| OpenMS 2.5.0

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

Consumer class that writes MS data to disk using the mzML format. More...

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

Inheritance diagram for PlainMSDataWritingConsumer:

## Public Member Functions

| PlainMSDataWritingConsumer (String filename)
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 | setExperimentalSettings (const ExperimentalSettings &exp) override
| Set experimental settings for the whole file. More...
void | setExpectedSize (Size expectedSpectra, Size expectedChromatograms) override
| Set expected size of spectra and chromatograms to be written. More...
void | consumeSpectrum (SpectrumType &s) override
| Consume a spectrum. More...
void | consumeChromatogram (ChromatogramType &c) override
| Consume a chromatogram. 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 | 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 writes MS data to disk using the mzML format.

A very simple implementation of MSDataWritingConsumer, not offering the ability to modify the spectra before writing. This is probably the class you want if you want to write mzML files to disk by providing spectra and chromatograms sequentially.

## Constructor & Destructor Documentation

## ◆ PlainMSDataWritingConsumer()

PlainMSDataWritingConsumer | ( | String | filename | ) |

inline explicit

## Member Function Documentation

## ◆ 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.