SAX2 handler for imzML 1.1.0 files, extending OpenMS MzMLHandler. More...

#include <OpenMS/FORMAT/HANDLERS/ImzMLHandler.h>

Inheritance diagram for ImzMLHandler:

Collaboration diagram for ImzMLHandler:

Classes
struct	ArrayMeta

struct	SpecIMS

Public Member Functions
	ImzMLHandler (PeakMap &exp, const std::string &filename, const ProgressLogger &logger)
	Construct an ImzMLHandler.

	~ImzMLHandler () override
	Closes the .ibd FILE* if open.

	ImzMLHandler (const ImzMLHandler &)=delete

ImzMLHandler &	operator= (const ImzMLHandler &)=delete

void	openIBD (const std::string &ibd_path)
	Open the companion .ibd file for random-access binary reads.

const ImzMLMeta &	getImzMLMeta () const noexcept
	Imaging metadata accumulated during SAX parse (read after parse_() returns).

ImzMLMeta &	getImzMLMeta () noexcept
	Non-const access for ImzMLFile to set the .ibd path before parse.

const std::vector< ImzMLSpectrumIndex > &	getIndex () const noexcept
	Per-spectrum binary index built during parse (one entry per spectrum).

void	connectDecodeConsumer (Interfaces::IMSDataConsumer *downstream, bool append_spectra_to_map, bool decode_ibd=true)
	Wire `ImzMLInterceptConsumer` between MzMLHandler and an optional downstream consumer.

void	startElement (const XMLCh uri, const XMLCh localname, const XMLCh *qname, const xercesc::Attributes &attrs) override

void	endElement (const XMLCh uri, const XMLCh localname, const XMLCh *qname) override

Public Member Functions inherited from MzMLHandler
	MzMLHandler (MapType &exp, const std::string &filename, const std::string &version, const ProgressLogger &logger)
	Constructor for a read-only handler.

	MzMLHandler (const MapType &exp, const std::string &filename, const std::string &version, const ProgressLogger &logger)
	Constructor for a write-only handler.

	~MzMLHandler () override
	Destructor.

void	endElement (const XMLCh const, const XMLCh const, const XMLCh *const qname) override
	Docu in base class XMLHandler::endElement.

void	startElement (const XMLCh const, const XMLCh const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
	Docu in base class XMLHandler::startElelement.

void	characters (const XMLCh *const chars, const XMLSize_t length) override
	Docu in base class XMLHandler::characters.

void	writeTo (std::ostream &os) override
	Docu in base class XMLHandler::writeTo.

void	setOptions (const PeakFileOptions &opt)
	Set the peak file options.

PeakFileOptions &	getOptions ()
	Get the peak file options.

void	getCounts (Size &spectra_counts, Size &chromatogram_counts)
	Get the spectra and chromatogram counts of a file.

void	setMSDataConsumer (Interfaces::IMSDataConsumer *consumer)
	Set the IMSDataConsumer consumer which will consume the read data.

LOADDETAIL	getLoadDetail () const override
	handler which support partial loading, implement this method

void	setLoadDetail (const LOADDETAIL d) override
	handler which support partial loading, implement this method

Public Member Functions inherited from XMLHandler
	XMLHandler (const std::string &filename, const std::string &version)
	Default constructor.

	~XMLHandler () override
	Destructor.

void	reset ()
	Release internal memory used for parsing (call.

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 std::string &msg, UInt line=0, UInt column=0) const
	Fatal error handler. Throws a ParseError exception.

void	error (ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const
	Error handler for recoverable errors.

void	warning (ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const
	Warning handler.

void	characters (const XMLCh *const chars, const XMLSize_t length) override
	Parsing method for character data.

void	startElement (const XMLCh const uri, const XMLCh const localname, const XMLCh *const qname, const xercesc::Attributes &attrs) override
	Parsing method for opening tags.

void	endElement (const XMLCh const uri, const XMLCh const localname, const XMLCh *const qname) override
	Parsing method for closing tags.

DataValue	cvParamToValue (const ControlledVocabulary &cv, const std::string &parent_tag, const std::string &accession, const std::string &name, const std::string &value, const std::string &unit_accession) const
	Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit.

