OpenMS::Internal Namespace Reference

Initialization procedures. More...

Namespaces
namespace	ClassTest
	Namespace for class tests.
namespace	PASEFHillCentroider
namespace	SqliteHelper

Classes
class	AcqusHandler
	Read-only acqus File handler for XMass Analysis. More...
class	AreaIterator
	Forward iterator for an area of peaks in an experiment. More...
class	CachedMzMLHandler
	An class that uses on-disk caching to read and write spectra and chromatograms. More...
class	ConsensusXMLHandler
	This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation. More...
class	DIntervalBase
	A base class for D-dimensional interval. More...
class	FeatureXMLHandler
	This class provides Input/Output functionality for feature maps. More...
class	FidHandler
	Read-only fid File handler for XMass Analysis. More...
class	FilterableList
	A widget which shows a list of text items, which can be filtered. More...
class	FilterList
	A widget which shows a list of DataFilter items. More...
struct	FractionGroupAbundanceData
	Parsed parallel arrays carrying protein quantities at (fraction_group, label) grain. More...
class	IDBoostGraph
	Creates and maintains a boost graph based on the OpenMS ID datastructures. More...
class	Identification
class	IdentificationHit
	Represents a object which can store the information of an analysisXML instance. More...
class	ImzMLHandler
	SAX2 handler for imzML 1.1.0 files, extending OpenMS MzMLHandler. More...
class	ImzMLWriter
	Writer for imzML 1.1.0 files (.imzML + companion .ibd). More...
class	IndexedMzMLHandler
	A low-level class to read an indexedmzML file. More...
class	InputFileList
	A widget shows a list of input files (i.e. existing files on a mounted drive), which allows adding/removing files and supports drag'n'drop from the window manager. More...
class	IntensityIteratorWrapper
	An iterator wrapper to access peak intensities instead of the peak itself. More...
class	LinearResampling
	Shared linear resampling implementation without parameter or progress handling. More...
class	ListEditorDelegate
	Internal delegate class. More...
class	ListTable
struct	Looper
struct	Looper< grid_size, grid_size, EvalResult, Tuple, TupleTypes... >
struct	Looper< param_index, grid_size, EvalResult, Tuple, FirstTupleType, TupleTypes... >
class	MascotXMLHandler
	Handler that is used for parsing MascotXML data. More...
class	MessagePasserFactory
class	MzDataHandler
class	MzDataValidator
	Semantic validator for mzData files. More...
class	MzIdentMLDOMHandler
	XML DOM handler for MzIdentMLFile. More...
class	MzIdentMLHandler
	XML STREAM handler for MzIdentMLFile. More...
class	MzIdentMLValidator
	Semantic validator for mzIdentML files. More...
class	MzMLHandler
	Handler for mzML file format. More...
class	MzMLHandlerHelper
	Helper for mzML file format. More...
class	MzMLSqliteHandler
	Sqlite handler for storing spectra and chromatograms in sqMass format. More...
class	MzMLSqliteSwathHandler
	Read-only accessor for SWATH/DIA spectrum indices stored in an sqMass file. More...
class	MzMLValidator
	Semantic validator for mzML files. More...
class	MzXMLHandler
class	OMSFileLoad
	Helper class for loading .oms files (SQLite format) More...
class	OMSFileStore
	Helper class for storing .oms files (SQLite format) More...
struct	OpenMSBuildInfo
	Build-configuration accessors: build type, OpenMP availability, and OpenMP thread count. More...
