XML handler for MzDataFile. More...
#include <OpenMS/FORMAT/HANDLERS/MzDataHandler.h>
 
  
 | 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... | |
| void | writeTo (std::ostream &os) | 
| Writes the contents to a stream.  More... | |
| void | setOptions (const PeakFileOptions &options) | 
| Sets the options.  More... | |
| Constructors and destructor | |
| MzDataHandler (MapType &exp, const String &filename, const String &version, ProgressLogger &logger) | |
| Constructor for a write-only handler.  More... | |
| MzDataHandler (const MapType &exp, const String &filename, const String &version, const ProgressLogger &logger) | |
| Constructor for a read-only handler.  More... | |
| virtual | ~MzDataHandler () | 
| 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 MSSpectrum< PeakType > | SpectrumType | 
| Spectrum type.  More... | |
| Protected Member Functions | |
| void | fillData_ () | 
| fills the current spectrum with peaks and meta data  More... | |
| void | writeBinary_ (std::ostream &os, Size size, const String &tag, const String &name="", SignedSize id=-1) | 
| write binary data to stream (first one)  More... | |
| cvParam and userParam handling methods (for mzData and featureXML) | |
| void | writeCVS_ (std::ostream &os, DoubleReal value, const String &acc, const String &name, UInt indent=4) const | 
| write cvParam containing strings to stream  More... | |
| void | writeCVS_ (std::ostream &os, const String &value, const String &acc, const String &name, UInt indent=4) const | 
| write cvParam containing strings to stream  More... | |
| void | writeCVS_ (std::ostream &os, UInt value, UInt map, const String &acc, const String &name, UInt indent=4) | 
| write cvParam element to stream  More... | |
| void | writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent=4) | 
| Writing the MetaInfo as UserParam to the file.  More... | |
| void | cvParam_ (const String &name, const String &value) | 
| read attributes of MzData's cvParamType  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 MzData.  More... | |
| bool | skip_spectrum_ | 
| Flag that indicates whether this spectrum should be skipped (due to options)  More... | |
| const ProgressLogger & | logger_ | 
| Progress logger.  More... | |
| DataProcessing | data_processing_ | 
| temporary datastructures to hold parsed data | |
| UInt | peak_count_ | 
| The number of peaks in the current spectrum.  More... | |
| SpectrumType | spec_ | 
| The current spectrum.  More... | |
| std::vector< std::pair< String, MetaInfoDescription > > | meta_id_descs_ | 
| An array of pairs MetaInfodescriptions and their ids.  More... | |
| std::vector< String > | data_to_decode_ | 
| encoded data which is read and has to be decoded  More... | |
| std::vector< Real > | data_to_encode_ | 
| floating point numbers which have to be encoded and written  More... | |
| std::vector< std::vector< Real > > | decoded_list_ | 
| std::vector< std::vector < DoubleReal > > | decoded_double_list_ | 
| std::vector< String > | precisions_ | 
| std::vector< String > | endians_ | 
|  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... | |
| Private Member Functions | |
| void | init_ () | 
| 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 MzDataFile.
MapType has to be a MSExperiment or have the same interface. Do not use this class. It is only needed in MzDataFile.
| 
 | protected | 
Peak type.
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 | protected | 
Spectrum type.
| 
 | inline | 
Constructor for a write-only handler.
| 
 | inline | 
Constructor for a read-only handler.
References MzDataHandler< MapType >::init_().
| 
 | inlinevirtual | 
Destructor.
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 | virtual | 
read attributes of MzData's cvParamType
Example: <cvParam cvLabel="psi" accession="PSI:1000001" name="@p name" value="@p value"/> name and sometimes value are defined in the MzData ontology. 
References DataProcessing::CHARGE_DECONVOLUTION, InstrumentSettings::CNG, InstrumentSettings::CNL, InstrumentSettings::CRM, DataProcessing::DEISOTOPING, InstrumentSettings::MASSSPECTRUM, InstrumentSettings::MSNSPECTRUM, IonSource::NEGATIVE, DataProcessing::PEAK_PICKING, IonSource::POSITIVE, InstrumentSettings::PRECURSOR, InstrumentSettings::SIM, and InstrumentSettings::SRM.
| 
 | virtual | 
Parsing method for closing tags.
Reimplemented from XMLHandler.
| 
 | protected | 
fills the current spectrum with peaks and meta data
References Base64::BYTEORDER_BIGENDIAN, and Base64::BYTEORDER_LITTLEENDIAN.
| 
 | inlineprivate | 
References XMLHandler::cv_terms_, and String::split().
Referenced by MzDataHandler< MapType >::MzDataHandler().
| 
 | inline | 
Sets the options.
References MzDataHandler< MapType >::options_.
Referenced by MzDataFile::load(), and MzDataFile::store().
| 
 | virtual | 
Parsing method for opening tags.
Reimplemented from XMLHandler.
References ScanWindow::begin, ScanWindow::end, SpectrumSettings::PEAKS, SpectrumSettings::RAWDATA, and SpectrumSettings::UNKNOWN.
| 
 | inlineprotected | 
write binary data to stream (first one)
The name and id are only used if the tag is supDataArrayBinary or supDataArray. 
