| OpenMS 2.5.0

Public Member Functions | Private Member Functions | List of all members
NoopMSDataWritingConsumer Class Reference

Consumer class that perform no operation. More...

`#include <OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h>`

Inheritance diagram for NoopMSDataWritingConsumer:

## Public Member Functions

| NoopMSDataWritingConsumer (String filename)
void | setExperimentalSettings (const ExperimentalSettings &) override
| Set experimental settings for the whole file. More...
void | consumeSpectrum (SpectrumType &) override
| Consume a spectrum. More...
void | consumeChromatogram (ChromatogramType &) override
| Consume a chromatogram. More...
Public Member Functions inherited from MSDataWritingConsumer
| MSDataWritingConsumer (String filename)
| Constructor. More...
| ~MSDataWritingConsumer () override
| Destructor. More...
virtual void | addDataProcessing (DataProcessing d)
| Optionally add a data processing method to each chromatogram and spectrum. More...
virtual Size | getNrSpectraWritten ()
| Return the number of spectra written. More...
virtual Size | getNrChromatogramsWritten ()
| Return the number of chromatograms written. More...
void | setExpectedSize (Size expectedSpectra, Size expectedChromatograms) override
| Set expected size of spectra and chromatograms to be written. More...
Public Member Functions inherited from MzMLHandler
void | getCounts (Size &spectra_counts, Size &chromatogram_counts)
| Get the spectra and chromatogram counts of a file. More...
virtual LOADDETAIL | getLoadDetail () const override
| handler which support partial loading, implement this method More...
virtual void | setLoadDetail (const LOADDETAIL d) override
| handler which support partial loading, implement this method More...
| MzMLHandler (MapType &exp, const String &filename, const String &version, const 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...
| ~MzMLHandler () override
| Destructor. More...
void | endElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
| Docu in base class XMLHandler::endElement. More...
void | startElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
| Docu in base class XMLHandler::startElelement. More...
void | characters (const XMLCh *const chars, const XMLSize_t length) override
| Docu in base class XMLHandler::characters. More...
void | writeTo (std::ostream &os) override
| Docu in base class XMLHandler::writeTo. More...
void | setOptions (const PeakFileOptions &opt)
| Set the peak file options. More...
PeakFileOptions & | getOptions ()
| Get the peak file options. More...
void | setMSDataConsumer (Interfaces::IMSDataConsumer *consumer)
| Set the IMSDataConsumer consumer which will consume the read data. More...
Public Member Functions inherited from XMLHandler
| XMLHandler (const String &filename, const String &version)
| Default constructor. More...
| ~XMLHandler () override
| 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...
void | characters (const XMLCh *const chars, const XMLSize_t length) override
| Parsing method for character data. More...
void | startElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname, const xercesc::Attributes &attrs) override
| Parsing method for opening tags. More...
void | endElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname) override
| Parsing method for closing tags. More...
String | errorString ()
| Returns the last error description. More...
void | checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids)
void | fatalError (const xercesc::SAXParseException &exception) override
void | error (const xercesc::SAXParseException &exception) override
void | warning (const xercesc::SAXParseException &exception) override
Public Member Functions inherited from IMSDataConsumer
virtual | ~IMSDataConsumer ()

## Private Member Functions

void | doCleanup_ () override
| Cleanup function called by the destructor. More...
void | processSpectrum_ (MapType::SpectrumType &) override
| Process a spectrum before storing to disk. More...
void | processChromatogram_ (MapType::ChromatogramType &) override
| Process a chromatogram before storing to disk. More...

