonDetector::ELECTRONMULTIPLIER, IonDetector::ELECTRONMULTIPLIERTUBE, IonSource::ELECTROSPRAYINLET, InstrumentSettings::EMC, InstrumentSettings::EMISSION, ChromatogramSettings::EMISSION_CHROMATOGRAM, InstrumentSettings::EMR, Sample::EMULSION, DRange< D >::encloses(), MassAnalyzer::ESA, IonSource::ESI, Precursor::ETD, ControlledVocabulary::exists(), MzMLHandler< MapType >::exp_, IonSource::FA, IonSource::FAB, IonDetector::FARADAYCUP, IonSource::FD, IonSource::FIB, IonSource::FII, DataProcessing::FILTERING, Instrument::FIRST_STABILITY_REGION, IonSource::FLOWINJECTIONANALYSIS, IonDetector::FOCALPLANEARRAY, IonDetector::FOCALPLANECOLLECTOR, DataProcessing::FORMAT_CONVERSION, MassAnalyzer::FOURIERTRANSFORM, Instrument::FRINGING_FIELD, Sample::GAS, IonSource::GD_MS, SpectrumSettings::getAcquisitionInfo(), Precursor::getActivationMethods(), SpectrumSettings::getInstrumentSettings(), MSSpectrum< PeakT >::getMSLevel(), Precursor::getPossibleChargeStates(), ChromatogramSettings::getPrecursor(), SpectrumSettings::getPrecursors(), ChromatogramSettings::getProduct(), SpectrumSettings::getProducts(), MSSpectrum< PeakT >::getRT(), PeakFileOptions::getRTRange(), InstrumentSettings::getScanWindows(), ControlledVocabulary::getTerm(), ControlledVocabulary::CVTerm::getXRefTypeName(), PeakFileOptions::hasMSLevels(), String::hasPrefix(), PeakFileOptions::hasRTRange(), Precursor::HCID, ControlledVocabulary::CVTerm::id, Precursor::IMD, MzMLHandler< MapType >::in_spectrum_list_, IonDetector::INDUCTIVEDETECTOR, IonSource::INDUCTIVELYCOUPLEDPLASMA, IonSource::INFUSION, MzMLHandler< MapType >::instruments_, IonSource::IONMETHODNULL, IonDetector::IONTOPHOTONDETECTOR, ControlledVocabulary::isChildOf(), MassAnalyzer::IT, IonSource::JETSEPARATOR, Instrument::KINETIC_ENERGY_ANALYZER, Precursor::LCID, IonSource::LD, Sample::LIQUID, MassAnalyzer::LIT, XMLHandler::LOAD, IonSource::LSI, Instrument::MAGNETIC_DEFLECTION, IonSource::MALDI, ChromatogramSettings::MASS_CHROMATOGRAM, InstrumentSettings::MASSSPECTRUM, SourceFile::MD5, IonSource::MEMBRANE, IonSource::MEMBRANESEPARATOR, IonSource::MESI, IonDetector::MICROCHANNELPLATEDETECTOR, IonSource::MOVINGBELT, IonSource::MOVINGWIRE, IonSource::MPI, InstrumentSettings::MS1SPECTRUM, InstrumentSettings::MSNSPECTRUM, IonDetector::MULTICOLLECTOR, SemanticValidator::CVTerm::name, ControlledVocabulary::CVTerm::name, IonSource::NANOSPRAY, IonSource::NEGATIVE, IonSource::NESI, IonSource::NICI, ControlledVocabulary::CVTerm::NONE, DataProcessing::NORMALIZATION, IonSource::NRMS, ControlledVocabulary::CVTerm::obsolete, MassAnalyzer::OFF, MassAnalyzer::ON, IonSource::OPENSPLIT, MzMLHandler< MapType >::options_, MassAnalyzer::ORBITRAP, IonSource::PARTICLEBEAM, MassAnalyzer::PAULIONTRAP, IonSource::PD, Precursor::PD, DataProcessing::PEAK_PICKING, SpectrumSettings::PEAKS, IonSource::PEI, Precursor::PHD, IonDetector::PHOTODIODEARRAYDETECTOR, IonDetector::PHOTOMULTIPLIER, IonSource::PI, IonDetector::POINTCOLLECTOR, IonSource::POSITIVE, IonDetector::POSTACCELERATIONDETECTOR, Precursor::PQD, InstrumentSettings::PRECURSOR, DataProcessing::PRECURSOR_RECALCULATION, MzMLHandler< MapType >::processing_, Precursor::PSD, IonDetector::PULSECOUNTING, IonSource::PYMS, MassAnalyzer::QUADRUPOLE, MassAnalyzer::RADIALEJECTIONLINEARIONTRAP, SpectrumSettings::RAWDATA, MzMLHandler< MapType >::ref_param_, Instrument::REFLECTRON, IonSource::REMPI, IonSource::RESERVOIR, IonSource::SALDI, MzMLHandler< MapType >::samples_, MassAnalyzer::SECTOR, IonSource::SELDI, MzMLHandler< MapType >::selected_ion_count_, ChromatogramSettings::SELECTED_ION_CURRENT_CHROMATOGRAM, Instrument::SELECTED_ION_FLOW_TUBE, ChromatogramSettings::SELECTED_ION_MONITORING_CHROMATOGRAM, ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM, IonSource::SEND, IonSource::SEPTUM, DateTime::set(), Precursor::setActivationEnergy(), Precursor::setCharge(), ChromatogramSettings::setChromatogramType(), Peak1D::setIntensity(), Product::setIsolationWindowLowerOffset(), Precursor::setIsolationWindowLowerOffset(), Product::setIsolationWindowUpperOffset(), Precursor::setIsolationWindowUpperOffset(), MetaInfoInterface::setMetaValue(), AcquisitionInfo::setMethodOfCombination(), MSSpectrum< PeakT >::setMSLevel(), Product::setMZ(), Peak1D::setMZ(), MSChromatogram< PeakT >::setName(), InstrumentSettings::setPolarity(), MSSpectrum< PeakT >::setRT(), InstrumentSettings::setScanMode(), SpectrumSettings::setType(), DataValue::setUnit(), InstrumentSettings::setZoomScan(), SourceFile::SHA1, IonSource::SI, Precursor::SID, IonSource::SILI, InstrumentSettings::SIM, MzMLHandler< MapType >::skip_spectrum_, DataProcessing::SMOOTHING, MzMLHandler< MapType >::software_, IonSource::SOI, Sample::SOLID, Sample::SOLUTION, Precursor::SORI, MzMLHandler< MapType >::source_files_, MzMLHandler< MapType >::spec_, IonSource::SPI, InstrumentSettings::SRM, Instrument::STATIC_FIELD, IonSource::SUI, Sample::SUSPENSION, MassAnalyzer::SWIFT, IonDetector::TDC, InstrumentSettings::TDF, IonSource::THERMOSPRAYINLET, IonSource::TI, Instrument::TIME_LAG_FOCUSING, String::toDouble(), MassAnalyzer::TOF, String::toInt(), ChromatogramSettings::TOTAL_ION_CURRENT_CHROMATOGRAM, IonDetector::TRANSIENTRECORDER, String::trim(), IonDetector::TYPENULL, SemanticValidator::CVTerm::unit_accession, SpectrumSettings::UNKNOWN, SemanticValidator::CVTerm::value, IonSource::VI, XMLHandler::warning(), ControlledVocabulary::CVTerm::xref_type, ControlledVocabulary::CVTerm::XSD_DATE, ControlledVocabulary::CVTerm::XSD_DECIMAL, ControlledVocabulary::CVTerm::XSD_INTEGER, ControlledVocabulary::CVTerm::XSD_NEGATIVE_INTEGER, ControlledVocabulary::CVTerm::XSD_NON_NEGATIVE_INTEGER, ControlledVocabulary::CVTerm::XSD_NON_POSITIVE_INTEGER, ControlledVocabulary::CVTerm::XSD_POSITIVE_INTEGER, and ControlledVocabulary::CVTerm::XSD_STRING.

