OpenMS  3.0.0
FeatureFinderDefs.h
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34 
35 #pragma once
36 
37 
42 
43 namespace OpenMS
44 {
45 
46  // forward declaration
47  class FeatureFinder;
48 
50  struct OPENMS_DLLAPI FeatureFinderDefs
51  {
54 
57 
60 
62  enum Flag {UNUSED, USED};
63 
65  class OPENMS_DLLAPI NoSuccessor :
67  {
68 public:
69  NoSuccessor(const char * file, int line, const char * function, const IndexPair & index) :
70  BaseException(file, line, function, "NoSuccessor", String("there is no successor/predecessor for the given Index: ") + String(index.first) + "/" + String(index.second)),
71  index_(index)
72  {
74  }
75 
76  ~NoSuccessor() noexcept override = default;
77 
78 protected:
79  IndexPair index_; // index without successor/predecessor
80  };
81  };
82 }
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::MSExperiment::getExperimentalSettings
const ExperimentalSettings & getExperimentalSettings() const
returns the meta information of this experiment (const access)
Size
OpenMS::FeatureFinderDefs::IndexSet
IsotopeCluster::IndexSet IndexSet
A set of peak indices.
Definition: FeatureFinderDefs.h:59
OpenMS::FeatureFinderDefs
The purpose of this struct is to provide definitions of classes and typedefs which are used throughou...
Definition: FeatureFinderDefs.h:50
OpenMS::Exception::IllegalArgument
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
OpenMS::IsotopeCluster::ChargedIndexSet
index set with associated charge estimate
Definition: IsotopeCluster.h:52
OpenMS::FeatureFinder::getParameters
Param getParameters(const String &algorithm_name) const
Returns the default parameters for the algorithm with name algorithm_name.
OpenMS::IsotopeCluster::IndexPair
std::pair< Size, Size > IndexPair
An index e.g. in an MSExperiment.
Definition: IsotopeCluster.h:47
OpenMS::File::basename
static String basename(const String &file)
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::DRange
A D-dimensional half-open interval.
Definition: DRange.h:60
OpenMS::String::trim
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
FeatureXMLFile.h
OpenMS::FeatureFinderDefs::ChargedIndexSet
IsotopeCluster::ChargedIndexSet ChargedIndexSet
Index to peak consisting of two UInts (scan index / peak index) with charge information.
Definition: FeatureFinderDefs.h:56
FeatureFinderAlgorithmPicked.h
OpenMS::FeatureMap::setPrimaryMSRunPath
void setPrimaryMSRunPath(const StringList &s)
set the file path to the primary MS run (usually the mzML file obtained after data conversion from ra...
OpenMS::SpectrumSettings::PROFILE
profile data
Definition: SpectrumSettings.h:74
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:120
OpenMS::MzQuantMLFile
File adapter for MzQuantML files.
Definition: MzQuantMLFile.h:51
FeatureFinder.h
OpenMS::IsotopeCluster::IndexSet
std::set< IndexPair > IndexSet
A set of index pairs, usually referring to an MSExperiment.
Definition: IsotopeCluster.h:49
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Exception::GlobalExceptionHandler::setMessage
static void setMessage(const std::string &message)
Exception.h
OpenMS::MzMLFile::load
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...
OpenMS::SpectrumSettings::SpectrumType
SpectrumType
Spectrum peak type.
Definition: SpectrumSettings.h:70
MSQuantifications.h
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
RangeUtils.h
OpenMS::FeatureFinder
The main feature finder class.
Definition: FeatureFinder.h:56
OpenMS::UniqueIdInterface::setUniqueId
Size setUniqueId()
Assigns a new, valid unique id. Always returns 1.
OpenMS::Exception::BaseException
Exception base class.
Definition: Exception.h:89
OpenMS::FeatureMap::applyMemberFunction
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all features (including subordinates)....
Definition: FeatureMap.h:289
OpenMS::FeatureFinderDefs::IndexPair
IsotopeCluster::IndexPair IndexPair
Index to peak consisting of two UInts (scan index / peak index)
Definition: FeatureFinderDefs.h:53
OpenMS::Citation
Stores Citations for individual TOPP tools.
Definition: TOPPBase.h:73
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::FeatureFinderDefs::NoSuccessor::NoSuccessor
NoSuccessor(const char *file, int line, const char *function, const IndexPair &index)
Definition: FeatureFinderDefs.h:69
OpenMS::MSQuantifications::assignUIDs
void assignUIDs()
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::FeatureFinderAlgorithmPicked::getProductName
static const String getProductName()
OpenMS::MzQuantMLFile::store
void store(const String &filename, const MSQuantifications &cmsq) const
Stores a map in a MzQuantML file.
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::FeatureFinderDefs::NoSuccessor
Exception that is thrown if a method an invalid IndexPair is given.
Definition: FeatureFinderDefs.h:65
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::MSExperiment::getSpectra
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
OpenMS::FeatureFinderDefs::Flag
Flag
Flags that indicate if a peak is already used in a feature.
Definition: FeatureFinderDefs.h:62
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::DataProcessing::QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
MzQuantMLFile.h
String.h
OpenMS::MSExperiment::updateRanges
void updateRanges() override
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::PeakFileOptions::setIntensityRange
void setIntensityRange(const DRange< 1 > &range)
restricts the range of intensity values for peaks to load
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::PeakFileOptions::setMSLevels
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
OpenMS::MSQuantifications
Definition: MSQuantifications.h:52
OpenMS::FeatureFinder::run
void run(const String &algorithm_name, PeakMap &input_map, FeatureMap &features, const Param &param, const FeatureMap &seeds)
Executes the FeatureFinder using the given algorithm.
OpenMS::Exception::FileEmpty
File is empty.
Definition: Exception.h:594
IsotopeCluster.h
StandardTypes.h
GlobalExceptionHandler.h
File.h
OpenMS::MzMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h