OpenMS  3.0.0
PSProteinInference.h
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32 // $Authors: Alexandra Zerck $
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35 
36 #pragma once
37 
40 
41 namespace OpenMS
42 {
43 
47  class OPENMS_DLLAPI PSProteinInference
48  {
49 public:
50 
52 
53  virtual ~PSProteinInference();
54 
55 
56  Size findMinimalProteinList(const std::vector<PeptideIdentification> & peptide_ids);
57 
58  void calculateProteinProbabilities(const std::vector<PeptideIdentification> & ids);
59 
60 // double getProteinProbability(const String& acc,const std::vector<String>& accessions, const std::vector<double>& probabilities);
61 
62  double getProteinProbability(const String & acc);
63 
64  bool isProteinInMinimalList(const String & acc);
65  Int getNumberOfProtIds(double protein_id_threshold);
66  Int getNumberOfProtIdsPeptideRule(Int min_peptides, std::map<String, std::set<String> > & prot_id_counter);
67 
69  {
70  return solver_;
71  }
72 
73 private:
74  std::vector<String> minimal_protein_list_accessions_;
75  std::vector<String> accessions_;
76  std::vector<double> probabilities_;
78  };
79 
80 }
81 
82 
83 
OpenMS::FileTypes::IDXML
OpenMS identification format (.idXML)
Definition: FileTypes.h:64
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::MzIdentMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a MzIdentML file.
FileHandler.h
FileTypes.h
OpenMS::PercolatorFeatureSetHelper::addCONCATSEFeatures
static void addCONCATSEFeatures(std::vector< PeptideIdentification > &peptide_id_list, StringList &search_engines_used, StringList &feature_set)
addCONCATSEFeatures
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::PercolatorFeatureSetHelper::mergeMULTISEProteinIds
static void mergeMULTISEProteinIds(std::vector< ProteinIdentification > &all_protein_ids, std::vector< ProteinIdentification > &new_protein_ids)
mergeMULTISEProteinIds
OpenMS::PercolatorFeatureSetHelper::addMSGFFeatures
static void addMSGFFeatures(std::vector< PeptideIdentification > &peptide_ids, StringList &feature_set)
addMSGFFeatures
OpenMS::Exception::InvalidValue
Invalid value exception.
Definition: Exception.h:327
OpenMS::FileHandler::getTypeByFileName
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IdXMLFile.h
OpenMS::ListUtils::contains
static bool contains(const std::vector< T > &container, const E &elem)
Checks whether the element elem is contained in the given container.
Definition: ListUtils.h:162
OpenMS::PSProteinInference::getSolver
LPWrapper::SOLVER getSolver()
Definition: PSProteinInference.h:68
OpenMS::FileTypes::MZIDENTML
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:75
OpenMS::PercolatorFeatureSetHelper::addMULTISEFeatures
static void addMULTISEFeatures(std::vector< PeptideIdentification > &peptide_ids, StringList &search_engines_used, StringList &feature_set, bool complete_only=true, bool limits_imputation=false)
addMULTISEFeatures
OpenMS::PercolatorFeatureSetHelper::addMASCOTFeatures
static void addMASCOTFeatures(std::vector< PeptideIdentification > &peptide_ids, StringList &feature_set)
addMASCOTFeatures
OpenMS::PercolatorFeatureSetHelper::mergeMULTISEPeptideIds
static void mergeMULTISEPeptideIds(std::vector< PeptideIdentification > &all_peptide_ids, std::vector< PeptideIdentification > &new_peptide_ids, String search_engine)
mergeMULTISEPeptideIds
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:58
OPENMS_LOG_WARN
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
Constants.h
OpenMS::PercolatorFeatureSetHelper::checkExtraFeatures
static void checkExtraFeatures(const std::vector< PeptideHit > &psms, StringList &extra_features)
checkExtraFeatures
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::ListUtils::concatenate
static String concatenate(const std::vector< T > &container, const String &glue="")
Concatenates all elements of the container and puts the glue string between elements.
Definition: ListUtils.h:209
OpenMS::MzIdentMLFile
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::PSProteinInference::solver_
LPWrapper::SOLVER solver_
Definition: PSProteinInference.h:77
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
ProgressLogger.h
OpenMS::ProteinIdentification::SearchParameters::db
String db
The used database.
Definition: ProteinIdentification.h:261
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
OpenMS::PercolatorFeatureSetHelper::concatMULTISEPeptideIds
static void concatMULTISEPeptideIds(std::vector< PeptideIdentification > &all_peptide_ids, std::vector< PeptideIdentification > &new_peptide_ids, String search_engine)
concatMULTISEPeptideIds
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::PSProteinInference::probabilities_
std::vector< double > probabilities_
Definition: PSProteinInference.h:76
OPENMS_LOG_DEBUG
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::PercolatorFeatureSetHelper::addXTANDEMFeatures
static void addXTANDEMFeatures(std::vector< PeptideIdentification > &peptide_ids, StringList &feature_set)
addXTANDEMFeatures
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::PSProteinInference::accessions_
std::vector< String > accessions_
Definition: PSProteinInference.h:75
OpenMS::MzIdentMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::PSProteinInference
This class implements protein inference for the precursor ion selection strategies.
Definition: PSProteinInference.h:47
PercolatorFeatureSetHelper.h
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::FileTypes::nameToType
static Type nameToType(const String &name)
LPWrapper.h
OpenMS::LPWrapper::SOLVER
SOLVER
Definition: LPWrapper.h:130
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
PeptideIdentification.h
OpenMS::PercolatorFeatureSetHelper::addMSFRAGGERFeatures
static void addMSFRAGGERFeatures(StringList &extra_features)
addMSFraggerFeatures
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
MzIdentMLFile.h
OpenMS::PSProteinInference::minimal_protein_list_accessions_
std::vector< String > minimal_protein_list_accessions_
Definition: PSProteinInference.h:74
TOPPBase.h
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::PercolatorFeatureSetHelper::addCOMETFeatures
static void addCOMETFeatures(std::vector< PeptideIdentification > &peptide_ids, StringList &feature_set)
addCOMETFeatures
StringListUtils.h