Referenced by MzMLHandler< MapType >::startElement().

void handleUserParam_ ( const String &  parent_parent_tag,
const String &  parent_tag,
const String &  name,
const String &  type,
const String &  value 
) [protected]

Handles user terms.

References MzMLHandler< MapType >::chromatogram_, MzMLHandler< MapType >::current_id_, MzMLHandler< MapType >::data_, MzMLHandler< MapType >::exp_, SpectrumSettings::getAcquisitionInfo(), SpectrumSettings::getInstrumentSettings(), ChromatogramSettings::getPrecursor(), SpectrumSettings::getPrecursors(), ChromatogramSettings::getProduct(), SpectrumSettings::getProducts(), InstrumentSettings::getScanWindows(), MzMLHandler< MapType >::in_spectrum_list_, MzMLHandler< MapType >::instruments_, XMLHandler::LOAD, MzMLHandler< MapType >::processing_, MzMLHandler< MapType >::samples_, MzMLHandler< MapType >::selected_ion_count_, MetaInfoInterface::setMetaValue(), MzMLHandler< MapType >::software_, MzMLHandler< MapType >::source_files_, MzMLHandler< MapType >::spec_, String::toDouble(), String::toInt(), and XMLHandler::warning().

Referenced by MzMLHandler< MapType >::startElement().

void setOptions ( const PeakFileOptions &  opt  )  [inline]

References MzMLHandler< MapType >::options_.

Referenced by MzMLFile::load(), and MzMLFile::store().

void startElement ( const XMLCh *  uri,
const XMLCh *  localname,
const XMLCh *const   qname,
const xercesc::Attributes &  attrs 
) [virtual]

Parsing method for opening tags.

Reimplemented from XMLHandler.

References XMLHandler::asDateTime_(), XMLHandler::attributeAsInt_(), XMLHandler::attributeAsString_(), MzMLHandler< MapType >::chromatogram_, StringManager::convert(), MzMLHandler< MapType >::current_id_, MzMLHandler< MapType >::data_, MzMLHandler< MapType >::default_array_length_, MzMLHandler< MapType >::default_processing_, MzMLHandler< MapType >::exp_, XMLHandler::fatalError(), SpectrumSettings::getAcquisitionInfo(), SpectrumSettings::getInstrumentSettings(), PeakFileOptions::getMetadataOnly(), ChromatogramSettings::getPrecursor(), SpectrumSettings::getPrecursors(), SpectrumSettings::getProducts(), InstrumentSettings::getScanWindows(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), MzMLHandler< MapType >::in_spectrum_list_, MzMLHandler< MapType >::instruments_, XMLHandler::LOAD, LOG_ERROR, MzMLHandler< MapType >::logger_, XMLHandler::open_tags_, XMLHandler::optionalAttributeAsInt_(), XMLHandler::optionalAttributeAsString_(), MzMLHandler< MapType >::options_, MzMLHandler< MapType >::processing_, MzMLHandler< MapType >::ref_param_, MzMLHandler< MapType >::samples_, MzMLHandler< MapType >::selected_ion_count_, ChromatogramSettings::setDataProcessing(), SpectrumSettings::setDataProcessing(), Acquisition::setIdentifier(), MetaInfoInterface::setMetaValue(), ChromatogramSettings::setNativeID(), SpectrumSettings::setNativeID(), ChromatogramSettings::setPrecursor(), ChromatogramSettings::setProduct(), DataProcessing::setSoftware(), ChromatogramSettings::setSourceFile(), SpectrumSettings::setSourceFile(), MzMLHandler< MapType >::skip_spectrum_, XMLHandler::sm_, MzMLHandler< MapType >::software_, MzMLHandler< MapType >::source_files_, MzMLHandler< MapType >::spec_, ProgressLogger::startProgress(), String::toDouble(), String::toQString(), XMLHandler::version_, and XMLHandler::warning().

bool validateCV_ ( const ControlledVocabulary::CVTerm &  c,
const String &  path,
const Internal::MzMLValidator &  validator 
) const [protected]

Helper method to validate if the given CV is allowed in the current location (path).

References SemanticValidator::CVTerm::accession, SemanticValidator::CVTerm::has_unit_accession, SemanticValidator::CVTerm::has_unit_name, ControlledVocabulary::CVTerm::id, ControlledVocabulary::CVTerm::name, and SemanticValidator::CVTerm::name.

Referenced by MzMLHandler< MapType >::writeUserParam_().

String writeCV_ ( const ControlledVocabulary::CVTerm &  c,
const DataValue &  metaValue 
) const [protected]

Helper method to write an CV based on a meta value.

References MzMLHandler< MapType >::cv_, ControlledVocabulary::getTerm(), DataValue::getUnit(), DataValue::hasUnit(), ControlledVocabulary::CVTerm::id, DataValue::isEmpty(), ControlledVocabulary::CVTerm::name, String::prefix(), and String::substitute().

Referenced by MzMLHandler< MapType >::writeUserParam_().

void writeDataProcessing_ ( std::ostream &  os,
const String &  id,
const std::vector< DataProcessing > &  dps,
Internal::MzMLValidator &  validator 
) [protected]

Helper method that writes a data processing list.

References DataProcessing::ALIGNMENT, DataProcessing::BASELINE_REDUCTION, DataProcessing::CALIBRATION, DataProcessing::CHARGE_CALCULATION, DataProcessing::CHARGE_DECONVOLUTION, DataProcessing::CONVERSION_DTA, DataProcessing::CONVERSION_MZDATA, DataProcessing::CONVERSION_MZML, DataProcessing::CONVERSION_MZXML, DataProcessing::DATA_PROCESSING, DataProcessing::DEISOTOPING, DataProcessing::FILTERING, DataProcessing::FORMAT_CONVERSION, DataProcessing::NORMALIZATION, DataProcessing::PEAK_PICKING, DataProcessing::PRECURSOR_RECALCULATION, DataProcessing::SMOOTHING, and MzMLHandler< MapType >::writeUserParam_().

Referenced by MzMLHandler< MapType >::writeTo().

void writePrecursor_ ( std::ostream &  os,
const Precursor &  precursor,
Internal::MzMLValidator &  validator 
) [protected]

Helper method that write precursor information from spectra and chromatograms.

References Precursor::BIRD, Precursor::CID, Precursor::ECD, Precursor::ETD, Precursor::getActivationEnergy(), Precursor::getActivationMethods(), Precursor::getCharge(), Peak1D::getIntensity(), Precursor::getIsolationWindowLowerOffset(), Precursor::getIsolationWindowUpperOffset(), Peak1D::getMZ(), Precursor::getPossibleChargeStates(), Precursor::HCID, Precursor::IMD, Precursor::LCID, Precursor::PD, Precursor::PHD, Precursor::PQD, Precursor::PSD, Precursor::SID, Precursor::SORI, and MzMLHandler< MapType >::writeUserParam_().

Referenced by MzMLHandler< MapType >::writeTo().

void writeProduct_ ( std::ostream &  os,
const Product &  product,
Internal::MzMLValidator &  validator 
) [protected]

Helper method that write precursor information from spectra and chromatograms.

References Product::getIsolationWindowLowerOffset(), Product::getIsolationWindowUpperOffset(), Product::getMZ(), and MzMLHandler< MapType >::writeUserParam_().

