XML handler for MzMLFile. More...
#include <OpenMS/FORMAT/HANDLERS/MzMLHandler.h>
 
  
 | 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< PeakType > | SpectrumType | 
| 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_accessionwith the namename. 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 ProgressLogger & | logger_ | 
| 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< BinaryData > | data_ | 
| 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, SourceFile > | source_files_ | 
| The source files: id => SourceFile.  More... | |
| Map< String, Sample > | samples_ | 
| The sample list: id => Sample.  More... | |
| Map< String, Software > | software_ | 
| The software list: id => Software.  More... | |
| Map< String, Instrument > | instruments_ | 
| 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< String > | open_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... | |
XML handler for MzMLFile.
MapType has to be an MSExperiment or have the same interface.
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Chromatogram peak type.
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Spectrum type.
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Peak type.
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Spectrum type.
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Constructor for a read-only handler.
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Constructor for a write-only handler.
References VersionInfo::VersionDetails::create(), MzMLHandler< MapType >::cv_, VersionInfo::VersionDetails::EMPTY, File::find(), CVMappingFile::load(), ControlledVocabulary::loadFromOBO(), LOG_ERROR, MzMLHandler< MapType >::mapping_, and XMLHandler::version_.
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Destructor.
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Parsing method for closing tags.
Reimplemented from XMLHandler.
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Fills the current chromatogram with data points and meta data.
References Base64::BYTEORDER_LITTLEENDIAN, and OpenMS::Constants::k.
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Fills the current spectrum with peaks and meta data.
References Base64::BYTEORDER_LITTLEENDIAN, and OpenMS::Constants::k.
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Looks up a child CV term of parent_accession with the name name. If no such term is found, an empty term is returned. 
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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.
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Handles user terms.
References String::toDouble(), and String::toInt().
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 | inline | 
References MzMLHandler< MapType >::options_.
Referenced by MzMLFile::load(), and MzMLFile::store().
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 | virtual | 
Parsing method for opening tags.
Reimplemented from XMLHandler.
References VersionInfo::VersionDetails::create(), VersionInfo::VersionDetails::EMPTY, LOG_ERROR, Acquisition::setIdentifier(), MetaInfoInterface::setMetaValue(), and DataProcessing::setSoftware().
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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, SemanticValidator::CVTerm::name, and ControlledVocabulary::CVTerm::name.
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References ChromatogramSettings::ABSORPTION_CHROMATOGRAM, ChromatogramSettings::BASEPEAK_CHROMATOGRAM, Base64::BYTEORDER_LITTLEENDIAN, ChromatogramSettings::ELECTROMAGNETIC_RADIATION_CHROMATOGRAM, ChromatogramSettings::EMISSION_CHROMATOGRAM, ChromatogramSettings::getChromatogramType(), MSChromatogram< PeakT >::getFloatDataArrays(), MSChromatogram< PeakT >::getIntegerDataArrays(), ChromatogramSettings::getNativeID(), ChromatogramSettings::getPrecursor(), ChromatogramSettings::getProduct(), MSChromatogram< PeakT >::getStringDataArrays(), ControlledVocabulary::CVTerm::id, ChromatogramSettings::MASS_CHROMATOGRAM, ControlledVocabulary::CVTerm::name, ChromatogramSettings::SELECTED_ION_CURRENT_CHROMATOGRAM, ChromatogramSettings::SELECTED_ION_MONITORING_CHROMATOGRAM, ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM, and ChromatogramSettings::TOTAL_ION_CURRENT_CHROMATOGRAM.
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Helper method to write an CV based on a meta value.
References DataValue::getUnit(), DataValue::hasUnit(), ControlledVocabulary::CVTerm::id, DataValue::isEmpty(), ControlledVocabulary::CVTerm::name, String::prefix(), and String::substitute().
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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, and DataProcessing::SMOOTHING.
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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.
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 | 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, and Precursor::SORI.
