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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

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. More...
 
virtual void startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes)
 Parsing method for opening tags. More...
 
virtual void characters (const XMLCh *const chars, const XMLSize_t length)
 Parsing method for character data. More...
 
virtual void writeTo (std::ostream &os)
 Writes the contents to a stream. More...
 
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. More...
 
 MzMLHandler (const MapType &exp, const String &filename, const String &version, const ProgressLogger &logger)
 Constructor for a write-only handler. More...
 
virtual ~MzMLHandler ()
 Destructor. More...
 
- Public Member Functions inherited from XMLHandler
 XMLHandler (const String &filename, const String &version)
 Default constructor. More...
 
virtual ~XMLHandler ()
 Destructor. More...
 
void reset ()
 Release internal memory used for parsing (call. More...
 
void fatalError (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
 Fatal error handler. Throws a ParseError exception. More...
 
void error (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
 Error handler for recoverable errors. More...
 
void warning (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
 Warning handler. More...
 
String errorString ()
 Returns the last error description. More...
 
void fatalError (const xercesc::SAXParseException &exception)
 
void error (const xercesc::SAXParseException &exception)
 
void warning (const xercesc::SAXParseException &exception)
 

Protected Types

typedef MapType::PeakType PeakType
 Peak type. More...
 
typedef
MapType::ChromatogramPeakType 
ChromatogramPeakType
 Chromatogram peak type. More...
 
typedef MSSpectrum< PeakTypeSpectrumType
 Spectrum type. More...
 
typedef MSChromatogram
< ChromatogramPeakType
ChromatogramType
 Spectrum type. More...
 

Protected Member Functions

void writeSpectrum_ (std::ostream &os, const SpectrumType &spec, Size s, Internal::MzMLValidator &validator, bool renew_native_ids, std::vector< std::vector< DataProcessing > > &dps)
 
void writeChromatogram_ (std::ostream &os, const ChromatogramType &chromatogram, Size c, Internal::MzMLValidator &validator)
 
void writeHeader_ (std::ostream &os, const MapType &exp, std::vector< std::vector< DataProcessing > > &dps, Internal::MzMLValidator &validator)
 
void writeFooter_ (std::ostream &os)
 
void fillData_ ()
 Fills the current spectrum with peaks and meta data. More...
 
void fillChromatogramData_ ()
 Fills the current chromatogram with data points and meta data. More...
 
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. More...
 
void handleUserParam_ (const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value)
 Handles user terms. More...
 
void writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent, String path, Internal::MzMLValidator &validator) const
 Writes user terms. More...
 
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. More...
 
void writeSoftware_ (std::ostream &os, const String &id, const Software &software, Internal::MzMLValidator &validator)
 Helper method that writes a software. More...
 
void writeSourceFile_ (std::ostream &os, const String &id, const SourceFile &software, Internal::MzMLValidator &validator)
 Helper method that writes a source file. More...
 
void writeDataProcessing_ (std::ostream &os, const String &id, const std::vector< DataProcessing > &dps, Internal::MzMLValidator &validator)
 Helper method that writes a data processing list. More...
 
void writePrecursor_ (std::ostream &os, const Precursor &precursor, Internal::MzMLValidator &validator)
 Helper method that write precursor information from spectra and chromatograms. More...
 
void writeProduct_ (std::ostream &os, const Product &product, Internal::MzMLValidator &validator)
 Helper method that write precursor information from spectra and chromatograms. More...
 
String writeCV_ (const ControlledVocabulary::CVTerm &c, const DataValue &metaValue) const
 Helper method to write an CV based on a meta value. More...
 
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) More...
 
- Protected Member Functions inherited from XMLHandler
bool equal_ (const XMLCh *a, const XMLCh *b)
 Returns if two xerces strings are equal. More...
 
void writeUserParam_ (const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
 Writes the content of MetaInfoInterface to the file. More...
 
Int asInt_ (const String &in)
 Conversion of a String to an integer value. More...
 
Int asInt_ (const XMLCh *in)
 Conversion of a Xerces string to an integer value. More...
 