class	OpenMSLineEdit
	Custom QLineEdit which emits a signal when losing focus (such that we can commit its data) More...
class	OpenMSOSInfo
	Snapshot of the runtime operating system: name, version, and pointer-width architecture. More...
class	ParamEditorDelegate
	Internal delegate class for QTreeWidget. More...
class	ParamTree
	QTreeWidget that emits a signal whenever a new row is selected. More...
class	ParamXMLHandler
	XML Handler for Param files. More...
class	Plot1DPrefDialog
	Preferences dialog for Plot1DWidget. More...
class	Plot2DPrefDialog
	Preferences dialog for Plot2DWidget. More...
class	Plot3DPrefDialog
	Preferences dialog for Plot3DWidget. More...
class	PTMXMLHandler
	Handler that is used for parsing PTMXML data. More...
struct	QuantChannel
	One label of a quantification unit and the sample it resolves to in the design. More...
class	QuantificationUnits
struct	QuantUnit
	One QPX quantification unit: exactly one OpenMS experimental-design fraction group. More...
class	SAX2HandlerAdapter
	Adapts an OpenMS XMLHandler to the Xerces SAX2 DefaultHandler interface. More...
class	ScopedResamplingWarningSuppression
	Internal RAII guard for temporary resampling warning suppression. More...
class	SemanticValidator
	Semantically validates XML files using CVMappings and a ControlledVocabulary. More...
class	shared_xerces_ptr
	Shared-ownership handle for a Xerces object or string, which releases it the way Xerces requires. More...
class	SpectrumIdentification
struct	SqliteConnectorFriend
class	StringManager
	Helper class for XML parsing that handles the conversions of Xerces strings. More...
struct	ThermoPrecursor
	One precursor of an MSn scan as reconstructed by ThermoRawFileMetadata::precursors(). More...
class	ThermoRawFileMetadata
	Resolve the precursor hierarchy from bridge metadata without fetching peaks. Keeps isolation targets distinct from selected ions, and retains SPS selections and supplemental reactions. The filter fallback follows ThermoRawFileParser. More...
class	ThermoRawScanReader
	Scan-by-scan conversion of a Thermo RAW file into OpenMS spectra (private). More...
struct	ThermoReaction
	One reaction (isolation plus activation step) of a Thermo MSn scan event. More...
struct	ThermoScan
	The per-scan metadata needed to reconstruct the precursor hierarchy. More...
struct	ThermoTrailerEntry
	One "trailer extra" label/value pair of a Thermo scan. More...
class	ThermoTrailerIndex
	Per-file trailer label lookup. More...
struct	ToolDescription
struct	ToolDescriptionInternal
	What the TOPP tool registry knows about one tool. More...
class	TOPPViewPrefDialog
	Preferences dialog for TOPPView. More...
class	TraMLHandler
	XML handler for TraMLFile. More...
class	TraMLValidator
	Semantically validates MzXML files. More...
class	UnimodXMLHandler
	Handler that is used for parsing XTandemXML data. More...
class	UniProtXMLHandler
	SAX handler for UniProtKB XML <entry> documents. More...
class	unique_xerces_ptr
class	XMLAttributes
	Xerces-free, lightweight view over the attribute list of an XML element. More...
class	XMLFile
	Base class for loading and storing XML files via Xerces, with optional schema validation and transparent gzip / bzip2 / zip decompression on load. More...
class	XMLHandler
	Base class for XML handlers. More...
class	XQuestResultXMLHandler
	XMLHandler for the result files of XQuest. More...

