OpenMS  3.0.0
XFDRAlgorithm.h
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32 // $Authors: Lukas Zimmermann, Eugen Netz $
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34 
35 #pragma once
36 
44 
45 namespace OpenMS
46 {
47 
48  //-------------------------------------------------------------
49  // Doxygen docu
50  //-------------------------------------------------------------
51 
65  class OPENMS_DLLAPI XFDRAlgorithm :
66  public DefaultParamHandler, public ProgressLogger
67  {
68 
69  public:
70 
72  enum ExitCodes
73  {
76  UNEXPECTED_RESULT
77  };
78 
80  XFDRAlgorithm();
81 
83  ~XFDRAlgorithm() override;
84 
91  ExitCodes run(std::vector<PeptideIdentification>& peptide_ids, ProteinIdentification& protein_id);
92 
97  ExitCodes validateClassArguments() const;
98 
99 private:
100  void updateMembers_() override;
101 
111  void initDataStructures_(std::vector<PeptideIdentification>& peptide_ids, ProteinIdentification& protein_id);
112 
118  static void assignTypes_(PeptideHit& pep_id, StringList& types);
119 
125  void fdr_xprophet_(std::map< String, Math::Histogram<> >& cum_histograms,
126  const String& targetclass, const String& decoyclass, const String& fulldecoyclass,
127  std::vector< double >& fdr, bool mono) const;
128 
134  static void calc_qfdr_(const std::vector< double >& fdr, std::vector< double >& qfdr);
135 
136  void findTopUniqueHits_(std::vector<PeptideIdentification>& peptide_ids);
137 
138  void writeArgumentsLog_() const;
139 
140  String getId_(const PeptideHit& ph) const;
141 
143  {
144  Size alpha_ions = Size(ph.getMetaValue("matched_linear_alpha")) + Size(ph.getMetaValue("matched_xlink_alpha"));
145  Size beta_ions = Size(ph.getMetaValue("matched_linear_beta")) + Size(ph.getMetaValue("matched_xlink_beta"));
146  return std::min(alpha_ions, beta_ions);
147  }
148 
149  inline static void setIntraProtein_(PeptideHit& ph, const bool value)
150  {
151  ph.setMetaValue("XFDR:is_intraprotein", DataValue(value ? "true" : "false"));
152  }
153 
154  inline static void setInterProtein_(PeptideHit& ph, const bool value)
155  {
156  ph.setMetaValue("XFDR:is_interprotein", DataValue(value ? "true" : "false"));
157  }
158 
162  static bool isSameProtein_(
163  String prot1,
164  String prot2,
165  const String &decoy_string)
166  {
167  prot1.substitute(decoy_string, "");
168  prot2.substitute(decoy_string, "");
169  assert( ! prot1.hasSubstring(decoy_string));
170  assert( ! prot2.hasSubstring(decoy_string));
171  return prot1 == prot2;
172  }
173 
174  // Score range for this of the tool
177 
178  // unique top hits
179  std::vector<String> unique_ids_;
180  std::vector<double> unique_id_scores_;
181 
182  // maps index of peptide id all_pep_ids_ to vector of cross link class
183  std::map<String, std::vector<String>> cross_link_classes_;
184 
185  // Program arguments
194  double arg_binsize_;
195 
196  // Names of the class parameters
198  static const String param_minborder_;
199  static const String param_maxborder_;
200  static const String param_mindeltas_;
202  static const String param_uniquexl_;
203  static const String param_no_qvalues_;
204  static const String param_minscore_;
205  static const String param_binsize_;
206 
207  // Constants related to particular crosslink classes
220  };
221 }
DefaultParamHandler.h
OpenMS::XFDRAlgorithm::param_maxborder_
static const String param_maxborder_
Definition: XFDRAlgorithm.h:199
OpenMS::FileTypes::IDXML
OpenMS identification format (.idXML)
Definition: FileTypes.h:64
OpenMS::XFDRAlgorithm::param_mindeltas_
static const String param_mindeltas_
Definition: XFDRAlgorithm.h:200
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
XMLFile.h
Size
XQuestResultXMLFile.h
XFDRAlgorithm.h
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::XFDRAlgorithm::arg_minscore_
double arg_minscore_
Definition: XFDRAlgorithm.h:191
OpenMS::XFDRAlgorithm::arg_uniquex_
bool arg_uniquex_
Definition: XFDRAlgorithm.h:192
OpenMS::String::substitute
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
OpenMS::XFDRAlgorithm::crosslink_class_intradecoys_
static const String crosslink_class_intradecoys_
Definition: XFDRAlgorithm.h:208
OpenMS::MetaInfoInterface::getMetaValue
const DataValue & getMetaValue(const String &name, const DataValue &default_value=DataValue::EMPTY) const
Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not fo...