UInt asUInt_ (const String &in)
 Conversion of a String to an unsigned integer value. More...
 
double asDouble_ (const String &in)
 Conversion of a String to a double value. More...
 
float asFloat_ (const String &in)
 Conversion of a String to a float value. More...
 
bool asBool_ (const String &in)
 Conversion of a string to a boolean value. More...
 
DateTime asDateTime_ (String date_string)
 Conversion of a xs:datetime string to a DataTime value. More...
 
char * attributeAsString_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a String. More...
 
Int attributeAsInt_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a Int. More...
 
DoubleReal attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a DoubleReal. More...
 
DoubleList attributeAsDoubleList_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a DoubleList. More...
 
IntList attributeAsIntList_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to an IntList. More...
 
StringList attributeAsStringList_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to an StringList. More...
 
bool optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the String value if the attribute is present. More...
 
bool optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the Int value if the attribute is present. More...
 
bool optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the UInt value if the attribute is present. More...
 
bool optionalAttributeAsDouble_ (DoubleReal &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the DoubleReal value if the attribute is present. More...
 
bool optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the DoubleList value if the attribute is present. More...
 
bool optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the StringList value if the attribute is present. More...
 
bool optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the IntList value if the attribute is present. More...
 
char * attributeAsString_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a String. More...
 
Int attributeAsInt_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a Int. More...
 
DoubleReal attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a DoubleReal. More...
 
DoubleList attributeAsDoubleList_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a DoubleList. More...
 
IntList attributeAsIntList_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a IntList. More...
 
StringList attributeAsStringList_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a StringList. More...
 
bool optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the String value if the attribute is present. More...
 
bool optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the Int value if the attribute is present. More...
 
bool optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the UInt value if the attribute is present. More...
 
bool optionalAttributeAsDouble_ (DoubleReal &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the DoubleReal value if the attribute is present. More...
 
bool optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the DoubleList value if the attribute is present. More...
 
bool optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the IntList value if the attribute is present. More...
 
bool optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the StringList value if the attribute is present. More...
 
SignedSize cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0)
 

Protected Attributes

MapType * exp_
 map pointer for reading More...
 
const MapType * cexp_
 map pointer for writing More...
 
PeakFileOptions options_
 Options that can be set for loading/storing. More...
 
Base64 decoder_
 Decoder/Encoder for Base64-data in MzML. More...
 
const ProgressLoggerlogger_
 Progress logger. More...
 
bool skip_spectrum_
 Flag that indicates whether this spectrum should be skipped (due to options) More...
 
ControlledVocabulary cv_
 Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) More...
 
CVMappings mapping_
 
UInt selected_ion_count_
 Count of selected ions. More...
 
temporary data structures to hold parsed data
SpectrumType spec_
 The current spectrum. More...
 
ChromatogramType chromatogram_
 The current chromatogram. More...
 
std::vector< BinaryDatadata_
 The spectrum data (or chromatogram data) More...
 
Size default_array_length_
 The default number of peaks in the current spectrum. More...
 
bool in_spectrum_list_
 Flag that indicates that we're inside a spectrum (in contrast to a chromatogram) More...
 
String current_id_
 Id of the current list. Used for referencing param group, source file, sample, software, ... More...
 
Map< String, std::vector
< SemanticValidator::CVTerm > > 
ref_param_
 The referencing param groups: id => array (accession, value) More...
 
Map< String, SourceFilesource_files_
 The source files: id => SourceFile. More...
 
Map< String, Samplesamples_
 The sample list: id => Sample. More...
 
Map< String, Softwaresoftware_
 The software list: id => Software. More...
 
Map< String, Instrumentinstruments_
 The data processing list: id => Instrument. More...
 
Map< String, std::vector
< DataProcessing > > 
processing_
 The data processing list: id => Instrument. More...
 
String default_processing_
 id of the default data processing (used when no processing is defined) More...
 
- Protected Attributes inherited from XMLHandler
String error_message_
 Error message of the last error. More...
 
String file_
 File name. More...
 
String version_
 Schema version. More...
 
StringManager sm_
 Helper class for string conversion. More...
 
std::vector< Stringopen_tags_
 Stack of open XML tags. More...
 
std::vector< std::vector
< String > > 
cv_terms_
 Array of CV term lists (one sublist denotes one term and it's children) More...
 

