Namespace used to hide implementation details from users. More...

Namespaces
	ClassTest
	Namespace for class tests.

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	DIntervalBase
	A base class for D-dimensional interval. More...

class	FidHandler
	Read-only fid File handler for XMass Analysis. More...

struct	FileMapping
	Maps input/output files to filenames for the external program. More...

class	IndexedMzMLHandler
	A low-level class to read an indexedmzML file. More...

class	IntensityIteratorWrapper
	An iterator wrapper to access peak intensities instead of the peak itself. More...

class	ListEditorDelegate
	Internal delegate class. More...

class	ListTable

struct	MappingParam
	Filename mappings for all input/output files. More...

class	MascotXMLHandler
	Handler that is used for parsing MascotXML data. More...

class	MzDataHandler

class	MzDataValidator
	Semantically validates MzXML files. More...

class	MzIdentMLDOMHandler
	XML DOM handler for MzIdentMLFile. More...

class	MzIdentMLHandler
	XML STREAM handler for MzIdentMLFile. More...

class	MzIdentMLValidator
	Semantically validates MzXML files. More...

class	MzMLHandler

class	MzMLHandlerHelper

class	MzMLSqliteHandler
	Sqlite handler for storing spectra and chromatograms in sqMass format. More...

class	MzMLSqliteSwathHandler
	Sqlite handler for SWATH data sets. More...

class	MzMLValidator
	Semantically validates MzXML files. More...

class	MzQuantMLHandler
	XML handler for MzQuantMLFile. More...

class	MzQuantMLValidator
	Semantically validates MzQuantML files. More...

class	MzXMLHandler

class	OpenMSLineEdit
	Custom QLineEdit which emits a signal when losing focus (such that we can commit its data) More...

struct	OpenMSOSInfo

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	PTMXMLHandler
	Handler that is used for parsing PTMXML data. More...

class	RNPxlFragmentAnnotationHelper

class	SemanticValidator
	Semantically validates XML files using CVMappings and a ControlledVocabulary. More...

class	Spectrum1DPrefDialog
	Preferences dialog for Spectrum1DWidget. More...

class	Spectrum2DPrefDialog
	Preferences dialog for Spectrum2DWidget. More...

class	Spectrum3DPrefDialog
	Preferences dialog for Spectrum3DWidget. More...

class	StringManager

struct	ToolDescription

class	ToolDescriptionHandler
	XML handler for ToolDescriptionFile. More...

struct	ToolDescriptionInternal
	ToolDescription Class. More...

struct	ToolExternalDetails

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	XMLFile
	Base class for loading/storing XML files that have a handler derived from XMLHandler. More...

class	XMLHandler
	Base class for XML handlers. More...

class	XQuestResultXMLHandler
	XMLHandler for the result files of XQuest. More...

Typedefs
typedef PeakMap	MapType
	XML handler for MzDataFile. More...

typedef MSSpectrum	SpectrumType

typedef MSChromatogram	ChromatogramType

Enumerations
enum	OpenMS_OS { OS_UNKNOWN, OS_MACOS, OS_WINDOWS, OS_LINUX }

enum	OpenMS_Architecture { ARCH_UNKNOWN, ARCH_32BIT, ARCH_64BIT }

Functions
bool	PermutScoreComparator (const CompNovoIdentificationBase::Permut &p1, const CompNovoIdentificationBase::Permut &p2)

template<UInt D>
std::ostream &	operator<< (std::ostream &os, const DIntervalBase< D > &rhs)
	Print the contents to a stream. More...

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. More...

String	encodeTab (const String &to_encode)
	Encodes tabs '' in the string as and returns the encoded string. More...

static OpenMSOSInfo	getOSInfo ()

OpenMS_Architecture	getBinaryArchitecture ()

Variables
const char *	OpenMS_locale

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

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

Detailed Description

Namespace used to hide implementation details from users.

Typedef Documentation

◆ ChromatogramType

typedef MSChromatogram ChromatogramType

◆ MapType

typedef PeakMap MapType

XML handler for MzDataFile.

XML handlers for MzXMLFile.

XML handler for MzMLFile.

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 an MSExperiment or have the same interface. In read-mode, this class will parse an MzML XML file and append the input spectra to the provided MapType object or (if provided separately through setMSDataConsumer) to the provided IMSDataConsumer Interface.

Note: Do not use this class. It is only needed in MzMLFile.; Only upon destruction of this class it can be guaranteed that all data has been appended to the appropriate consumer of the data. Do not try to access the data before that.

Todo:: replace hardcoded cv stuff with more flexible handling via obo r/w.

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 OpenMS_Architecture

Enumerator
ARCH_UNKNOWN
ARCH_32BIT
ARCH_64BIT

◆ OpenMS_OS

enum OpenMS_OS

Enumerator
OS_UNKNOWN
OS_MACOS
OS_WINDOWS
OS_LINUX

Function Documentation

◆ encodeTab()

String OpenMS::Internal::encodeTab ( const String & to_encode )

Encodes tabs '' in the string as 	 and returns the encoded string.

Parameters

to_encode The String to encode.

Returns: The encoded string.

◆ getBinaryArchitecture()

OpenMS_Architecture OpenMS::Internal::getBinaryArchitecture ( )

References ARCH_32BIT, ARCH_64BIT, and ARCH_UNKNOWN.

◆ getOSInfo()

static OpenMSOSInfo OpenMS::Internal::getOSInfo ( )

static

References OpenMSOSInfo::arch, ARCH_32BIT, ARCH_64BIT, OpenMSOSInfo::os, OS_LINUX, OS_MACOS, OpenMSOSInfo::os_version, and OS_WINDOWS.

◆ intensityIteratorWrapper()

IntensityIteratorWrapper<IteratorT> OpenMS::Internal::intensityIteratorWrapper ( const IteratorT & rhs )

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

Referenced by MorphologicalFilter::filter().

◆ operator<<()

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

Print the contents to a stream.

References DIntervalBase< D >::minPosition().

◆ PermutScoreComparator()

bool OpenMS::Internal::PermutScoreComparator	(	const CompNovoIdentificationBase::Permut &	p1,
		const CompNovoIdentificationBase::Permut &	p2
	)

Variable Documentation

◆ OpenMS_ArchNames

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

Referenced by OpenMSOSInfo::getArchAsString().

◆ OpenMS_locale

const char* OpenMS_locale

Used to set the locale to "C", to avoid problems on machines with incompatible locale settings (this overwrites the locale setting of the environment!)

◆ OpenMS_OSNames

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

Referenced by OpenMSOSInfo::getOSAsString().

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables