OpenMS  3.0.0
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 
ConsensusXMLFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
FileHandler.h
VersionInfo.h
OpenMS::ConsensusXMLFile::store
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
OpenMS::Param::setValue
void setValue(const std::string &key, const ParamValue &value, const std::string &description="", const std::vector< std::string > &tags=std::vector< std::string >())
Sets a value.
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.
OpenMS::Param::insert
void insert(const std::string &prefix, const Param &param)
StopWatch.h
IDMergerAlgorithm.h
OpenMS::FileHandler::getTypeByFileName
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
OpenMS::ProteinInference
[experimental class] given a peptide quantitation, infer corresponding protein quantities
Definition: ProteinInference.h:54
OpenMS::FalseDiscoveryRate::applyPickedProteinFDR
void applyPickedProteinFDR(ProteinIdentification &id, String decoy_string="", bool prefix=true, bool groups_too=true)
Applies a picked protein FDR. Behaves like a normal target-decoy FDR where only the score of the best...
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::FileTypes::CONSENSUSXML
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:65
IdXMLFile.h
OpenMS::StopWatch::clear
void clear()
OpenMS::ConsensusMapMergerAlgorithm::mergeAllIDRuns
void mergeAllIDRuns(ConsensusMap &cmap) const
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
ConsensusMapMergerAlgorithm.h
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_LOG_FATAL_ERROR
#define OPENMS_LOG_FATAL_ERROR
Macro to be used if fatal error are reported (processing stops)
Definition: LogStream.h:450
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::BasicProteinInferenceAlgorithm
Algorithm class that implements simple protein inference by aggregation of peptide scores....
Definition: BasicProteinInferenceAlgorithm.h:60
Peak2D.h
OpenMS::ConsensusMapMergerAlgorithm
Merges identification data in ConsensusMaps.
Definition: ConsensusMapMergerAlgorithm.h:63
OpenMS::StopWatch::reset
void reset()
Clear the stop watch but keep running.
OpenMS::ConsensusMap::getProteinIdentifications
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
OpenMS::FalseDiscoveryRate::applyBasic
void applyBasic(const std::vector< ProteinIdentification > &run_info, std::vector< PeptideIdentification > &ids)
simpler reimplementation of the apply function above for PSMs. With charge and identifier info from r...
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::StopWatch::start
void start()
Start the stop watch.
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
BasicProteinInferenceAlgorithm.h
OpenMS::StopWatch::stop
void stop()
Stop the stop watch (can be resumed later). If the stop watch was not running an exception is thrown.
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to 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:82
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::StopWatch
This class is used to determine the current process' CPU (user and/or kernel) and wall time.
Definition: StopWatch.h:65
OpenMS::FalseDiscoveryRate
Calculates false discovery rates (FDR) from identifications.
Definition: FalseDiscoveryRate.h:77
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::BasicProteinInferenceAlgorithm::run
void run(std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids) const
float
OpenMS::FileTypes::nameToType
static Type nameToType(const String &name)
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
FalseDiscoveryRate.h
OpenMS::ProteinInference::IntensityType
Peak2D::IntensityType IntensityType
Definition: ProteinInference.h:59
TOPPBase.h
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:58
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68