Additional Inherited Members

- Public Types inherited from XMLHandler
enum  ActionMode { LOAD, STORE }
 Action to set the current mode (for error messages) More...
 

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.

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.

MzMLHandler ( const MapType &  exp,
const String filename,
const String version,
const ProgressLogger logger 
)
inline
virtual ~MzMLHandler ( )
inlinevirtual

Destructor.

Member Function Documentation

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

Parsing method for character data.

Reimplemented from XMLHandler.

References String::trim().

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

Parsing method for closing tags.

Reimplemented from XMLHandler.

void fillChromatogramData_ ( )
protected

Fills the current chromatogram with data points and meta data.

References Base64::BYTEORDER_LITTLEENDIAN, and OpenMS::Constants::k.

void fillData_ ( )
protected

Fills the current spectrum with peaks and meta data.

References Base64::BYTEORDER_LITTLEENDIAN, and OpenMS::Constants::k.

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.

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, 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, IonSource::CHROMATOGRAPHY, IonSource::CI, Precursor::CID, InstrumentSettings::CNG, InstrumentSettings::CNL, Instrument::COLLISION_QUADRUPOLE, IonSource::CONTINUOUSFLOWFASTATOMBOMBARDMENT, DataProcessing::CONVERSION_DTA, DataProcessing::CONVERSION_MZDATA, DataProcessing::CONVERSION_MZML, DataProcessing::CONVERSION_MZXML, IonDetector::CONVERSIONDYNODE, IonDetector::CONVERSIONDYNODEELECTRONMULTIPLIER, IonDetector::CONVERSIONDYNODEPHOTOMULTIPLIER, InstrumentSettings::CRM, MassAnalyzer::CYCLOTRON, IonDetector::DALYDETECTOR, 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, MassAnalyzer::ESA, IonSource::ESI, Precursor::ETD, 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, ControlledVocabulary::CVTerm::getXRefTypeName(), String::hasPrefix(), Precursor::HCID, ControlledVocabulary::CVTerm::id, Precursor::IMD, IonDetector::INDUCTIVEDETECTOR, IonSource::INDUCTIVELYCOUPLEDPLASMA, IonSource::INFUSION, IonSource::IONMETHODNULL, IonDetector::IONTOPHOTONDETECTOR, MassAnalyzer::IT, IonSource::JETSEPARATOR, Instrument::KINETIC_ENERGY_ANALYZER, Precursor::LCID, IonSource::LD, Sample::LIQUID, MassAnalyzer::LIT, 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, MassAnalyzer::ORBITRAP, IonSource::PARTICLEBEAM, MassAnalyzer::PAULIONTRAP, Precursor::PD, IonSource::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, Precursor::PSD, IonDetector::PULSECOUNTING, IonSource::PYMS, MassAnalyzer::QUADRUPOLE, MassAnalyzer::RADIALEJECTIONLINEARIONTRAP, SpectrumSettings::RAWDATA, Instrument::REFLECTRON, IonSource::REMPI, IonSource::RESERVOIR, IonSource::SALDI, MassAnalyzer::SECTOR, IonSource::SELDI, 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(), DataValue::setUnit(), SourceFile::SHA1, IonSource::SI, Precursor::SID, IonSource::SILI, InstrumentSettings::SIM, DataProcessing::SMOOTHING, IonSource::SOI, Sample::SOLID, Sample::SOLUTION, Precursor::SORI, 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, 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.

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 String::toDouble(), and String::toInt().

void setOptions ( const PeakFileOptions opt)
inline
void startElement ( const XMLCh *  uri,
const XMLCh *  localname,
const XMLCh *const  qname,
const xercesc::Attributes &  attrs 
)
virtual
bool validateCV_ ( const ControlledVocabulary::CVTerm c,
const String path,
const Internal::MzMLValidator validator 
) const
protected
void writeChromatogram_ ( std::ostream &  os,
const ChromatogramType chromatogram,
Size  c,
Internal::MzMLValidator validator 
)
protected
String writeCV_ ( const ControlledVocabulary::CVTerm c,
const DataValue metaValue 
) const
protected
void writeDataProcessing_ ( std::ostream &  os,
const String id,
const std::vector< DataProcessing > &  dps,
Internal::MzMLValidator validator 
)
protected
void writeFooter_ ( std::ostream &  os)
protected
void writeHeader_ ( std::ostream &  os,
const MapType &  exp,
std::vector< std::vector< DataProcessing > > &  dps,
Internal::MzMLValidator validator 
)
protected

