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

Namespaces
	ClassTest
	Namespace for class tests.

	SqliteHelper

Classes
class	IDBoostGraph
	Creates and maintains a boost graph based on the OpenMS ID datastructures. More...

class	MessagePasserFactory

class	RNPxlFragmentAnnotationHelper
	Convenience functions to construct appealing fragment annotation strings and store them as PeptideHit::PeakAnnotation. More...

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

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

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

struct	ToolDescriptionInternal
	ToolDescription Class. More...

struct	ToolExternalDetails

struct	ToolDescription

class	AcqusHandler
	Read-only acqus File handler for XMass Analysis. 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	FeatureXMLHandler
	This class provides Input/Output functionality for feature maps. More...

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

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

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

class	MzDataHandler

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

class	IdentificationHit
	Represents a object which can store the information of an analysisXML instance. More...

class	SpectrumIdentification

class	Identification

class	MzIdentMLHandler
	XML STREAM handler for MzIdentMLFile. 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
	Sqlite handler for SWATH data sets. More...

class	MzXMLHandler

class	ParamXMLHandler
	XML Handler for Param files. More...

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

class	ToolDescriptionHandler
	XML handler for ToolDescriptionFile. More...

class	TraMLHandler
	XML handler for TraMLFile. More...

class	UnimodXMLHandler
	Handler that is used for parsing XTandemXML data. More...

class	shared_xerces_ptr

class	unique_xerces_ptr

class	StringManager

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

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

class	OMSFileLoad
	Helper class for loading .oms files (SQLite format) More...

class	OMSFileStore
	Helper class for storing .oms files (SQLite format) More...

class	MzDataValidator
	Semantically validates MzXML files. More...

class	MzIdentMLValidator
	Semantically validates MzXML files. More...

class	MzMLValidator
	Semantically validates MzXML files. More...

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

class	TraMLValidator
	Semantically validates MzXML files. More...

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

class	AreaIterator
	Forward iterator for an area of peaks in an experiment. More...

struct	Looper

struct	Looper< grid_size, grid_size, EvalResult, Tuple, TupleTypes... >

struct	Looper< param_index, grid_size, EvalResult, Tuple, FirstTupleType, TupleTypes... >

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

class	OpenMSOSInfo

struct	OpenMSBuildInfo
	Struct with some static methods to get informations on the build configuration. More...

class	FLASHDeconvTabWidget
	A multi-tabbed widget for the FLASHDeconvWizard offering setting of parameters, input-file specification and running FLASHDeconv and more. More...

class	Plot1DPrefDialog
	Preferences dialog for Plot1DWidget. More...

class	Plot2DPrefDialog
	Preferences dialog for Plot2DWidget. More...

class	Plot3DPrefDialog
	Preferences dialog for Plot3DWidget. More...

class	PythonModuleRequirement

class	PythonSelector

class	SwathTabWidget
	A multi-tabbed widget for the SwathWizard offering setting of parameters, input-file specification and running Swath and more. More...

class	TOPPViewPrefDialog
	Preferences dialog for TOPPView. More...

class	WizardGUILock
	RAII class to switch to certain TabWidget, disable the GUI and go back to the orignal Tab when this class is destroyed. More...

struct	Args
	custom arguments to allow for looping calls More...

struct	Command

class	FilterList
	A widget which shows a list of DataFilter items. 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	ListTable

class	ListEditorDelegate
	Internal delegate class. More...

class	FilterableList
	A widget which shows a list of text items, which can be filtered. More...

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

class	ParamEditorDelegate
	Internal delegate class for QTreeWidget. More...

class	ParamTree
	QTreeWidget that emits a signal whenever a new row is selected. More...

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

typedef MSSpectrum	SpectrumType

typedef MSChromatogram	ChromatogramType

typedef std::vector< Args >	ArgLoop

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

enum	OpenMS_Architecture { ARCH_UNKNOWN , ARCH_32BIT , ARCH_64BIT }

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

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

void	raiseDBError_ (const String &error, int line, const char *function, const String &context, const String &query="")
	Raise a more informative database error. More...

bool	execAndReset (SQLite::Statement &query, int expected_modifications)
	Execute and reset an SQL query. More...

void	execWithExceptionAndReset (SQLite::Statement &query, int expected_modifications, int line, const char function, const char context)
	If execAndReset() returns false, call raiseDBError_() More...

String	encodeTab (const String &to_encode)
	Encodes tabs '\t' in the string as and returns the encoded string. 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...

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.

Class Documentation

◆ OpenMS::Internal::ToolExternalDetails

struct OpenMS::Internal::ToolExternalDetails

Collaboration diagram for ToolExternalDetails:

[legend]

Class Members
String	category
String	commandline
Param	param
String	path	filename to external tool
String	text_fail
String	text_finish
String	text_startup
MappingParam	tr_table
String	working_directory	folder where the command will be executed from

◆ 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::Args

struct OpenMS::Internal::Args

custom arguments to allow for looping calls

Collaboration diagram for Args:

[legend]

Class Members
size_t	insert_pos	where to insert in the target argument list (index is 0-based)
QStringList	loop_arg	list of arguments to insert; one for every loop

Typedef Documentation

◆ ArgLoop

typedef std::vector<Args> ArgLoop

◆ 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 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 '\t' in the string as 	 and returns the encoded string.

Parameters

to_encode The String to encode.

Returns: The encoded string.

◆ execAndReset()

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

If execAndReset() returns false, call raiseDBError_()

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

◆ operator==()

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

Referenced by ChromatogramPeak::operator!=(), NASequence::ConstIterator::operator!=(), Interpretation::operator!=(), NASequence::Iterator::operator!=(), MobilityPeak1D::operator!=(), MobilityPeak2D::operator!=(), Mobilogram::operator!=(), MSChromatogram::operator!=(), MSSpectrum::operator!=(), OnDiscMSExperiment::operator!=(), Peak1D::operator!=(), Peak2D::operator!=(), RichPeak2D::operator!=(), and Matrix< Value >::operator==().

◆ raiseDBError_()

void OpenMS::Internal::raiseDBError_	(	const String &	error,
		int	line,
		const char *	function,
		const String &	context,
		const 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

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

Exceptions

Exception::FailedAPICall Throw this exception

Variable Documentation

◆ OpenMS_ArchNames

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

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

◆ OpenMS_locale

const char* OpenMS_locale

extern

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