OpenMS
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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"} |
Namespace used to hide implementation details from users.
struct OpenMS::Internal::ToolExternalDetails |
Class Members | ||
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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 |
struct OpenMS::Internal::Looper |
struct OpenMS::Internal::Args |
custom arguments to allow for looping calls
Class Members | ||
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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 MSChromatogram ChromatogramType |
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.
MapType has to be a MSExperiment or have the same interface. Do not use this class. It is only needed in MzXMLFile.
typedef MSSpectrum SpectrumType |
enum OpenMS_Architecture |
enum OpenMS_OS |
Encodes tabs '\t' in the string as 	 and returns the encoded string.
to_encode | The String to encode. |
bool OpenMS::Internal::execAndReset | ( | SQLite::Statement & | query, |
int | expected_modifications | ||
) |
Execute and reset an SQL query.
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<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().
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().
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==().
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.
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) |
Exception::FailedAPICall | Throw this exception |
std::string OpenMS_ArchNames[] = {"unknown", "32 bit", "64 bit"} |
Referenced by OpenMSOSInfo::getArchAsString(), and OpenMSOSInfo::getBinaryArchitecture().
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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!)
std::string OpenMS_OSNames[] = {"unknown", "MacOS", "Windows", "Linux"} |
Referenced by OpenMSOSInfo::getOSAsString().