OpenMS::XQuestResultXMLFile::load
void load(const String &filename, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids)
Load the content of the xquest.xml file into the provided data structures.
OpenMS::XFDRAlgorithm::crosslink_class_monolinks_
static const String crosslink_class_monolinks_
Definition: XFDRAlgorithm.h:215
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::XFDRAlgorithm::unique_ids_
std::vector< String > unique_ids_
Definition: XFDRAlgorithm.h:179
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::XFDRAlgorithm::param_minborder_
static const String param_minborder_
Definition: XFDRAlgorithm.h:198
OpenMS::XFDRAlgorithm::arg_minborder_
double arg_minborder_
Definition: XFDRAlgorithm.h:188
OpenMS::XFDRAlgorithm::arg_maxborder_
double arg_maxborder_
Definition: XFDRAlgorithm.h:189
OpenMS::XFDRAlgorithm::arg_binsize_
double arg_binsize_
Definition: XFDRAlgorithm.h:194
OpenMS::XFDRAlgorithm::arg_mindeltas_
double arg_mindeltas_
Definition: XFDRAlgorithm.h:187
OpenMS::XFDRAlgorithm::ILLEGAL_PARAMETERS
Definition: XFDRAlgorithm.h:75
OpenMS::FileTypes::MZIDENTML
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:75
OpenMS::XFDRAlgorithm::getMinIonsMatched_
static Size getMinIonsMatched_(const PeptideHit &ph)
Definition: XFDRAlgorithm.h:142
XMLHandler.h
OpenMS::XFDRAlgorithm
Calculates false discovery rate estimates on crosslink identifications.
Definition: XFDRAlgorithm.h:65
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::XFDRAlgorithm::arg_no_qvalues_
bool arg_no_qvalues_
Definition: XFDRAlgorithm.h:193
OpenMS::XFDRAlgorithm::run
ExitCodes run(std::vector< PeptideIdentification > &peptide_ids, ProteinIdentification &protein_id)
Performs the main function of this class, the FDR estimation for cross-linked peptide experiments.
OpenMS::String::hasSubstring
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
OpenMS::XFDRAlgorithm::max_score_
Int max_score_
Definition: XFDRAlgorithm.h:176
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
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::XFDRAlgorithm::ExitCodes
ExitCodes
Exit codes.
Definition: XFDRAlgorithm.h:72
OpenMS::XFDRAlgorithm::min_score_
Int min_score_
Definition: XFDRAlgorithm.h:175
XQuestResultXMLHandler.h
OpenMS::XFDRAlgorithm::param_decoy_string_
static const String param_decoy_string_
Definition: XFDRAlgorithm.h:197
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::Math::Histogram
Representation of a histogram.
Definition: Histogram.h:63
OpenMS::XFDRAlgorithm::validateClassArguments
ExitCodes validateClassArguments() const
Checks whether the parameters of the object are valid.
PeptideHit.h
OpenMS::XQuestResultXMLFile
Used to load and store xQuest result files.