Concepts
concept	Evaluator

Typedefs
typedef PeakMap	MapType
	XML handler for MzDataFile.
typedef MSSpectrum	SpectrumType
typedef MSChromatogram	ChromatogramType

Enumerations
enum class	OpenMS_OS {   OS_UNKNOWN , OS_MACOS , OS_WINDOWS , OS_LINUX ,   SIZE_OF_OPENMS_OS }
	Operating systems OpenMSOSInfo can report. SIZE_OF_OPENMS_OS is a sentinel for array sizing. More...
enum class	OpenMS_Architecture { ARCH_UNKNOWN , ARCH_32BIT , ARCH_64BIT , SIZE_OF_OPENMS_ARCHITECTURE }
	Pointer-width architectures OpenMSOSInfo can report. SIZE_OF_OPENMS_ARCHITECTURE is a sentinel for array sizing. More...

Functions
bool	operator== (const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
void	xercesInitialize ()
	Calls xercesc::XMLPlatformUtils::Initialize() under a process-wide lock.
void	xercesTerminate ()
	Calls xercesc::XMLPlatformUtils::Terminate() under the lock of xercesInitialize()
template<UInt D>
std::ostream &	operator<< (std::ostream &os, const DIntervalBase< D > &rhs)
	Print the contents to a stream.
void	raiseDBError_ (const std::string &error, int line, const char *function, const std::string &context, const std::string &query="")
	Raise a more informative database error.
bool	execAndReset (SQLite::Statement &query, int expected_modifications)
	Execute and reset an SQL query.
void	execWithExceptionAndReset (SQLite::Statement &query, int expected_modifications, int line, const char *function, const char *context)
	If execAndReset() returns false, call raiseDBError_()
const ProteinIdentification::ProteinGroup::FloatDataArray *	sampleAbundances (const ProteinIdentification::ProteinGroup &group)
FractionGroupAbundanceData	fractionGroupAbundances (const ProteinIdentification::ProteinGroup &group)
	Read PeptideAndProteinQuant's named unit-level arrays and validate their parallel-key contract.
std::string	validateQuantificationAnnotations (const ProteinIdentification::ProteinGroup::FloatDataArray *sample_abundances, const FractionGroupAbundanceData &quantities, Size design_samples, const QuantificationUnits &units, const std::set< std::pair< UInt, UInt > > &expected_quantity_keys)
	Validate one protein group's complete QPX 1.1 quantification annotation contract.
std::string	encodeTab (const std::string &to_encode)
	Encodes tabs '\t' in the string as &#x9; and returns the encoded string.
template<typename GetSpectrum >
IonImage	extractIonImage (const MSImagingGeometry &geom, double mz, double tolerance_ppm, const std::vector< Size > &pixel_indices, Size n_spectra, GetSpectrum &&get_spectrum)
	Build an IonImage by summing peak intensities in an m/z window over a pixel subset.
template<typename IteratorT >
IntensityIteratorWrapper< IteratorT >	intensityIteratorWrapper (const IteratorT &rhs)
	make-function so that we need no write out all those type names to get the wrapped iterator.
std::string	getOSVersionString_ ()
	Return the running OS version using a platform-specific probe.

Variables
const std::string	OpenMS_OSNames [] = {"unknown", "MacOS", "Windows", "Linux"}
	String labels paired with OpenMS_OS; index by static_cast<size_t>(enum_value).
const std::string	OpenMS_ArchNames [] = {"unknown", "32 bit", "64 bit"}
	String labels paired with OpenMS_Architecture; index by static_cast<size_t>(enum_value).

Detailed Description

Initialization procedures.

Namespace used to hide implementation details from users.

Part of the library needs to be initialized to be used properly, these procedures need to be run at startup (and preferably only once).

---

Class Documentation

OpenMS::Internal::FractionGroupAbundanceData

struct OpenMS::Internal::FractionGroupAbundanceData

Parsed parallel arrays carrying protein quantities at (fraction_group, label) grain.

Class Members
string	error
bool	present = false
bool	valid = true
map< pair< UInt, UInt >, float >	values

OpenMS::Internal::Looper

struct OpenMS::Internal::Looper

template<size_t param_index, size_t grid_size, typename EvalResult, typename Tuple, typename... TupleTypes>
struct OpenMS::Internal::Looper< param_index, grid_size, EvalResult, Tuple, TupleTypes >

OpenMS::Internal::QuantChannel

struct OpenMS::Internal::QuantChannel

One label of a quantification unit and the sample it resolves to in the design.

Class Members
unsigned	label = 1	design label / channel number, 1-based
string	qpx_label	QPX intensity label ("LFQ", "TMT126", ...)
Size	sample = 0	design sample, retained to validate consistent run/sample resolution

OpenMS::Internal::QuantUnit

struct OpenMS::Internal::QuantUnit

One QPX quantification unit: exactly one OpenMS experimental-design fraction group.

Class Members
vector< QuantChannel >	channels	one per label the unit's runs carry
UInt	fraction_group = 0	OpenMS fraction_group defining this unit.
vector< string >	runs	QPX run names, in fraction order.

OpenMS::Internal::ThermoPrecursor

struct OpenMS::Internal::ThermoPrecursor

One precursor of an MSn scan as reconstructed by ThermoRawFileMetadata::precursors().

