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SequestOutfile.h
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34 
35 #ifndef OPENMS_FORMAT_SEQUESTOUTFILE_H
36 #define OPENMS_FORMAT_SEQUESTOUTFILE_H
37 
41 
42 #include <map>
43 #include <vector>
44 #include <cmath>
45 
46 namespace OpenMS
47 {
48  class ProteinIdentification;
49  class DateTime;
50 
62  class OPENMS_DLLAPI SequestOutfile
63  {
64 public:
67 
69  SequestOutfile(const SequestOutfile & sequest_outfile);
70 
72  virtual ~SequestOutfile();
73 
75  SequestOutfile & operator=(const SequestOutfile & sequest_outfile);
76 
78  bool operator==(const SequestOutfile & sequest_outfile) const;
79 
98  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);
99 
100 // /// retrieve the p-values from the out files
101 // void getPValuesFromOutFiles(vector< pair < String, vector< double > > >& filenames_and_pvalues) throw (Exception::FileNotFound, Exception::ParseError);
102 
104  bool getColumns(const String & line, std::vector<String> & substrings, Size number_of_columns, Size reference_column);
105 
114  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);
115 
118  void getACAndACType(String line, String & accession, String & accession_type);
119 
125  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);
126 
127 private:
128 
129  static double const_weights_[];
130  static double xcorr_weights_[];
131  static double delta_cn_weights_[];
132  static double rank_sp_weights_[];
133  static double delta_mass_weights_[];
134  static Size max_pep_lens_[];
135  static Size num_frags_[];
136  };
137 
138 } //namespace OpenMS
139 
140 #endif // OPENMS_FORMAT_SEQUESTOUTFILE_H
Representation of a protein identification run.
Definition: ProteinIdentification.h:62
A more convenient string class.
Definition: String.h:57
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Representation of a Sequest output file.
Definition: SequestOutfile.h:62
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
DateTime Class.
Definition: DateTime.h:55
int Int
Signed integer type.
Definition: Types.h:103

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:03 using doxygen 1.8.13