DataValue	cvParamToValue (const ControlledVocabulary &cv, const CVTerm &raw_term) const
	Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit.

void	checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids) const

Private Types
using	CvPair = std::pair< std::string, std::string >

Private Member Functions
void	handleIMSCvParam_ (const std::string &acc, const std::string &val)

void	applyRefGroup_ (const std::string &id)

Private Attributes
FILE *	ibd_ { nullptr }

ImzMLMeta	meta_

bool	in_spectrum_ { false }

bool	in_scan_ { false }

bool	in_bda_ { false }

uint32_t	cur_x_ { 0 }

uint32_t	cur_y_ { 0 }

uint32_t	cur_z_ { 1 }

ArrayMeta	cur_array_

ArrayMeta	cur_mz_meta_

ArrayMeta	cur_int_meta_

std::vector< SpecIMS >	spec_ims_
	IMS state per spectrum (document order)

std::vector< ImzMLSpectrumIndex >	index_
	Full index for OnDiscImzMLExperiment.

std::unordered_map< std::string, std::vector< CvPair > >	ref_groups_

std::string	cur_ref_id_

bool	in_ref_group_ { false }

bool	decode_ibd_ { true }

bool	cur_x_seen_ { false }

bool	cur_y_seen_ { false }

std::unique_ptr< ImzMLInterceptConsumer >	decode_bridge_

Friends
class	ImzMLInterceptConsumer

Additional Inherited Members
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 }

Static Public Member Functions inherited from XMLHandler
static std::string	writeXMLEscape (const std::string &to_escape)
	Escapes a string and returns the escaped string.

static DataValue	fromXSDString (const std::string &type, const std::string &value)
	Convert an XSD type (e.g. 'xsd:double') to a DataValue.

Protected Types inherited from MzMLHandler
typedef MapType::PeakType	PeakType
	Peak type.

typedef MapType::ChromatogramPeakType	ChromatogramPeakType
	Chromatogram peak type.

typedef MSSpectrum	SpectrumType
	Spectrum type.

typedef MSChromatogram	ChromatogramType
	Spectrum type.

typedef MzMLHandlerHelper::BinaryData	BinaryData

Protected Member Functions inherited from MzMLHandler
void	populateSpectraWithData_ ()
	Populate all spectra on the stack with data from input.

void	populateChromatogramsWithData_ ()
	Populate all chromatograms on the stack with data from input.

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.

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.

void	fillChromatogramData_ ()
	Fills the current chromatogram with data points and meta data.

void	handleCVParam_ (const std::string &parent_parent_tag, const std::string &parent_tag, const std::string &accession, const std::string &name, const std::string &value, const std::string &unit_accession="")
	Handles CV terms.

void	handleUserParam_ (const std::string &parent_parent_tag, const std::string &parent_tag, const std::string &name, const std::string &type, const std::string &value, const std::string &unit_accession="")
	Handles user terms.

	MzMLHandler (const std::string &filename, const std::string &version, const ProgressLogger &logger)
	delegated constructor for the two public versions

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.

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.

void	writeChromatogram_ (std::ostream &os, const ChromatogramType &chromatogram, Size chrom_idx, const Internal::MzMLValidator &validator)
	Write out a single chromatogram.

template<typename ContainerT >
void	writeContainerData_ (std::ostream &os, const PeakFileOptions &pf_options_, const ContainerT &container, const std::string &array_type)

template<typename DataType >
void	writeBinaryDataArray_ (std::ostream &os, const PeakFileOptions &options, std::vector< DataType > &data, bool is32bit, std::string array_type)
	Write a single <binaryDataArray> element to the output.

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.

void	writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent, const std::string &path, const Internal::MzMLValidator &validator, const std::set< std::string > &exclude={}) const
	Writes user terms.

void	writeSoftware_ (std::ostream &os, const std::string &id, const Software &software, const Internal::MzMLValidator &validator)
	Helper method that writes a software.

void	writeSourceFile_ (std::ostream &os, const std::string &id, const SourceFile &software, const Internal::MzMLValidator &validator)
	Helper method that writes a source file.

void	writeDataProcessing_ (std::ostream &os, const std::string &id, const std::vector< ConstDataProcessingPtr > &dps, const Internal::MzMLValidator &validator)
	Helper method that writes a data processing list.

void	writePrecursor_ (std::ostream &os, const Precursor &precursor, const Internal::MzMLValidator &validator)
	Helper method that write precursor information from spectra and chromatograms.

void	writeProduct_ (std::ostream &os, const Product &product, const Internal::MzMLValidator &validator)
	Helper method that write precursor information from spectra and chromatograms.

std::string	writeCV_ (const ControlledVocabulary::CVTerm &c, const DataValue &metaValue) const
	Helper method to write an CV based on a meta value.

bool	validateCV_ (const ControlledVocabulary::CVTerm &c, const std::string &path, const Internal::MzMLValidator &validator) const
	Helper method to validate if the given CV is allowed in the current location (path)

ControlledVocabulary::CVTerm	getChildWithName_ (const std::string &parent_accession, const std::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.

