OpenMS  3.0.0
SequestOutfile.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Martin Langwisch $
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34 
35 #pragma once
36 
40 
41 #include <map>
42 #include <vector>
43 #include <cmath>
44 
45 namespace OpenMS
46 {
47  class ProteinIdentification;
48  class DateTime;
49 
61  class OPENMS_DLLAPI SequestOutfile
62  {
63 public:
66 
68  SequestOutfile(const SequestOutfile & sequest_outfile);
69 
71  virtual ~SequestOutfile();
72 
74  SequestOutfile & operator=(const SequestOutfile & sequest_outfile);
75 
77  bool operator==(const SequestOutfile & sequest_outfile) const;
78 
97  void load(const String & result_filename, std::vector<PeptideIdentification> & peptide_identifications, ProteinIdentification & protein_identification, const double p_value_threshold, std::vector<double> & pvalues, const String & database = "", const bool ignore_proteins_per_peptide = false);
98 
99 // /// retrieve the p-values from the out files
100 // void getPValuesFromOutFiles(vector< pair < String, vector< double > > >& filenames_and_pvalues) throw (Exception::FileNotFound&, Exception::ParseError);
101 
103  bool getColumns(const String & line, std::vector<String> & substrings, Size number_of_columns, Size reference_column);
104 
113  void getSequences(const String & database_filename, const std::map<String, Size> & ac_position_map, std::vector<String> & sequences, std::vector<std::pair<String, Size> > & found, std::map<String, Size> & not_found);
114 
117  void getACAndACType(String line, String & accession, String & accession_type);
118 
124  void readOutHeader(const String & result_filename, DateTime & datetime, double & precursor_mz_value, Int & charge, Size & precursor_mass_type, Size & ion_mass_type, Size & displayed_peptides, String & sequest, String & sequest_version, String & database_type, Int & number_column, Int & rank_sp_column, Int & id_column, Int & mh_column, Int & delta_cn_column, Int & xcorr_column, Int & sp_column, Int & sf_column, Int & ions_column, Int & reference_column, Int & peptide_column, Int & score_column, Size & number_of_columns);
125 
126 private:
127 
128  static double const_weights_[];
129  static double xcorr_weights_[];
130  static double delta_cn_weights_[];
131  static double rank_sp_weights_[];
132  static double delta_mass_weights_[];
133  static Size max_pep_lens_[];
134  static Size num_frags_[];
135  };
136 
137 } //namespace OpenMS
138 
OpenMS::SequestOutfile
Representation of a Sequest output file.
Definition: SequestOutfile.h:61
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
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Exception.h
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
String.h
PeptideIdentification.h
OpenMS::DateTime
DateTime Class.
Definition: DateTime.h:58