References Base64::BYTEORDER_LITTLEENDIAN, MzDataHandler< MapType >::data_to_encode_, MzDataHandler< MapType >::decoder_, and Base64::encode().
| 
 | inlineprotected | 
write cvParam containing strings to stream
value string value acc accession number defined by ontology name term defined by ontology indent number of tabs used in front of tag
Example: <cvParam cvLabel="psi" accession="PSI:@p acc" name="@p name" value="@p value"/>
Referenced by MzDataHandler< MapType >::writeCVS_().
| 
 | inlineprotected | 
write cvParam containing strings to stream
value string value acc accession number defined by ontology name term defined by ontology indent number of tabs used in front of tag
Example: <cvParam cvLabel="psi" accession="PSI:@p acc" name="@p name" value="@p value"/>
| 
 | inlineprotected | 
write cvParam element to stream
os Output stream value enumeration value map index if the terms in cv_terms_ acc accession number defined by ontology name term defined by ontology indent number of tabs used in front of tag
Example: <cvParam cvLabel="psi" accession="PSI:@p acc" name="@p name" value=""/>
References XMLHandler::cv_terms_, XMLHandler::STORE, XMLHandler::warning(), and MzDataHandler< MapType >::writeCVS_().
| 
 | virtual | 
Writes the contents to a stream.
Reimplemented from XMLHandler.
References InstrumentSettings::ABSORBTION, DataProcessing::CHARGE_DECONVOLUTION, InstrumentSettings::CNG, InstrumentSettings::CNL, InstrumentSettings::CRM, DataProcessing::DEISOTOPING, InstrumentSettings::EMC, DateTime::get(), MassAnalyzer::getAccuracy(), SpectrumSettings::getAcquisitionInfo(), Precursor::getActivationEnergy(), Precursor::getActivationMethods(), Precursor::getCharge(), DataProcessing::getCompletionTime(), Sample::getConcentration(), Instrument::getCustomizations(), MassAnalyzer::getFinalMSExponent(), MSSpectrum< PeakT >::getFloatDataArrays(), Acquisition::getIdentifier(), SpectrumSettings::getInstrumentSettings(), Peak1D::getIntensity(), Instrument::getIonDetectors(), Instrument::getIonSources(), MassAnalyzer::getIsolationWidth(), MassAnalyzer::getMagneticFieldStrength(), Sample::getMass(), Instrument::getMassAnalyzers(), AcquisitionInfo::getMethodOfCombination(), Instrument::getModel(), MSSpectrum< PeakT >::getMSLevel(), Peak1D::getMZ(), Software::getName(), Sample::getName(), Instrument::getName(), SpectrumSettings::getNativeID(), Sample::getNumber(), InstrumentSettings::getPolarity(), SpectrumSettings::getPrecursors(), DataProcessing::getProcessingActions(), MassAnalyzer::getReflectronState(), MassAnalyzer::getResolution(), MassAnalyzer::getResolutionMethod(), MassAnalyzer::getResolutionType(), MSSpectrum< PeakT >::getRT(), MassAnalyzer::getScanDirection(), MassAnalyzer::getScanLaw(), InstrumentSettings::getScanMode(), MassAnalyzer::getScanRate(), MassAnalyzer::getScanTime(), InstrumentSettings::getScanWindows(), DataProcessing::getSoftware(), Sample::getState(), MassAnalyzer::getTOFTotalPathLength(), SpectrumSettings::getType(), MassAnalyzer::getType(), Instrument::getVendor(), Software::getVersion(), Sample::getVolume(), InstrumentSettings::getZoomScan(), Map< Key, T >::has(), String::hasPrefix(), MetaInfoInterface::isMetaEmpty(), InstrumentSettings::MASSSPECTRUM, InstrumentSettings::MS1SPECTRUM, InstrumentSettings::MSNSPECTRUM, InstrumentSettings::NamesOfScanMode, IonSource::NEGATIVE, DataProcessing::PEAK_PICKING, SpectrumSettings::PEAKS, IonSource::POSITIVE, InstrumentSettings::PRECURSOR, SpectrumSettings::RAWDATA, InstrumentSettings::SIM, InstrumentSettings::SRM, String::substr(), InstrumentSettings::TDF, String::toInt(), and InstrumentSettings::UNKNOWN.
| 
 | inlineprotected | 
Writing the MetaInfo as UserParam to the file.
References MetaInfoInterface::getKeys(), and MetaInfoInterface::getMetaValue().
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 | protected | 
map pointer for writing
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 | protected | 
| 
 | protected | 
encoded data which is read and has to be decoded
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 | protected | 
floating point numbers which have to be encoded and written
Referenced by MzDataHandler< MapType >::writeBinary_().
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 | protected | 
| 
 | protected | 
| 
 | protected | 
Decoder/Encoder for Base64-data in MzData.
Referenced by MzDataHandler< MapType >::writeBinary_().
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 | protected | 
| 
 | protected | 
map pointer for reading
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 | protected | 
Progress logger.
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 | protected | 
An array of pairs MetaInfodescriptions and their ids.
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 | protected | 
Options that can be set for loading/storing.
Referenced by MzDataHandler< MapType >::setOptions().
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 | protected | 
The number of peaks in the current spectrum.
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 | protected | 
| 
 | protected | 
Flag that indicates whether this spectrum should be skipped (due to options)
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 | 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 |