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OpenMS
2.6.0
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70 BaseException(file, line, function,
"NoSuccessor",
"no successor/predecessor"),
73 what_ =
String(
"there is no successor/predecessor for the given Index: ") + index_.first +
"/" + index_.second;
Base class for TOPP applications.
Definition: TOPPBase.h:144
const ExperimentalSettings & getExperimentalSettings() const
returns the meta information of this experiment (const access)
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
IsotopeCluster::IndexSet IndexSet
A set of peak indices.
Definition: FeatureFinderDefs.h:59
The purpose of this struct is to provide definitions of classes and typedefs which are used throughou...
Definition: FeatureFinderDefs.h:50
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
index set with associated charge estimate
Definition: IsotopeCluster.h:52
Base::iterator Iterator
Definition: FeatureMap.h:143
Param getParameters(const String &algorithm_name) const
Returns the default parameters for the algorithm with name algorithm_name.
std::pair< Size, Size > IndexPair
An index e.g. in an MSExperiment.
Definition: IsotopeCluster.h:47
static String basename(const String &file)
Returns the basename of the file (without the path).
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:59
A D-dimensional half-open interval.
Definition: DRange.h:60
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
static GlobalExceptionHandler & getInstance()
The accessor for the singleton. It also serves as a replacement for the constructor.
Definition: GlobalExceptionHandler.h:88
IndexPair index_
Definition: FeatureFinderDefs.h:82
IsotopeCluster::ChargedIndexSet ChargedIndexSet
Index to peak consisting of two UInts (scan index / peak index) with charge information.
Definition: FeatureFinderDefs.h:56
void setPrimaryMSRunPath(const StringList &s)
set the file path to the primary MS run (usually the mzML file obtained after data conversion from ra...
profile data
Definition: SpectrumSettings.h:74
~NoSuccessor() override
Definition: FeatureFinderDefs.h:77
Size size() const
Definition: MSExperiment.h:127
File adapter for MzQuantML files.
Definition: MzQuantMLFile.h:51
std::set< IndexPair > IndexSet
A set of index pairs, usually referring to an MSExperiment.
Definition: IsotopeCluster.h:49
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
static void setMessage(const std::string &message)
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
SpectrumType
Spectrum peak type.
Definition: SpectrumSettings.h:70
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
The main feature finder class.
Definition: FeatureFinder.h:56
Size setUniqueId()
Assigns a new, valid unique id. Always returns 1.
Definition: UniqueIdInterface.h:146
Exception base class.
Definition: Exception.h:89
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all features (including subordinates)....
Definition: FeatureMap.h:284
IsotopeCluster::IndexPair IndexPair
Index to peak consisting of two UInts (scan index / peak index)
Definition: FeatureFinderDefs.h:53
Stores Citations for individual TOPP tools.
Definition: TOPPBase.h:70
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
NoSuccessor(const char *file, int line, const char *function, const IndexPair &index)
Definition: FeatureFinderDefs.h:69
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
static const String getProductName()
void store(const String &filename, const MSQuantifications &cmsq) const
Stores a map in a MzQuantML file.
A container for features.
Definition: FeatureMap.h:97
Exception that is thrown if a method an invalid IndexPair is given.
Definition: FeatureFinderDefs.h:65
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
Flag
Flags that indicate if a peak is already used in a feature.
Definition: FeatureFinderDefs.h:62
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
Quantitation.
Definition: DataProcessing.h:72
void updateRanges() override
Updates minimum and maximum position/intensity.
Management and storage of parameters / INI files.
Definition: Param.h:73
void setIntensityRange(const DRange< 1 > &range)
restricts the range of intensity values for peaks to load
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
Definition: MSQuantifications.h:52
void run(const String &algorithm_name, PeakMap &input_map, FeatureMap &features, const Param ¶m, const FeatureMap &seeds)
Executes the FeatureFinder using the given algorithm.
File is empty.
Definition: Exception.h:594
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!