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OpenMS
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Consumer class that perform no operation. More...
#include <OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h>
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 (const String &filename) | |
| Constructor. More... | |
| ~MSDataWritingConsumer () override | |
| Destructor. More... | |
| void | setExpectedSize (Size expectedSpectra, Size expectedChromatograms) override |
| Set expected size of spectra and chromatograms to be written. 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... | |
| Public Member Functions inherited from MzMLHandler | |
| 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 | getCounts (Size &spectra_counts, Size &chromatogram_counts) |
| Get the spectra and chromatogram counts of a file. More... | |
| void | setMSDataConsumer (Interfaces::IMSDataConsumer *consumer) |
| Set the IMSDataConsumer consumer which will consume the read data. More... | |
| LOADDETAIL | getLoadDetail () const override |
| handler which support partial loading, implement this method More... | |
| void | setLoadDetail (const LOADDETAIL d) override |
| handler which support partial loading, implement this method 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 (const xercesc::SAXParseException &exception) override |
| void | error (const xercesc::SAXParseException &exception) override |
| void | warning (const xercesc::SAXParseException &exception) override |
| 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) const |
| 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... | |
| static DataValue | fromXSDString (const String &type, const String &value) |
| Convert an XSD type (e.g. 'xsd:double') to a DataValue. 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 | |
| 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 &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... | |
| MzMLHandler (const String &filename, const String &version, const ProgressLogger &logger) | |
| delegated constructor for the two public versions 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, const 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 &options, const OpenMS::DataArrays::FloatDataArray &array, const Size spec_chrom_idx, const Size array_idx, bool is_spectrum, 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 | |
| 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) const |
| Conversion of a String to an integer value. More... | |
| Int | asInt_ (const XMLCh *in) const |
| Conversion of a Xerces string to an integer value. More... | |
| UInt | asUInt_ (const String &in) const |
| Conversion of a String to an unsigned integer value. More... | |
| double | asDouble_ (const String &in) const |
| Conversion of a String to a double value. More... | |
| float | asFloat_ (const String &in) const |
| Conversion of a String to a float value. More... | |
| bool | asBool_ (const String &in) const |
| Conversion of a string to a boolean value. More... | |
| DateTime | asDateTime_ (String date_string) const |
| Conversion of a xs:datetime string to a DateTime value. More... | |
| bool | equal_ (const XMLCh *a, const XMLCh *b) const |
| Returns if two Xerces strings are equal. More... | |
| SignedSize | cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0) |
| 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... | |
| 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 | |
| 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... | |
| std::map< String, std::vector< SemanticValidator::CVTerm > > | ref_param_ |
| The referencing param groups: id => array (accession, value) More... | |
| std::map< String, SourceFile > | source_files_ |
| The source files: id => SourceFile. More... | |
| std::map< String, Sample > | samples_ |
| The sample list: id => Sample. More... | |
| std::map< String, Software > | software_ |
| The software list: id => Software. More... | |
| std::map< String, Instrument > | instruments_ |
| The data processing list: id => Instrument. More... | |
| std::map< std::pair< String, String >, bool > | cached_terms_ |
| CV terms-path-combinations that have been checked in validateCV_() More... | |
| std::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... | |
| const ProgressLogger & | logger_ |
| Progress logger. More... | |
| Interfaces::IMSDataConsumer * | consumer_ { nullptr } |
| Consumer class to work on spectra. 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... | |
| const ControlledVocabulary & | cv_ |
| Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) More... | |
| CVMappings | mapping_ |
| 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... | |
| 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... | |
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.
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inlineexplicit |
|
inlineoverridevirtual |
Consume a chromatogram.
The chromatogram will be processed using the processChromatogram_ method of the current implementation and then written to the mzML file.
| c | The chromatogram to be written to mzML |
Reimplemented from MSDataWritingConsumer.
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inlineoverridevirtual |
Consume a spectrum.
The spectrum will be processed using the processSpectrum_ method of the current implementation and then written to the mzML file.
| s | The spectrum to be written to mzML |
Reimplemented from MSDataWritingConsumer.
|
inlineoverrideprivatevirtual |
Cleanup function called by the destructor.
Will write the last tags to the file and close the file stream.
Reimplemented from MSDataWritingConsumer.
|
inlineoverrideprivatevirtual |
Process a chromatogram before storing to disk.
Redefine this function to determine chromatogram processing before writing to disk.
Implements MSDataWritingConsumer.
|
inlineoverrideprivatevirtual |
Process a spectrum before storing to disk.
Redefine this function to determine spectra processing before writing to disk.
Implements MSDataWritingConsumer.
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inlineoverridevirtual |
Set experimental settings for the whole file.
| 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.
1.9.1 