Definition: XQuestResultXMLFile.h:55
OpenMS::XFDRAlgorithm::crosslink_class_decoys_
static const String crosslink_class_decoys_
Definition: XFDRAlgorithm.h:216
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
OpenMS::DataValue
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:58
ProgressLogger.h
OpenMS::XFDRAlgorithm::arg_minionsmatched_
Int arg_minionsmatched_
Definition: XFDRAlgorithm.h:190
OpenMS::XFDRAlgorithm::crosslink_class_hybriddecoysintralinks_
static const String crosslink_class_hybriddecoysintralinks_
Definition: XFDRAlgorithm.h:218
OpenMS::XFDRAlgorithm::crosslink_class_fulldecoysintralinks_
static const String crosslink_class_fulldecoysintralinks_
Definition: XFDRAlgorithm.h:209
OpenMS::XFDRAlgorithm::crosslink_class_interlinks_
static const String crosslink_class_interlinks_
Definition: XFDRAlgorithm.h:214
ProteinIdentification.h
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::FileTypes::XQUESTXML
xQuest XML file format for protein-protein cross-link identifications (.xquest.xml)
Definition: FileTypes.h:110
OpenMS::XFDRAlgorithm::param_minionsmatched_
static const String param_minionsmatched_
Definition: XFDRAlgorithm.h:201
OpenMS::XFDRAlgorithm::unique_id_scores_
std::vector< double > unique_id_scores_
Definition: XFDRAlgorithm.h:180
OpenMS::XFDRAlgorithm::crosslink_class_interdecoys_
static const String crosslink_class_interdecoys_
Definition: XFDRAlgorithm.h:210
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::XFDRAlgorithm::isSameProtein_
static bool isSameProtein_(String prot1, String prot2, const String &decoy_string)
Determines whether the Peptide Evidences belong to the same protein, modulo decoy.
Definition: XFDRAlgorithm.h:162
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::XFDRAlgorithm::crosslink_class_monodecoys_
static const String crosslink_class_monodecoys_
Definition: XFDRAlgorithm.h:212
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to the parameters.
OpenMS::XFDRAlgorithm::EXECUTION_OK
Definition: XFDRAlgorithm.h:74
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::MzIdentMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
OpenMS::XFDRAlgorithm::param_binsize_
static const String param_binsize_
Definition: XFDRAlgorithm.h:205
OpenMS::XFDRAlgorithm::param_minscore_
static const String param_minscore_
Definition: XFDRAlgorithm.h:204
OpenMS::XFDRAlgorithm::setIntraProtein_
static void setIntraProtein_(PeptideHit &ph, const bool value)
Definition: XFDRAlgorithm.h:149
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::XFDRAlgorithm::cross_link_classes_
std::map< String, std::vector< String > > cross_link_classes_
Definition: XFDRAlgorithm.h:183
Histogram.h
OpenMS::Param::update
bool update(const Param &p_outdated, const bool add_unknown=false)
Rescue parameter values from p_outdated to current param.
OpenMS::XFDRAlgorithm::crosslink_class_hybriddecoysinterlinks_
static const String crosslink_class_hybriddecoysinterlinks_
Definition: XFDRAlgorithm.h:219
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::OpenMS_Log_debug
Logger::LogStream OpenMS_Log_debug
Global static instance of a LogStream to capture messages classified as debug output....
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::XFDRAlgorithm::crosslink_class_intralinks_
static const String crosslink_class_intralinks_
Definition: XFDRAlgorithm.h:213
OpenMS::XFDRAlgorithm::param_no_qvalues_
static const String param_no_qvalues_
Definition: XFDRAlgorithm.h:203
OpenMS::XFDRAlgorithm::crosslink_class_fulldecoysinterlinks_
static const String crosslink_class_fulldecoysinterlinks_
Definition: XFDRAlgorithm.h:211
OpenMS::XFDRAlgorithm::setInterProtein_
static void setInterProtein_(PeptideHit &ph, const bool value)
Definition: XFDRAlgorithm.h:154
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::XQuestResultXMLFile::getNumberOfHits
int getNumberOfHits() const
Returns the total number of hits in the file.
OpenMS::FileTypes
Centralizes the file types recognized by FileHandler.
Definition: FileTypes.h:52
OpenMS::XQuestResultXMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a xQuest XML file.
PeptideIdentification.h
StandardTypes.h
OpenMS::XFDRAlgorithm::decoy_string_
String decoy_string_
Definition: XFDRAlgorithm.h:186
MzIdentMLFile.h
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::XFDRAlgorithm::param_uniquexl_
static const String param_uniquexl_
Definition: XFDRAlgorithm.h:202
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::XFDRAlgorithm::crosslink_class_targets_
static const String crosslink_class_targets_
Definition: XFDRAlgorithm.h:217
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55