References InstrumentSettings::ABSORBTION, IonSource::AD, IonDetector::ADC, IonSource::AI, MassAnalyzer::ANALYZERNULL, IonSource::AP_MALDI, IonSource::APCI, IonSource::API, IonSource::APPI, IonDetector::ARRAYDETECTOR, IonSource::ASI, IonSource::AUI, MassAnalyzer::AXIALEJECTIONLINEARIONTRAP, IonSource::BATCH, IonSource::CEI, IonDetector::CHANNELTRON, IonSource::CHEMI, IonSource::CHROMATOGRAPHY, IonSource::CI, InstrumentSettings::CNG, InstrumentSettings::CNL, Instrument::COLLISION_QUADRUPOLE, IonSource::CONTINUOUSFLOWFASTATOMBOMBARDMENT, IonDetector::CONVERSIONDYNODE, IonDetector::CONVERSIONDYNODEELECTRONMULTIPLIER, IonDetector::CONVERSIONDYNODEPHOTOMULTIPLIER, InstrumentSettings::CRM, MassAnalyzer::CYCLOTRON, IonDetector::DALYDETECTOR, Instrument::DELAYED_EXTRACTION, IonSource::DI, IonSource::DIRECT, IonSource::DISSI, IonDetector::DYNODE, IonSource::EI, Instrument::EINZEL_LENS, IonDetector::ELECTRONMULTIPLIER, IonDetector::ELECTRONMULTIPLIERTUBE, IonSource::ELECTROSPRAYINLET, InstrumentSettings::EMC, InstrumentSettings::EMISSION, InstrumentSettings::EMR, Sample::EMULSION, MassAnalyzer::ESA, IonSource::ESI, IonSource::FA, IonSource::FAB, IonDetector::FARADAYCUP, IonSource::FD, IonSource::FI, IonSource::FIB, Instrument::FIRST_STABILITY_REGION, IonSource::FLOWINJECTIONANALYSIS, IonDetector::FOCALPLANEARRAY, IonDetector::FOCALPLANECOLLECTOR, MassAnalyzer::FOURIERTRANSFORM, Instrument::FRINGING_FIELD, Sample::GAS, IonSource::GD_MS, MassAnalyzer::getAccuracy(), ContactPerson::getAddress(), Sample::getComment(), Sample::getConcentration(), ContactPerson::getContactInfo(), Instrument::getCustomizations(), ContactPerson::getEmail(), MassAnalyzer::getFinalMSExponent(), ContactPerson::getFirstName(), IonSource::getInletType(), ContactPerson::getInstitution(), Instrument::getIonDetectors(), IonSource::getIonizationMethod(), Instrument::getIonOptics(), Instrument::getIonSources(), ContactPerson::getLastName(), MassAnalyzer::getMagneticFieldStrength(), Sample::getMass(), Instrument::getMassAnalyzers(), Sample::getName(), Instrument::getName(), Sample::getNumber(), IonSource::getOrder(), MassAnalyzer::getOrder(), MassAnalyzer::getReflectronState(), Sample::getState(), MassAnalyzer::getTOFTotalPathLength(), MassAnalyzer::getType(), ContactPerson::getURL(), Sample::getVolume(), Map< Key, T >::has(), ControlledVocabulary::CVTerm::id, IonDetector::INDUCTIVEDETECTOR, IonSource::INDUCTIVELYCOUPLEDPLASMA, IonSource::INFUSION, IonSource::IONMETHODNULL, IonDetector::IONTOPHOTONDETECTOR, MassAnalyzer::IT, IonSource::JETSEPARATOR, Instrument::KINETIC_ENERGY_ANALYZER, IonSource::LD, Sample::LIQUID, MassAnalyzer::LIT, IonSource::LSI, Instrument::MAGNETIC_DEFLECTION, IonSource::MALDI, InstrumentSettings::MASSSPECTRUM, IonSource::MEMBRANE, IonSource::MEMBRANESEPARATOR, IonSource::MESI, IonDetector::MICROCHANNELPLATEDETECTOR, IonSource::MOVINGBELT, IonSource::MOVINGWIRE, IonSource::MPI, InstrumentSettings::MS1SPECTRUM, InstrumentSettings::MSNSPECTRUM, IonDetector::MULTICOLLECTOR, ControlledVocabulary::CVTerm::name, IonSource::NANOSPRAY, IonSource::NESI, IonSource::NICI, IonSource::NRMS, MassAnalyzer::OFF, MassAnalyzer::ON, IonSource::OPENSPLIT, MassAnalyzer::ORBITRAP, IonSource::PARTICLEBEAM, MassAnalyzer::PAULIONTRAP, IonSource::PD, IonSource::PEI, IonDetector::PHOTODIODEARRAYDETECTOR, IonDetector::PHOTOMULTIPLIER, IonSource::PI, IonDetector::POINTCOLLECTOR, IonDetector::POSTACCELERATIONDETECTOR, InstrumentSettings::PRECURSOR, IonDetector::PULSECOUNTING, IonSource::PYMS, MassAnalyzer::QUADRUPOLE, MassAnalyzer::RADIALEJECTIONLINEARIONTRAP, Instrument::REFLECTRON, IonSource::REMPI, IonSource::RESERVOIR, IonSource::SALDI, MassAnalyzer::SECTOR, IonSource::SELDI, Instrument::SELECTED_ION_FLOW_TUBE, IonSource::SEND, IonSource::SEPTUM, IonSource::SI, IonSource::SILI, InstrumentSettings::SIM, IonSource::SOI, Sample::SOLID, Sample::SOLUTION, 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, MassAnalyzer::TOF, IonDetector::TRANSIENTRECORDER, IonDetector::TYPENULL, InstrumentSettings::UNKNOWN, and IonSource::VI.

