OpenMS
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  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< ArgsArgLoop
 

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...
 
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...
 
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 &#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.


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::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

◆ 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

Enumeration Type Documentation

◆ 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 &#x9; and returns the encoded string.

Parameters
to_encodeThe 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==()

◆ 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
errorThe error that occurred
lineLine in the code where error occurred
functionName of the function where error occurred
contextContext for the error
queryText of the query that was executed (optional)
Exceptions
Exception::FailedAPICallThrow this exception

Variable Documentation

◆ OpenMS_ArchNames

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

◆ 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"}