Referenced by MzMLHandler< MapType >::writeTo().

void writeSoftware_ ( std::ostream &  os,
const String &  id,
const Software &  software,
Internal::MzMLValidator &  validator 
) [protected]

Helper method that writes a software.

References MzMLHandler< MapType >::getChildWithName_(), Software::getName(), Software::getVersion(), ControlledVocabulary::CVTerm::id, ControlledVocabulary::CVTerm::name, and MzMLHandler< MapType >::writeUserParam_().

Referenced by MzMLHandler< MapType >::writeTo().

void writeSourceFile_ ( std::ostream &  os,
const String &  id,
const SourceFile &  software,
Internal::MzMLValidator &  validator 
) [protected]

Helper method that writes a source file.

References SourceFile::getChecksum(), SourceFile::getChecksumType(), MzMLHandler< MapType >::getChildWithName_(), SourceFile::getFileType(), SourceFile::getNameOfFile(), SourceFile::getNativeIDType(), SourceFile::getPathToFile(), ControlledVocabulary::CVTerm::id, ControlledVocabulary::CVTerm::name, and MzMLHandler< MapType >::writeUserParam_().

Referenced by MzMLHandler< MapType >::writeTo().

void writeTo ( std::ostream &   )  [virtual]

Writes the contents to a stream.

Reimplemented from XMLHandler.