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 | protected | 
Helper method that write precursor information from spectra and chromatograms.
References Product::getIsolationWindowLowerOffset(), Product::getIsolationWindowUpperOffset(), and Product::getMZ().
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 | protected | 
Helper method that writes a software.
References Software::getName(), Software::getVersion(), ControlledVocabulary::CVTerm::id, and ControlledVocabulary::CVTerm::name.
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 | protected | 
Helper method that writes a source file.
References SourceFile::getChecksum(), SourceFile::getChecksumType(), SourceFile::getFileType(), SourceFile::getNameOfFile(), SourceFile::getNativeIDType(), SourceFile::getPathToFile(), ControlledVocabulary::CVTerm::id, SourceFile::MD5, ControlledVocabulary::CVTerm::name, and SourceFile::SHA1.
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 | protected | 
References InstrumentSettings::ABSORBTION, Base64::BYTEORDER_LITTLEENDIAN, InstrumentSettings::CNG, InstrumentSettings::CNL, InstrumentSettings::CRM, InstrumentSettings::EMC, InstrumentSettings::EMISSION, InstrumentSettings::EMR, SpectrumSettings::getAcquisitionInfo(), SpectrumSettings::getDataProcessing(), MSSpectrum< PeakT >::getFloatDataArrays(), Acquisition::getIdentifier(), SpectrumSettings::getInstrumentSettings(), MSSpectrum< PeakT >::getIntegerDataArrays(), AcquisitionInfo::getMethodOfCombination(), MSSpectrum< PeakT >::getMSLevel(), SpectrumSettings::getNativeID(), InstrumentSettings::getPolarity(), SpectrumSettings::getPrecursors(), SpectrumSettings::getProducts(), MSSpectrum< PeakT >::getRT(), InstrumentSettings::getScanMode(), InstrumentSettings::getScanWindows(), SpectrumSettings::getSourceFile(), MSSpectrum< PeakT >::getStringDataArrays(), SpectrumSettings::getType(), InstrumentSettings::getZoomScan(), ControlledVocabulary::CVTerm::id, InstrumentSettings::MASSSPECTRUM, InstrumentSettings::MS1SPECTRUM, InstrumentSettings::MSNSPECTRUM, ControlledVocabulary::CVTerm::name, IonSource::NEGATIVE, SpectrumSettings::PEAKS, IonSource::POSITIVE, InstrumentSettings::PRECURSOR, SpectrumSettings::RAWDATA, InstrumentSettings::SIM, InstrumentSettings::SRM, and InstrumentSettings::TDF.
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 | virtual | 
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 | protected | 
Writes user terms.
References OpenMS::Constants::c, DataValue::DOUBLE_VALUE, DataValue::EMPTY, MetaInfoInterface::getKeys(), MetaInfoInterface::getMetaValue(), DataValue::INT_VALUE, String::substitute(), and DataValue::valueType().
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map pointer for writing
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The current chromatogram.
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Id of the current list. Used for referencing param group, source file, sample, software, ...
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Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Referenced by MzMLHandler< MapType >::MzMLHandler().
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The spectrum data (or chromatogram data)
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Decoder/Encoder for Base64-data in MzML.
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 | protected | 
The default number of peaks in the current spectrum.
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id of the default data processing (used when no processing is defined)
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map pointer for reading
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Flag that indicates that we're inside a spectrum (in contrast to a chromatogram)
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 | protected | 
The data processing list: id => Instrument.
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Progress logger.
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 | protected | 
Referenced by MzMLHandler< MapType >::MzMLHandler().
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Options that can be set for loading/storing.
Referenced by MzMLHandler< MapType >::setOptions().
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The data processing list: id => Instrument.
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The referencing param groups: id => array (accession, value)
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Count of selected ions.
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 | protected | 
Flag that indicates whether this spectrum should be skipped (due to options)
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The source files: id => SourceFile.
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The current spectrum.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:37 using doxygen 1.8.5 |