## Additional Inherited Members

Public Types inherited from MSDataWritingConsumer
typedef PeakMap | MapType
typedef MapType::SpectrumType | SpectrumType
typedef MapType::ChromatogramType | ChromatogramType
Public Types inherited from XMLHandler
enum | ActionMode { LOAD, STORE }
| Action to set the current mode (for error messages) More...
enum | LOADDETAIL { LD_ALLDATA, LD_RAWCOUNTS, LD_COUNTS_WITHOPTIONS }
Public Types inherited from IMSDataConsumer
typedef MSSpectrum | SpectrumType
typedef MSChromatogram | ChromatogramType
Static Public Member Functions inherited from XMLHandler
static String | writeXMLEscape (const String &to_escape)
| Escapes a string and returns the escaped string. More...
Protected Types inherited from MzMLHandler
typedef MapType::PeakType | PeakType
| Peak type. More...
typedef MapType::ChromatogramPeakType | ChromatogramPeakType
| Chromatogram peak type. More...
typedef MSSpectrum | SpectrumType
| Spectrum type. More...
typedef MSChromatogram | ChromatogramType
| Spectrum type. More...
typedef MzMLHandlerHelper::BinaryData | BinaryData
Protected Member Functions inherited from MzMLHandler
| MzMLHandler (const String &filename, const String &version, const ProgressLogger &logger)
| delegated constructor for the two public versions More...
void | populateSpectraWithData_ ()
| Populate all spectra on the stack with data from input. More...
void | populateChromatogramsWithData_ ()
| Populate all chromatograms on the stack with data from input. More...
void | addSpectrumMetaData_ (const std::vector< MzMLHandlerHelper::BinaryData > &input_data, const Size n, SpectrumType &spectrum) const
| Add extra data arrays to a spectrum. More...
void | populateSpectraWithData_ (std::vector< MzMLHandlerHelper::BinaryData > &input_data, Size &length, const PeakFileOptions &peak_file_options, SpectrumType &spectrum)
| Fill a single spectrum with data from input. More...
void | populateChromatogramsWithData_ (std::vector< MzMLHandlerHelper::BinaryData > &input_data, Size &length, const PeakFileOptions &peak_file_options, ChromatogramType &inp_chromatogram)
| Fill a single chromatogram with data from input. 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, const String &unit_accession="")
| Handles user terms. More...
void | writeHeader_ (std::ostream &os, const MapType &exp, std::vector< std::vector< ConstDataProcessingPtr > > &dps, const Internal::MzMLValidator &validator)
| Write out XML header including (everything up to spectrumList / chromatogramList. More...
void | writeSpectrum_ (std::ostream &os, const SpectrumType &spec, Size spec_idx, const Internal::MzMLValidator &validator, bool renew_native_ids, std::vector< std::vector< ConstDataProcessingPtr > > &dps)
| Write out a single spectrum. More...
void | writeChromatogram_ (std::ostream &os, const ChromatogramType &chromatogram, Size chrom_idx, const Internal::MzMLValidator &validator)
| Write out a single chromatogram. More...
template<typename ContainerT >
void | writeContainerData_ (std::ostream &os, const PeakFileOptions &pf_options_, const ContainerT &container, String array_type)
template<typename DataType >
void | writeBinaryDataArray_ (std::ostream &os, const PeakFileOptions &options, std::vector< DataType > &data, bool is32bit, String array_type)
| Write a single <binaryDataArray> element to the output. More...
void | writeBinaryFloatDataArray_ (std::ostream &os, const PeakFileOptions &pf_options_, const OpenMS::DataArrays::FloatDataArray &array, const Size spec_chrom_idx, const Size array_idx, bool isSpectrum, const Internal::MzMLValidator &validator)
| Write a single <binaryDataArray> element for a float data array to the output. More...
void | writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent, const String &path, const Internal::MzMLValidator &validator, const std::set< String > &exclude={}) const
| Writes user terms. More...
void | writeSoftware_ (std::ostream &os, const String &id, const Software &software, const Internal::MzMLValidator &validator)
| Helper method that writes a software. More...
void | writeSourceFile_ (std::ostream &os, const String &id, const SourceFile &software, const Internal::MzMLValidator &validator)
| Helper method that writes a source file. More...
void | writeDataProcessing_ (std::ostream &os, const String &id, const std::vector< ConstDataProcessingPtr > &dps, const Internal::MzMLValidator &validator)
| Helper method that writes a data processing list. More...
void | writePrecursor_ (std::ostream &os, const Precursor &precursor, const Internal::MzMLValidator &validator)
| Helper method that write precursor information from spectra and chromatograms. More...
void | writeProduct_ (std::ostream &os, const Product &product, const 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...
ControlledVocabulary::CVTerm | getChildWithName_ (const String &parent_accession, const String &name) const
| Helper method to look up a child CV term of `parent_accession` with the name `name`. If no such term is found, an empty term is returned. More...
Protected Member Functions inherited from XMLHandler
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 DateTime value. More...
String | 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...
String | 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 inherited from MSDataWritingConsumer
std::ofstream | ofs_
| File stream (to write mzML) More...
bool | started_writing_
| Stores whether we have already started writing any data. More...
bool | writing_spectra_
| Stores whether we are currently writing spectra. More...
bool | writing_chromatograms_
| Stores whether we are currently writing chromatograms. More...
Size | spectra_written_
| Number of spectra written. More...
Size | chromatograms_written_
| Number of chromatograms written. More...
Size | spectra_expected_
| Number of spectra expected. More...
Size | chromatograms_expected_
| Number of chromatograms expected. More...
bool | add_dataprocessing_
| Whether to add dataprocessing term to the data before writing. More...
Internal::MzMLValidator * | validator_
| Validator that knows about CV terms. More...
ExperimentalSettings | settings_
| Experimental settings to use for the whole file. More...
std::vector< std::vector< ConstDataProcessingPtr > > | dps_
| Vector of data processing objects -> will be filled by writeHeader_. More...
DataProcessingPtr | additional_dataprocessing_
| The dataprocessing to be added to each spectrum/chromatogram. More...
Protected Attributes inherited from MzMLHandler
MapType * | exp_ { nullptr }
| map pointer for reading More...
const MapType * | cexp_ { nullptr }
| map pointer for writing More...
PeakFileOptions | options_
| Options that can be set for loading/storing. More...
const ProgressLogger & | logger_
| Progress logger. More...
Interfaces::IMSDataConsumer * | consumer_ { nullptr }
| Consumer class to work on spectra. More...
ControlledVocabulary | cv_
| Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) More...
CVMappings | mapping_
SpectrumType | spec_
| The current spectrum. More...
ChromatogramType | chromatogram_
| The current chromatogram. More...
std::vector< BinaryData > | bin_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_ { false }
| Flag that indicates that we're inside a spectrum (in contrast to a chromatogram) More...
bool | skip_spectrum_ { false }
| Flag that indicates whether this spectrum should be skipped (e.g. due to options) More...
bool | skip_chromatogram_ { false }
| Flag that indicates whether this chromatogram should be skipped (e.g. due to options) More...
bool | rt_set_ { false }
| Remember whether the RT of the spectrum was set or not. 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< DataProcessingPtr > > | processing_
| The data processing list: id => Instrument. More...
String | default_processing_
| id of the default data processing (used when no processing is defined) More...
UInt | selected_ion_count_ { 0 }
| Count of selected ions. More...
std::vector< SpectrumData > | spectrum_data_
| Vector of spectrum data stored for later parallel processing. More...
std::vector< ChromatogramData > | chromatogram_data_
| Vector of chromatogram data stored for later parallel processing. More...
std::vector< std::pair< std::string, Int64 > > | spectra_offsets_
| Stores binary offsets for each <spectrum> tag. More...
std::vector< std::pair< std::string, Int64 > > | chromatograms_offsets_
| Stores binary offsets for each <chromatogram> tag. More...
UInt | scan_count_ { 0 }
| number of scans which pass the options-filter More...
UInt | chromatogram_count_ { 0 }
| number of chromatograms which pass the options-filter More...
Int | scan_count_total_ { -1 }
| total number of scans in mzML file (according to 'count' attribute) More...
Int | chrom_count_total_ { -1 }
| total number of chromatograms in mzML file (according to 'count' attribute) 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...
LOADDETAIL | load_detail_
| parse only until total number of scans and chroms have been determined from attributes More...
std::vector< std::vector< String > > | cv_terms_
| Array of CV term lists (one sublist denotes one term and it's children) More...

