Consumer class that writes MS data to disk using the mzML format. More...
#include <OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h>
Public Member Functions | |
PlainMSDataWritingConsumer (String filename) | |
Public Member Functions inherited from MSDataWritingConsumer | |
MSDataWritingConsumer (String filename) | |
Constructor. More... | |
virtual | ~MSDataWritingConsumer () |
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... | |
virtual void | setExperimentalSettings (const ExperimentalSettings &exp) |
Set experimental settings for the whole file. More... | |
virtual void | setExpectedSize (Size expectedSpectra, Size expectedChromatograms) |
Set expected size of spectra and chromatograms to be written. More... | |
virtual void | consumeSpectrum (SpectrumType &s) |
Consume a spectrum. More... | |
virtual void | consumeChromatogram (ChromatogramType &c) |
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... | |
void | setMSDataConsumer (Interfaces::IMSDataConsumer *consumer) |
Set the IMSDataConsumer consumer which will consume the read data. More... | |
MzMLHandler (MapType &exp, const String &filename, const String &version, 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... | |
virtual | ~MzMLHandler () |
Destructor. More... | |
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... | |
virtual void | writeTo (std::ostream &os) |
Writes the contents to a stream. More... | |
void | setOptions (const PeakFileOptions &opt) |
Set the peak file options. More... | |
PeakFileOptions & | getOptions () |
Get the peak file options. 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) |
Public Member Functions inherited from IMSDataConsumer | |
virtual | ~IMSDataConsumer () |
Private Member Functions | |
void | processSpectrum_ (MapType::SpectrumType &) |
Process a spectrum before storing to disk. More... | |
void | processChromatogram_ (MapType::ChromatogramType &) |
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... | |
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 | |
void | writeSpectrum_ (std::ostream &os, const SpectrumType &spec, Size s, Internal::MzMLValidator &validator, bool renew_native_ids, std::vector< std::vector< ConstDataProcessingPtr > > &dps) |
void | writeChromatogram_ (std::ostream &os, const ChromatogramType &chromatogram, Size c, Internal::MzMLValidator &validator) |
template<typename ContainerT > | |
void | writeContainerData (std::ostream &os, const PeakFileOptions &pf_options_, const ContainerT &container, String array_type) |
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 |
void | populateSpectraWithData_ (std::vector< MzMLHandlerHelper::BinaryData > &input_data, Size &default_arr_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 &default_arr_length, const PeakFileOptions &peak_file_options, ChromatogramType &inp_chromatogram) |
Fill a single chromatogram with data from input. More... | |
template<typename DataType > | |
void | writeBinaryDataArray (std::ostream &os, const PeakFileOptions &pf_options_, std::vector< DataType > data_to_encode, bool is32bit, String array_type) |
void | writeHeader_ (std::ostream &os, const MapType &exp, std::vector< std::vector< ConstDataProcessingPtr > > &dps, Internal::MzMLValidator &validator) |
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) |
Handles user terms. More... | |
void | writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent, String path, Internal::MzMLValidator &validator) const |
Writes user terms. More... | |
ControlledVocabulary::CVTerm | getChildWithName_ (const String &parent_accession, const String &name) const |
Looks up a child CV term of parent_accession with the name name . If no such term is found, an empty term is returned. More... | |
void | writeSoftware_ (std::ostream &os, const String &id, const Software &software, Internal::MzMLValidator &validator) |
Helper method that writes a software. More... | |
void | writeSourceFile_ (std::ostream &os, const String &id, const SourceFile &software, Internal::MzMLValidator &validator) |
Helper method that writes a source file. More... | |
void | writeDataProcessing_ (std::ostream &os, const String &id, const std::vector< ConstDataProcessingPtr > &dps, Internal::MzMLValidator &validator) |
Helper method that writes a data processing list. More... | |
void | writePrecursor_ (std::ostream &os, const Precursor &precursor, Internal::MzMLValidator &validator) |
Helper method that write precursor information from spectra and chromatograms. More... | |
void | writeProduct_ (std::ostream &os, const Product &product, 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... | |
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... | |
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 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_ |
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 MzML. More... | |
const ProgressLogger & | logger_ |
Progress logger. More... | |
Interfaces::IMSDataConsumer * | consumer_ |
Consumer class to work on spectra. More... | |
UInt | scan_count |
Counting spectra and chromatograms. More... | |
UInt | chromatogram_count |
bool | skip_chromatogram_ |
Flag that indicates whether this spectrum should be skipped (due to options) More... | |
bool | skip_spectrum_ |
bool | rt_set_ |
ControlledVocabulary | cv_ |
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) More... | |
CVMappings | mapping_ |
UInt | selected_ion_count_ |
Count of selected ions. More... | |
SpectrumType | spec_ |
The current spectrum. More... | |
ChromatogramType | chromatogram_ |
The current chromatogram. More... | |
std::vector< BinaryData > | 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_ |
Flag that indicates that we're inside a spectrum (in contrast to a chromatogram) 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... | |
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, long > > | spectra_offsets |
std::vector< std::pair< std::string, long > > | chromatograms_offsets |
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... | |
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.
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inlineexplicit |
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inlineprivatevirtual |
Process a chromatogram before storing to disk.
Redefine this function to determine chromatogram processing before writing to disk.
Implements MSDataWritingConsumer.
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inlineprivatevirtual |
Process a spectrum before storing to disk.
Redefine this function to determine spectra processing before writing to disk.
Implements MSDataWritingConsumer.
OpenMS / TOPP release 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:12 using doxygen 1.8.13 |