OpenMS::Internal Namespace Reference

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	IntensityIteratorWrapper
	An iterator wrapper to access peak intensities instead of the peak itself. More...
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	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	MzQuantMLHandler
	XML handler for MzQuantMLFile. 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	MzQuantMLValidator
	Semantically validates MzQuantML 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	OpenMSOSInfo
struct	OpenMSBuildInfo
	Struct with some static methods to get informations on the build configuration. 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	SwathGUILock
	RAII class to switch to certain TabWidget, disable the GUI and go back to the orignal Tab when this class is destroyed. More...
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	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

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)
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...
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...
bool	tableExists_ (const String &db_name, const String &table_name)
	Check if a specified database table exists. More...
void	raiseDBError_ (const QSqlError &error, int line, const char *function, const String &context)
	Raise a more informative database error. More...
String	encodeTab (const String &to_encode)
	Encodes tabs '\t' in the string as &#x9; and returns the encoded string. 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.

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Class Documentation

OpenMS::Internal::ToolExternalDetails

struct OpenMS::Internal::ToolExternalDetails

Collaboration diagram for ToolExternalDetails:

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

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 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.

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 Map< Key, T >::equals(), ChromatogramPeak::operator!=(), NASequence::ConstIterator::operator!=(), Interpretation::operator!=(), NASequence::Iterator::operator!=(), MSChromatogram::operator!=(), MSSpectrum::operator!=(), OnDiscMSExperiment::operator!=(), Peak1D::operator!=(), Peak2D::operator!=(), and RichPeak2D::operator!=().

PermutScoreComparator()

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

raiseDBError_()

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

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

Exceptions

Exception::FailedAPICall

Throw this exception

tableExists_()

bool OpenMS::Internal::tableExists_	(	const String &	db_name,
		const String &	table_name
	)

Check if a specified database table exists.

Parameters

db_name	Name of the database (as used by Qt/QSqlDatabase)
table_name	Name of the table to check

Returns

True if table exists, false if not

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().