## Detailed Description

Consumer class that perform no operation.

This is sometimes necessary to fulfill the requirement of passing an valid MSDataWritingConsumer object or pointer but no operation is required.

## Constructor & Destructor Documentation

## ◆ NoopMSDataWritingConsumer()

NoopMSDataWritingConsumer | ( | String | filename | ) |

inline explicit

## Member Function Documentation

## ◆ consumeChromatogram()

void consumeChromatogram | ( | ChromatogramType & | c | ) |

inline override virtual

Consume a chromatogram.

The chromatogram will be processed using the processChromatogram_ method of the current implementation and then written to the mzML file.

Parameters

  c | The chromatogram to be written to mzML

Reimplemented from MSDataWritingConsumer.

## ◆ consumeSpectrum()

void consumeSpectrum | ( | SpectrumType & | s | ) |

inline override virtual

Consume a spectrum.

The spectrum will be processed using the processSpectrum_ method of the current implementation and then written to the mzML file.

Parameters

  s | The spectrum to be written to mzML

Reimplemented from MSDataWritingConsumer.

## ◆ doCleanup_()

void doCleanup_ | ( |  | ) |

inline override private virtual

Cleanup function called by the destructor.

Will write the last tags to the file and close the file stream.

Reimplemented from MSDataWritingConsumer.

## ◆ processChromatogram_()

void processChromatogram_ | ( | MapType::ChromatogramType & | c | ) |

inline override private virtual

Process a chromatogram before storing to disk.

Redefine this function to determine chromatogram processing before writing to disk.

Implements MSDataWritingConsumer.

## ◆ processSpectrum_()

void processSpectrum_ | ( | MapType::SpectrumType & | s | ) |

inline override private virtual

Process a spectrum before storing to disk.

Redefine this function to determine spectra processing before writing to disk.

Implements MSDataWritingConsumer.

## ◆ setExperimentalSettings()

void setExperimentalSettings | ( | const ExperimentalSettings & | exp | ) |

inline override virtual

Set experimental settings for the whole file.

Parameters

  exp | Experimental settings to be used for this file (from this and the first spectrum/chromatogram, the class will deduce most of the header of the mzML file)

Reimplemented from MSDataWritingConsumer.