Class Members
ThermoReaction	activation	primary reaction
optional< int >	charge	unset if unknown or not positive
bool	estimate_intensity = true	false for additional SPS selections
double	lower_offset = 0.0	width / 2 - isolation offset (0 if the width is unknown)
int	parent_scan = 0	scan this precursor was isolated from (0 if unknown)
double	selected_mz = 0.0	monoisotopic m/z when plausible, otherwise the target
string	spectrum_ref	native ID of the parent scan ("" if unknown)
optional< ThermoReaction >	supplemental	supplemental activation (e.g. the HCD step of EThcD)
double	target_mz = 0.0	isolation window target m/z
double	upper_offset = 0.0	width / 2 + isolation offset
optional< double >	width	isolation width; unset if unknown or negative

OpenMS::Internal::ThermoReaction

struct OpenMS::Internal::ThermoReaction

One reaction (isolation plus activation step) of a Thermo MSn scan event.

Class Members
string	activation	vendor activation type name, e.g. "HigherEnergyCollisionalDissociation"
optional< double >	collision_energy	vendor value; meaningful only if collision_energy_valid
bool	collision_energy_valid = false	vendor flag for collision_energy
optional< double >	isolation_offset	isolation window offset from the target (Th)
optional< double >	isolation_width	isolation window width (Th)
optional< double >	precursor_mass	isolation target m/z

OpenMS::Internal::ThermoScan

struct OpenMS::Internal::ThermoScan

The per-scan metadata needed to reconstruct the precursor hierarchy.

Class Members
string	filter	scan filter string, e.g. "FTMS + c NSI Full ms2 500.00@hcd30.00 [100-1000]"
int	ms_level = 0	MS order (1 for full scans)
string	native_id	e.g. "controllerType=0 controllerNumber=1 scan=12"
vector< ThermoReaction >	reactions	reactions in acquisition order (MS2 first)
int	scan_number = 0	1-based scan number within the controller
vector< ThermoTrailerEntry >	trailer	trailer-extra entries in file order

OpenMS::Internal::ThermoTrailerEntry

struct OpenMS::Internal::ThermoTrailerEntry

One "trailer extra" label/value pair of a Thermo scan.

Class Members
string	label	e.g. "Monoisotopic M/Z:"
string	value	as reported by the instrument, numbers included

Typedef Documentation

ChromatogramType

typedef MSChromatogram ChromatogramType

MapType

typedef PeakMap MapType

XML handler for MzDataFile.

XML handlers for MzXMLFile.

MapType has to be a MSExperiment or have the same interface. Do not use this class. It is only needed in MzDataFile.

Improvement:

Add implementation and tests of 'supDataArray' to store IntegerDataArray and StringDataArray of MSSpectrum (Hiwi)

MapType has to be a MSExperiment or have the same interface.
Do not use this class. It is only needed in MzXMLFile.

SpectrumType

typedef MSSpectrum SpectrumType

Enumeration Type Documentation

OpenMS_Architecture

enum class OpenMS_Architecture

strong

Pointer-width architectures OpenMSOSInfo can report. SIZE_OF_OPENMS_ARCHITECTURE is a sentinel for array sizing.

Enumerator
ARCH_UNKNOWN
ARCH_32BIT
ARCH_64BIT
SIZE_OF_OPENMS_ARCHITECTURE

OpenMS_OS

enum class OpenMS_OS

strong

Operating systems OpenMSOSInfo can report. SIZE_OF_OPENMS_OS is a sentinel for array sizing.

Enumerator
OS_UNKNOWN
OS_MACOS
OS_WINDOWS
OS_LINUX
SIZE_OF_OPENMS_OS

Function Documentation

encodeTab()

std::string encodeTab

(

const std::string &

to_encode

)

Encodes tabs '\t' in the string as &#x9; and returns the encoded string.

Parameters

[in]

to_encode

The std::string to encode.

Returns

The encoded string.

execAndReset()

bool execAndReset	(	SQLite::Statement &	query,
		int	expected_modifications
	)

Execute and reset an SQL query.

Returns

Whether the number of modifications made by the query matches the expected number

execWithExceptionAndReset()

void execWithExceptionAndReset	(	SQLite::Statement &	query,
		int	expected_modifications,
		int	line,
		const char *	function,
		const char *	context
	)

If execAndReset() returns false, call raiseDBError_()

extractIonImage()

template<typename GetSpectrum >

IonImage extractIonImage	(	const MSImagingGeometry &	geom,
		double	mz,
		double	tolerance_ppm,
		const std::vector< Size > &	pixel_indices,
		Size	n_spectra,
		GetSpectrum &&	get_spectrum
	)

Build an IonImage by summing peak intensities in an m/z window over a pixel subset.

A single extraction kernel shared by MSImagingExperiment and OnDiscImzMLExperiment. The only substantive difference between the two callers is how a spectrum is obtained:

// In-memory (no copy): lambda must declare an explicit return type to avoid
// the silent decay-to-value footgun:
[this](Size i) -> const MSSpectrum& { return experiment_[i]; }
 
// On-disc (value, function-lifetime-extended):
[this](Size i) -> MSSpectrum { return pimpl_->decodeSpectrum(i); }

The const auto& binding inside the loop does the right thing for both cases: it binds the reference directly (no copy, in-memory) or lifetime-extends the temporary for the duration of the loop body (on-disc). A std::function<const MSSpectrum&(Size)> would not work for the on-disc case — it would dangle on the decoded value.

Note

The in-memory lambda must carry an explicit -> const MSSpectrum& return type. An unannotated auto-returning lambda decays to a by-value return and silently reintroduces a copy on the hot in-memory path.

Template Parameters

GetSpectrum

Callable with signature returning MSSpectrum (by value, on-disc) or const MSSpectrum& (by reference, in-memory). The deduced return category determines the binding in const auto& spec.

Parameters

[in]	geom	Imaging pixel grid (dimensions + pixel list).
[in]	mz	m/z center of the extraction window (>= 0).
[in]	tolerance_ppm	Half-window in ppm (>= 0).
[in]	pixel_indices	Indices into geom.getPixels() to process (all pixels or a region subset).
[in]	n_spectra	Total number of spectra in the source (used for bounds checking per pixel).
[in]	get_spectrum	Callable(spectrum_index) -> spectrum.

Returns

Ion image with the same dimensions as geom.

Exceptions

Exception::InvalidValue

if mz or tolerance_ppm is negative or non-finite, or if a pixel references an out-of-range spectrum_index.

References MSImagingGeometry::getHeight(), MSImagingGeometry::getPixels(), MSImagingGeometry::getWidth(), IonImage::setIntensity(), IonImage::setMzRange(), OpenMS::Math::sum(), and OpenMS::StringUtils::toStr().

fractionGroupAbundances()

FractionGroupAbundanceData fractionGroupAbundances ( const ProteinIdentification::ProteinGroup &  group )

inline

Read PeptideAndProteinQuant's named unit-level arrays and validate their parallel-key contract.

References FractionGroupAbundanceData::error, ProteinIdentification::ProteinGroup::getFloatDataArrays(), ProteinIdentification::ProteinGroup::getIntegerDataArrays(), FractionGroupAbundanceData::present, FractionGroupAbundanceData::valid, and FractionGroupAbundanceData::values.

getOSVersionString_()

std::string getOSVersionString_ ( )

inline

Return the running OS version using a platform-specific probe.

Windows uses RtlGetVersion from ntdll.dll to bypass the compatibility shim and return the real version as "MAJOR.MINOR.BUILD". macOS uses sysctlbyname("kern.osproductversion", ...). Linux (and other __unix__) parses /etc/os-release and returns the VERSION_ID value with surrounding quotes stripped.

Returns "unknown" if the platform query fails or the platform is unsupported.

References OpenMS::StringUtils::substr().

Referenced by OpenMSOSInfo::getOSInfo().

intensityIteratorWrapper()

template<typename IteratorT >

IntensityIteratorWrapper< IteratorT > intensityIteratorWrapper

(

const IteratorT &

rhs

)

make-function so that we need no write out all those type names to get the wrapped iterator.

operator<<()

template<UInt D>

std::ostream & operator<<	(	std::ostream &	os,
		const DIntervalBase< D > &	rhs
	)

Print the contents to a stream.