References InstrumentSettings::ABSORBTION, IonDetector::ADC, IonDetector::ARRAYDETECTOR, Base64::BYTEORDER_LITTLEENDIAN, OpenMS::Constants::c, MzMLHandler< MapType >::cexp_, IonDetector::CHANNELTRON, InstrumentSettings::CNG, InstrumentSettings::CNL, IonDetector::CONVERSIONDYNODE, IonDetector::CONVERSIONDYNODEELECTRONMULTIPLIER, IonDetector::CONVERSIONDYNODEPHOTOMULTIPLIER, InstrumentSettings::CRM, MzMLHandler< MapType >::cv_, IonDetector::DALYDETECTOR, MzMLHandler< MapType >::decoder_, IonDetector::DYNODE, IonDetector::ELECTRONMULTIPLIER, IonDetector::ELECTRONMULTIPLIERTUBE, InstrumentSettings::EMC, InstrumentSettings::EMISSION, InstrumentSettings::EMR, Base64::encode(), Base64::encodeIntegers(), Base64::encodeStrings(), ProgressLogger::endProgress(), IonDetector::FARADAYCUP, IonDetector::FOCALPLANEARRAY, IonDetector::FOCALPLANECOLLECTOR, MassAnalyzer::getAccuracy(), SpectrumSettings::getAcquisitionInfo(), ContactPerson::getAddress(), MzMLHandler< MapType >::getChildWithName_(), ChromatogramSettings::getChromatogramType(), Sample::getComment(), PeakFileOptions::getCompression(), Sample::getConcentration(), ContactPerson::getContactInfo(), Instrument::getCustomizations(), SpectrumSettings::getDataProcessing(), ContactPerson::getEmail(), MassAnalyzer::getFinalMSExponent(), ContactPerson::getFirstName(), MSChromatogram< PeakT >::getFloatDataArrays(), MSSpectrum< PeakT >::getFloatDataArrays(), Acquisition::getIdentifier(), IonSource::getInletType(), ContactPerson::getInstitution(), SpectrumSettings::getInstrumentSettings(), MSChromatogram< PeakT >::getIntegerDataArrays(), MSSpectrum< PeakT >::getIntegerDataArrays(), PeakFileOptions::getIntensity32Bit(), Instrument::getIonDetectors(), IonSource::getIonizationMethod(), Instrument::getIonOptics(), Instrument::getIonSources(), ContactPerson::getLastName(), MassAnalyzer::getMagneticFieldStrength(), Sample::getMass(), Instrument::getMassAnalyzers(), AcquisitionInfo::getMethodOfCombination(), MSSpectrum< PeakT >::getMSLevel(), PeakFileOptions::getMz32Bit(), Instrument::getName(), Sample::getName(), ChromatogramSettings::getNativeID(), SpectrumSettings::getNativeID(), Sample::getNumber(), MassAnalyzer::getOrder(), IonSource::getOrder(), InstrumentSettings::getPolarity(), ChromatogramSettings::getPrecursor(), SpectrumSettings::getPrecursors(), ChromatogramSettings::getProduct(), SpectrumSettings::getProducts(), MassAnalyzer::getReflectronState(), MSSpectrum< PeakT >::getRT(), InstrumentSettings::getScanMode(), InstrumentSettings::getScanWindows(), SpectrumSettings::getSourceFile(), Sample::getState(), MSChromatogram< PeakT >::getStringDataArrays(), MSSpectrum< PeakT >::getStringDataArrays(), MassAnalyzer::getTOFTotalPathLength(), SpectrumSettings::getType(), MassAnalyzer::getType(), ContactPerson::getURL(), Sample::getVolume(), InstrumentSettings::getZoomScan(), Map< Key, T >::has(), ControlledVocabulary::CVTerm::id, IonDetector::INDUCTIVEDETECTOR, IonDetector::IONTOPHOTONDETECTOR, MzMLHandler< MapType >::logger_, MzMLHandler< MapType >::mapping_, InstrumentSettings::MASSSPECTRUM, IonDetector::MICROCHANNELPLATEDETECTOR, InstrumentSettings::MS1SPECTRUM, InstrumentSettings::MSNSPECTRUM, IonDetector::MULTICOLLECTOR, ControlledVocabulary::CVTerm::name, MzMLHandler< MapType >::options_, IonDetector::PHOTODIODEARRAYDETECTOR, IonDetector::PHOTOMULTIPLIER, IonDetector::POINTCOLLECTOR, IonDetector::POSTACCELERATIONDETECTOR, InstrumentSettings::PRECURSOR, IonDetector::PULSECOUNTING, ProgressLogger::setProgress(), InstrumentSettings::SIM, InstrumentSettings::SRM, ProgressLogger::startProgress(), XMLHandler::STORE, IonDetector::TDC, InstrumentSettings::TDF, IonDetector::TRANSIENTRECORDER, IonDetector::TYPENULL, InstrumentSettings::UNKNOWN, XMLHandler::version_, XMLHandler::warning(), MzMLHandler< MapType >::writeDataProcessing_(), MzMLHandler< MapType >::writePrecursor_(), MzMLHandler< MapType >::writeProduct_(), MzMLHandler< MapType >::writeSoftware_(), MzMLHandler< MapType >::writeSourceFile_(), and MzMLHandler< MapType >::writeUserParam_().

void writeUserParam_ ( std::ostream &  os,
const MetaInfoInterface &  meta,
UInt  indent,
String  path,
Internal::MzMLValidator &  validator 
) const [protected]

Writes user terms.

References OpenMS::Constants::c, MzMLHandler< MapType >::cv_, DataValue::EMPTY, MetaInfoInterface::getKeys(), MetaInfoInterface::getMetaValue(), ControlledVocabulary::getTermByName(), ControlledVocabulary::hasTermWithName(), String::substitute(), MzMLHandler< MapType >::validateCV_(), DataValue::valueType(), and MzMLHandler< MapType >::writeCV_().

Referenced by MzMLHandler< MapType >::writeDataProcessing_(), MzMLHandler< MapType >::writePrecursor_(), MzMLHandler< MapType >::writeProduct_(), MzMLHandler< MapType >::writeSoftware_(), MzMLHandler< MapType >::writeSourceFile_(), and MzMLHandler< MapType >::writeTo().

Member Data Documentation

const MapType* cexp_ [protected]

map pointer for writing

Referenced by MzMLHandler< MapType >::writeTo().