Protected Member Functions inherited from XMLHandler
void	writeUserParam_ (const std::string &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
	Writes the content of MetaInfoInterface to the file.

Int	asInt_ (const std::string &in) const
	Conversion of a std::string to an integer value.

Int	asInt_ (const XMLCh *in) const
	Conversion of a Xerces string to an integer value.

UInt	asUInt_ (const std::string &in) const
	Conversion of a std::string to an unsigned integer value.

double	asDouble_ (const std::string &in) const
	Conversion of a std::string to a double value.

float	asFloat_ (const std::string &in) const
	Conversion of a std::string to a float value.

bool	asBool_ (const std::string &in) const
	Conversion of a string to a boolean value.

DateTime	asDateTime_ (std::string date_string) const
	Conversion of a xs:datetime string to a DateTime value.

bool	equal_ (const XMLCh a, const XMLCh b) const
	Returns if two Xerces strings are equal.

SignedSize	cvStringToEnum_ (const Size section, const std::string &term, const char *message, const SignedSize result_on_error=0)

std::string	attributeAsString_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a String.

Int	attributeAsInt_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a Int.

double	attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a double.

DoubleList	attributeAsDoubleList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a DoubleList.

IntList	attributeAsIntList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to an IntList.

StringList	attributeAsStringList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to an StringList.

bool	optionalAttributeAsString_ (std::string &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the String value if the attribute is present.

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.

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.

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.

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.

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.

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.

std::string	attributeAsString_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a String.

Int	attributeAsInt_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a Int.

double	attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a double.

DoubleList	attributeAsDoubleList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a DoubleList.

IntList	attributeAsIntList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a IntList.

StringList	attributeAsStringList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a StringList.

bool	optionalAttributeAsString_ (std::string &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the String value if the attribute is present.

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.

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.

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.

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.

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.

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.

Protected Attributes inherited from MzMLHandler
SpectrumType	spec_
	The current spectrum.

ChromatogramType	chromatogram_
	The current chromatogram.

std::vector< BinaryData >	bin_data_
	The spectrum data (or chromatogram data)

Size	default_array_length_
	The default number of peaks in the current spectrum.

bool	in_spectrum_list_ { false }
	Flag that indicates that we're inside a spectrum (in contrast to a chromatogram)

bool	skip_spectrum_ { false }
	Flag that indicates whether this spectrum should be skipped (e.g. due to options)

bool	skip_chromatogram_ { false }
	Flag that indicates whether this chromatogram should be skipped (e.g. due to options)

bool	rt_set_ { false }
	Remember whether the RT of the spectrum was set or not.

std::string	current_id_
	Id of the current list. Used for referencing param group, source file, sample, software, ...

std::map< std::string, std::vector< SemanticValidator::CVTerm > >	ref_param_
	The referencing param groups: id => array (accession, value)

std::map< std::string, SourceFile >	source_files_
	The source files: id => SourceFile.

std::map< std::string, Sample >	samples_
	The sample list: id => Sample.

std::map< std::string, Software >	software_
	The software list: id => Software.

std::map< std::string, Instrument >	instruments_
	The data processing list: id => Instrument.

std::map< std::pair< std::string, std::string >, bool >	cached_terms_
	CV terms-path-combinations that have been checked in validateCV_()

std::map< std::string, std::vector< DataProcessingPtr > >	processing_
	The data processing list: id => Instrument.

std::string	default_processing_
	id of the default data processing (used when no processing is defined)

UInt	selected_ion_count_ { 0 }
	Count of selected ions.

std::vector< SpectrumData >	spectrum_data_
	Vector of spectrum data stored for later parallel processing.

std::vector< ChromatogramData >	chromatogram_data_
	Vector of chromatogram data stored for later parallel processing.

std::vector< std::pair< std::string, Int64 > >	spectra_offsets_
	Stores binary offsets for each <spectrum> tag.

std::vector< std::pair< std::string, Int64 > >	chromatograms_offsets_
	Stores binary offsets for each <chromatogram> tag.

const ProgressLogger &	logger_
	Progress logger.

