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... | |
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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_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... | |
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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... | |
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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 | |
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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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References MzMLHandler< MapType >::options_.
Referenced by MzMLFile::load(), and MzMLFile::store().
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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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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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Helper method that write precursor information from spectra and chromatograms.
References Product::getIsolationWindowLowerOffset(), Product::getIsolationWindowUpperOffset(), and Product::getMZ().
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Helper method that writes a software.
References Software::getName(), Software::getVersion(), ControlledVocabulary::CVTerm::id, and ControlledVocabulary::CVTerm::name.
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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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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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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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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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The data processing list: id => Instrument.
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Progress logger.
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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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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 |