OpenMS  2.5.0
ProteinInference.h
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34 
35 #pragma once
36 
37 #include <OpenMS/KERNEL/Peak2D.h>
38 
39 #include <vector>
40 
41 namespace OpenMS
42 {
43 
44  class PeptideHit;
45  class ConsensusMap;
46 
54  class OPENMS_DLLAPI ProteinInference
55  {
56 
57 public:
58 
60 
63 
66 
68  ProteinInference& operator=(const ProteinInference& rhs);
69 
83  void infer(ConsensusMap& consensus_map, const UInt reference_map);
84 
85 
86 protected:
87 
88  void infer_(ConsensusMap& consensus_map,
89  const size_t protein_idenfication_index,
90  const UInt reference_map);
91 
92  bool sortByUnique_(std::vector<PeptideHit>& peptide_hits_local, const bool is_higher_score_better);
93 
94  }; // !class
95 
96 } // !namespace
97 
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
VersionInfo.h
OpenMS::StopWatch::stop
bool stop()
OpenMS::IdXMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
StopWatch.h
OpenMS::Exception::InvalidSize
Invalid UInt exception.
Definition: Exception.h:303
IDMergerAlgorithm.h
OpenMS::ProteinInference
[experimental class] given a peptide quantitation, infer corresponding protein quantities
Definition: ProteinInference.h:54
OpenMS::String
A more convenient string class.
Definition: String.h:58
IdXMLFile.h
OpenMS::StopWatch::clear
void clear()
OpenMS::IDMergerAlgorithm
Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but...
Definition: IDMergerAlgorithm.h:61
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::BasicProteinInferenceAlgorithm
Algorithm class that implements simple protein inference by aggregation of peptide scores....
Definition: BasicProteinInferenceAlgorithm.h:58
Peak2D.h
OpenMS::StopWatch::reset
void reset()
BasicProteinInferenceAlgorithm.h
IDBoostGraph.h
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::StopWatch::toString
String toString() const
get a compact representation of the current time status.
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::StopWatch
StopWatch Class.
Definition: StopWatch.h:59
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::StopWatch::start
bool start()
OpenMS::BasicProteinInferenceAlgorithm::run
void run(std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids) const
float
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::Internal::IDBoostGraph
Creates and maintains a boost graph based on the OpenMS ID datastructures.
Definition: IDBoostGraph.h:78
OpenMS::Param::insert
void insert(const String &prefix, const Param &param)
OpenMS::ProteinInference::IntensityType
Peak2D::IntensityType IntensityType
Definition: ProteinInference.h:59
TOPPBase.h
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63