Interfaces::IMSDataConsumer *	consumer_ { nullptr }
	Consumer class to work on spectra.

UInt	scan_count_ { 0 }
	number of scans which pass the options-filter

UInt	chromatogram_count_ { 0 }
	number of chromatograms which pass the options-filter

Int	scan_count_total_ { -1 }
	total number of scans in mzML file (according to 'count' attribute)

Int	chrom_count_total_ { -1 }
	total number of chromatograms in mzML file (according to 'count' attribute)

const ControlledVocabulary &	cv_
	Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)

CVMappings	mapping_

MapType *	exp_ { nullptr }
	map pointer for reading

const MapType *	cexp_ { nullptr }
	map pointer for writing

PeakFileOptions	options_
	Options that can be set for loading/storing.

Protected Attributes inherited from XMLHandler
std::string	file_
	File name.

std::string	version_
	Schema version.

StringManager	sm_
	Helper class for string conversion.

std::vector< std::string >	open_tags_
	Stack of open XML tags.

LOADDETAIL	load_detail_
	parse only until total number of scans and chroms have been determined from attributes

std::vector< std::vector< std::string > >	cv_terms_
	Array of CV term lists (one sublist denotes one term and it's children)

Detailed Description

SAX2 handler for imzML 1.1.0 files, extending OpenMS MzMLHandler.

imzML (HUPO-PSI v1.1.0) stores MSI data across two files:

.imzML — mzML 1.1.0 XML with IMS ontology CV extensions
.ibd — raw binary companion (m/z and intensity arrays)

This handler extends MzMLHandler so that all standard mzML metadata (instrument, data processing, scan settings, RT, MS level) is parsed by the base class at no extra cost. Only the ~15 IMS:* CV terms that MzMLHandler does not know are intercepted here.

Delivery timing. MzMLHandler batches spectrum delivery: it calls consumeSpectrum on the registered IMSDataConsumer only after the entire <spectrumList> has been parsed. ImzMLHandler therefore records per-spectrum IMS state in spec_ims_ at endElement("spectrum") and uses a spectrum counter inside ImzMLInterceptConsumer to re-associate each delivered MSSpectrum with the correct IMS entry.

Usage. Do not use this class directly. Use ImzMLFile::load() or OnDiscImzMLExperiment::open() instead.

Inheritance diagram:

xercesc::DefaultHandler
  └─ OpenMS::Internal::XMLHandler
        └─ OpenMS::Internal::MzMLHandler
              └─ OpenMS::Internal::ImzMLHandler  ← this class
                    └─ ImzMLInterceptConsumer : IMSDataConsumer

Class Documentation

◆ OpenMS::Internal::ImzMLHandler::SpecIMS

struct OpenMS::Internal::ImzMLHandler::SpecIMS

Collaboration diagram for ImzMLHandler::SpecIMS:

[legend]

Class Members
ArrayMeta	int_meta
ArrayMeta	mz_meta
uint32_t	x {0}
uint32_t	y {0}
uint32_t	z {1}

Member Typedef Documentation

◆ CvPair

using CvPair = std::pair<std::string, std::string>

private

Constructor & Destructor Documentation

◆ ImzMLHandler() [1/2]

ImzMLHandler	(	PeakMap &	exp,
		const std::string &	filename,
		const ProgressLogger &	logger
	)

Construct an ImzMLHandler.

Parameters

exp	PeakMap that receives `ExperimentalSettings` from MzMLHandler.
filename	Path to the .imzML file (for error messages and Xerces URI).
logger	ProgressLogger inherited from the owning `ImzMLFile`.

◆ ~ImzMLHandler()

~ImzMLHandler ( )

override

Closes the .ibd FILE* if open.

◆ ImzMLHandler() [2/2]

ImzMLHandler ( const ImzMLHandler & )

delete

Member Function Documentation

◆ applyRefGroup_()

void applyRefGroup_ ( const std::string & id )

private

◆ connectDecodeConsumer()

void connectDecodeConsumer	(	Interfaces::IMSDataConsumer *	downstream,
		bool	append_spectra_to_map,
		bool	decode_ibd = `true`
	)

Wire ImzMLInterceptConsumer between MzMLHandler and an optional downstream consumer.

Decodes .ibd peak data when spectra are delivered. When append_spectra_to_map is true, decoded spectra are also appended to the bound PeakMap.