ChromatogramType chromatogram_ [protected]

The current chromatogram.

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::fillChromatogramData_(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), and MzMLHandler< MapType >::startElement().

String current_id_ [protected]

Id of the current list. Used for referencing param group, source file, sample, software, ...

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), and MzMLHandler< MapType >::startElement().

ControlledVocabulary cv_ [protected]

Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo).

Referenced by MzMLHandler< MapType >::getChildWithName_(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::MzMLHandler(), MzMLHandler< MapType >::writeCV_(), MzMLHandler< MapType >::writeTo(), and MzMLHandler< MapType >::writeUserParam_().

std::vector<BinaryData> data_ [protected]

The spectrum data (or chromatogram data).

Referenced by MzMLHandler< MapType >::characters(), MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::fillChromatogramData_(), MzMLHandler< MapType >::fillData_(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), and MzMLHandler< MapType >::startElement().

Base64 decoder_ [protected]

Decoder/Encoder for Base64-data in MzML.

Referenced by MzMLHandler< MapType >::fillChromatogramData_(), MzMLHandler< MapType >::fillData_(), and MzMLHandler< MapType >::writeTo().

Size default_array_length_ [protected]

The default number of peaks in the current spectrum.

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::fillChromatogramData_(), MzMLHandler< MapType >::fillData_(), and MzMLHandler< MapType >::startElement().

String default_processing_ [protected]

id of the default data processing (used when no processing is defined)

Referenced by MzMLHandler< MapType >::startElement().

MapType* exp_ [protected]

map pointer for reading

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), and MzMLHandler< MapType >::startElement().

bool in_spectrum_list_ [protected]

Flag that indicates that we're inside a spectrum (in contrast to a chromatogram).

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), and MzMLHandler< MapType >::startElement().

Map<String, Instrument> instruments_ [protected]

The data processing list: id => Instrument.

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), and MzMLHandler< MapType >::startElement().

const ProgressLogger& logger_ [protected]

Progress logger.

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::startElement(), and MzMLHandler< MapType >::writeTo().

CVMappings mapping_ [protected]

Referenced by MzMLHandler< MapType >::MzMLHandler(), and MzMLHandler< MapType >::writeTo().

PeakFileOptions options_ [protected]

Options that can be set for loading/storing.

Referenced by MzMLHandler< MapType >::fillChromatogramData_(), MzMLHandler< MapType >::fillData_(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::setOptions(), MzMLHandler< MapType >::startElement(), and MzMLHandler< MapType >::writeTo().

Map<String, std::vector<DataProcessing> > processing_ [protected]

The data processing list: id => Instrument.

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), and MzMLHandler< MapType >::startElement().

Map<String, std::vector<SemanticValidator::CVTerm> > ref_param_ [protected]

The referencing param groups: id => array (accession, value).

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::handleCVParam_(), and MzMLHandler< MapType >::startElement().

Map<String, Sample> samples_ [protected]

The sample list: id => Sample.

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), and MzMLHandler< MapType >::startElement().

UInt selected_ion_count_ [protected]

Count of selected ions.

Referenced by MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), and MzMLHandler< MapType >::startElement().

bool skip_spectrum_ [protected]

Flag that indicates whether this spectrum should be skipped (due to options).

Referenced by MzMLHandler< MapType >::characters(), MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::handleCVParam_(), and MzMLHandler< MapType >::startElement().

Map<String, Software> software_ [protected]

The software list: id => Software.

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), and MzMLHandler< MapType >::startElement().

Map<String, SourceFile> source_files_ [protected]

The source files: id => SourceFile.

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), and MzMLHandler< MapType >::startElement().

SpectrumType spec_ [protected]

The current spectrum.

Referenced by MzMLHandler< MapType >::endElement(), MzMLHandler< MapType >::fillData_(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), and MzMLHandler< MapType >::startElement().

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:43:00 using doxygen 1.7.1