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... | |
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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 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, double 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... | |
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bool | equal_ (const XMLCh *a, const XMLCh *b) const |
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... | |
double | attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const |
Converts an attribute to a double. 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_ (double &value, const xercesc::Attributes &a, const char *name) const |
Assigns the attribute content to the double 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... | |
double | attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const |
Converts an attribute to a double. 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_ (double &value, const xercesc::Attributes &a, const XMLCh *name) const |
Assigns the attribute content to the double 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< float > | data_to_encode_ |
floating point numbers which have to be encoded and written More... | |
std::vector< std::vector< float > > | decoded_list_ |
std::vector< std::vector< double > > | decoded_double_list_ |
std::vector< String > | precisions_ |
std::vector< String > | endians_ |
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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... | |
Private Member Functions | |
void | init_ () |
Additional Inherited Members | |
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enum | ActionMode { LOAD, STORE } |
Action to set the current mode (for error messages) More... | |
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static String | writeXMLEscape (const String &to_escape) |
Escapes a string and returns the escaped string. 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.
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protected |
Peak type.
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protected |
Spectrum type.
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inline |
Constructor for a write-only handler.
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inline |
Constructor for a read-only handler.
References MzDataHandler< MapType >::init_().
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inlinevirtual |
Destructor.
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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.
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Parsing method for closing tags.
Reimplemented from XMLHandler.
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fills the current spectrum with peaks and meta data
References Base64::BYTEORDER_BIGENDIAN, Base64::BYTEORDER_LITTLEENDIAN, Peak1D::setIntensity(), and Peak1D::setMZ().
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inlineprivate |
References XMLHandler::cv_terms_, and String::split().
Referenced by MzDataHandler< MapType >::MzDataHandler().
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Sets the options.
References MzDataHandler< MapType >::options_.
Referenced by MzDataFile::load(), and MzDataFile::store().
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Parsing method for opening tags.
Reimplemented from XMLHandler.
References ScanWindow::begin, ScanWindow::end, SpectrumSettings::PEAKS, SpectrumSettings::RAWDATA, and SpectrumSettings::UNKNOWN.
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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, and Base64::encode().
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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_().
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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"/>
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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_().
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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.
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Writing the MetaInfo as UserParam to the file.
References MetaInfoInterface::getKeys(), and MetaInfoInterface::getMetaValue().
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map pointer for writing
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protected |
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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
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protected |
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protected |
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Decoder/Encoder for Base64-data in MzData.
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protected |
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map pointer for reading
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protected |
Progress logger.
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An array of pairs MetaInfodescriptions and their ids.
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Options that can be set for loading/storing.
Referenced by MzDataHandler< MapType >::setOptions().
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The number of peaks in the current spectrum.
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Flag that indicates whether this spectrum should be skipped (due to options)
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The current spectrum.
OpenMS / TOPP release 2.0.0 | Documentation generated on Thu Aug 20 2015 01:44:42 using doxygen 1.8.9.1 |