◆ endElement()

void endElement	(	const XMLCh *	uri,
		const XMLCh *	localname,
		const XMLCh *	qname
	)

override

◆ getImzMLMeta() [1/2]

const ImzMLMeta & getImzMLMeta ( ) const

inlinenoexcept

Imaging metadata accumulated during SAX parse (read after parse_() returns).

◆ getImzMLMeta() [2/2]

ImzMLMeta & getImzMLMeta ( )

inlinenoexcept

Non-const access for ImzMLFile to set the .ibd path before parse.

◆ getIndex()

const std::vector< ImzMLSpectrumIndex > & getIndex ( ) const

inlinenoexcept

Per-spectrum binary index built during parse (one entry per spectrum).

◆ handleIMSCvParam_()

void handleIMSCvParam_	(	const std::string &	acc,
		const std::string &	val
	)

private

◆ openIBD()

void openIBD ( const std::string & ibd_path )

Open the companion .ibd file for random-access binary reads.

Must be called before parse_() when peak data is needed. When loading metadata only (no IBD), skip this call.

Parameters

ibd_path Absolute path to the .ibd file.

Exceptions

Exception::FileNotFound if the file cannot be opened.

◆ operator=()

ImzMLHandler & operator= ( const ImzMLHandler & )

delete

◆ startElement()

void startElement	(	const XMLCh *	uri,
		const XMLCh *	localname,
		const XMLCh *	qname,
		const xercesc::Attributes &	attrs
	)

override

Friends And Related Symbol Documentation

◆ ImzMLInterceptConsumer

friend class ImzMLInterceptConsumer

friend

Member Data Documentation

◆ cur_array_

ArrayMeta cur_array_

private

◆ cur_int_meta_

ArrayMeta cur_int_meta_

private

◆ cur_mz_meta_

ArrayMeta cur_mz_meta_

private

◆ cur_ref_id_

std::string cur_ref_id_

private

◆ cur_x_

uint32_t cur_x_ { 0 }

private

◆ cur_x_seen_

bool cur_x_seen_ { false }

private

◆ cur_y_

uint32_t cur_y_ { 0 }

private

◆ cur_y_seen_

bool cur_y_seen_ { false }

private

◆ cur_z_

uint32_t cur_z_ { 1 }

private

◆ decode_bridge_

std::unique_ptr<ImzMLInterceptConsumer> decode_bridge_

private

◆ decode_ibd_

bool decode_ibd_ { true }

private

◆ ibd_

FILE* ibd_ { nullptr }

private

◆ in_bda_

bool in_bda_ { false }

private

◆ in_ref_group_

bool in_ref_group_ { false }

private

◆ in_scan_

bool in_scan_ { false }

private

◆ in_spectrum_

bool in_spectrum_ { false }

private

◆ index_

std::vector<ImzMLSpectrumIndex> index_

private

Full index for OnDiscImzMLExperiment.

◆ meta_

ImzMLMeta meta_

private

◆ ref_groups_

std::unordered_map<std::string, std::vector<CvPair> > ref_groups_

private

◆ spec_ims_

std::vector<SpecIMS> spec_ims_

private

IMS state per spectrum (document order)

Classes

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::Internal::ImzMLHandler::SpecIMS

Member Typedef Documentation

◆ CvPair

Constructor & Destructor Documentation

◆ ImzMLHandler() [1/2]

◆ ~ImzMLHandler()

◆ ImzMLHandler() [2/2]

Member Function Documentation

◆ applyRefGroup_()

◆ connectDecodeConsumer()

◆ endElement()

◆ getImzMLMeta() [1/2]

◆ getImzMLMeta() [2/2]

◆ getIndex()

◆ handleIMSCvParam_()

◆ openIBD()

◆ operator=()

◆ startElement()

Friends And Related Symbol Documentation

◆ ImzMLInterceptConsumer

Member Data Documentation

◆ cur_array_

◆ cur_int_meta_

◆ cur_mz_meta_

◆ cur_ref_id_

◆ cur_x_

◆ cur_x_seen_

◆ cur_y_

◆ cur_y_seen_

◆ cur_z_

◆ decode_bridge_

◆ decode_ibd_

◆ ibd_

◆ in_bda_

◆ in_ref_group_

◆ in_scan_

◆ in_spectrum_

◆ index_

◆ meta_

◆ ref_groups_

◆ spec_ims_