void writePrecursor_ ( std::ostream &  os,
const Precursor precursor,
Internal::MzMLValidator validator 
)
protected
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(), and Product::getMZ().

void writeSoftware_ ( std::ostream &  os,
const String id,
const Software software,
Internal::MzMLValidator validator 
)
protected
void writeSourceFile_ ( std::ostream &  os,
const String id,
const SourceFile software,
Internal::MzMLValidator validator 
)
protected
void writeSpectrum_ ( std::ostream &  os,
const SpectrumType spec,
Size  s,
Internal::MzMLValidator validator,
bool  renew_native_ids,
std::vector< std::vector< DataProcessing > > &  dps 
)
protected
void writeTo ( std::ostream &  )
virtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

References OpenMS::Constants::c.

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

Member Data Documentation

const MapType* cexp_
protected

map pointer for writing

ChromatogramType chromatogram_
protected

The current chromatogram.

String current_id_
protected

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

ControlledVocabulary cv_
protected

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

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

std::vector<BinaryData> data_
protected

The spectrum data (or chromatogram data)

Base64 decoder_
protected

Decoder/Encoder for Base64-data in MzML.

Size default_array_length_
protected

The default number of peaks in the current spectrum.

String default_processing_
protected

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

MapType* exp_
protected

map pointer for reading

bool in_spectrum_list_
protected

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

Map<String, Instrument> instruments_
protected

The data processing list: id => Instrument.

const ProgressLogger& logger_
protected

Progress logger.

CVMappings mapping_
protected
PeakFileOptions options_
protected

Options that can be set for loading/storing.

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

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

The data processing list: id => Instrument.

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

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

Map<String, Sample> samples_
protected

The sample list: id => Sample.

UInt selected_ion_count_
protected

Count of selected ions.

bool skip_spectrum_
protected

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

Map<String, Software> software_
protected

The software list: id => Software.

Map<String, SourceFile> source_files_
protected

The source files: id => SourceFile.

SpectrumType spec_
protected

The current spectrum.


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:37 using doxygen 1.8.5