References DIntervalBase< D >::maxPosition(), and DIntervalBase< D >::minPosition().

operator==()

bool operator==	(	const IDBoostGraph::ProteinGroup &	lhs,
		const IDBoostGraph::ProteinGroup &	rhs
	)

Referenced by ChromatogramPeak::operator!=(), NASequence::ConstIterator::operator!=(), Interpretation::operator!=(), NASequence::Iterator::operator!=(), MobilityPeak2D::operator!=(), Mobilogram::operator!=(), MSChromatogram::operator!=(), MSSpectrum::operator!=(), OnDiscMSExperiment::operator!=(), Peak1D::operator!=(), Peak2D::operator!=(), and RichPeak2D::operator!=().

raiseDBError_()

void raiseDBError_	(	const std::string &	error,
		int	line,
		const char *	function,
		const std::string &	context,
		const std::string &	query = ""
	)

Raise a more informative database error.

Add context to an SQL error encountered by Qt and throw it as a FailedAPICall exception.

Parameters

[in]	error	The error that occurred
[in]	line	Line in the code where error occurred
[in]	function	Name of the function where error occurred
[in]	context	Context for the error
[in]	query	Text of the query that was executed (optional)

Exceptions

Exception::FailedAPICall

Throw this exception

sampleAbundances()

const ProteinIdentification::ProteinGroup::FloatDataArray * sampleAbundances ( const ProteinIdentification::ProteinGroup &  group )

inline

The group's sample-level abundance array, or nullptr when it carries no quantification.

Looked up by NAME rather than by index: PeptideAndProteinQuant names it "abundances" (PeptideAndProteinQuant.cpp) and the positional convention – four float arrays in a fixed order – is an implementation detail of that one writer.

References ProteinIdentification::ProteinGroup::getFloatDataArrays().

validateQuantificationAnnotations()

std::string validateQuantificationAnnotations ( const ProteinIdentification::ProteinGroup::FloatDataArray *  sample_abundances, const FractionGroupAbundanceData &  quantities, Size  design_samples, const QuantificationUnits &  units, const std::set< std::pair< UInt, UInt > > &  expected_quantity_keys  )

inline

Validate one protein group's complete QPX 1.1 quantification annotation contract.

Parameters

[in]	sample_abundances	Optional legacy sample-level abundance array
[in]	quantities	Parsed fraction-group/label abundance arrays
[in]	design_samples	Number of samples in the experimental design
[in]	units	Quantification units derived from the design and ConsensusMap headers
[in]	expected_quantity_keys	Fraction-group/label keys required by units

Returns

An empty string when exportable, otherwise a diagnostic describing the first violation

References QuantificationUnits::empty(), FractionGroupAbundanceData::error, FractionGroupAbundanceData::present, FractionGroupAbundanceData::valid, and FractionGroupAbundanceData::values.

xercesInitialize()

void xercesInitialize

(

)

Calls xercesc::XMLPlatformUtils::Initialize() under a process-wide lock.

Xerces counts its initialisations in a plain integer and requires callers to serialise Initialize() and Terminate() (its threading FAQ). OpenMS initialises Xerces once when the library is loaded; every parser calls this again before parsing, also from several threads at once (e.g. the chunks of a parallel mzML read), so the calls are serialised here. Throws xercesc::XMLException as Initialize() does.

xercesTerminate()

void xercesTerminate

(

)

Calls xercesc::XMLPlatformUtils::Terminate() under the lock of xercesInitialize()

Variable Documentation

OpenMS_ArchNames

const std::string OpenMS_ArchNames[] = {"unknown", "32 bit", "64 bit"}

inline

String labels paired with OpenMS_Architecture; index by static_cast<size_t>(enum_value).

Referenced by OpenMSOSInfo::getArchAsString(), and OpenMSOSInfo::getBinaryArchitecture().

OpenMS_OSNames

const std::string OpenMS_OSNames[] = {"unknown", "MacOS", "Windows", "Linux"}

inline

String labels paired with OpenMS_OS; index by static_cast<size_t>(enum_value).

Referenced by OpenMSOSInfo::getOSAsString().