OpenMS  2.8.0
PercolatorInfile.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
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34 
35 #pragma once
36 
38 #include <OpenMS/FORMAT/TextFile.h>
39 
40 #include <vector>
41 
42 namespace OpenMS
43 {
44 
49  class OPENMS_DLLAPI PercolatorInfile
50  {
51  public:
52  static void store(const String& pin_file,
53  const std::vector<PeptideIdentification>& peptide_ids,
54  const StringList& feature_set,
55  const std::string& enz,
56  int min_charge,
57  int max_charge);
58 
59  // uses spectrum_reference, if empty uses spectrum_id, if also empty fall back to using index
60  static String getScanIdentifier(const PeptideIdentification& pid, size_t index);
61 
62  protected:
63 
64  //id <tab> label <tab> scannr <tab> calcmass <tab> expmass <tab> feature1 <tab> ... <tab> featureN <tab> peptide <tab> proteinId1 <tab> .. <tab> proteinIdM
66  const std::vector<PeptideIdentification>& peptide_ids,
67  const StringList& feature_set,
68  const std::string& enz,
69  int min_charge,
70  int max_charge);
71 
72 
73  static Int getScanNumber_(const String& scan_identifier);
74 
75  static bool isEnz_(const char& n, const char& c, const std::string& enz);
76 
77  static Size countEnzymatic_(const String& peptide, const std::string& enz);
78 
79  };
80 } // namespace OpenMS
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:65
Class for storing Percolator tab-delimited input files.
Definition: PercolatorInfile.h:50
static String getScanIdentifier(const PeptideIdentification &pid, size_t index)
static TextFile preparePin_(const std::vector< PeptideIdentification > &peptide_ids, const StringList &feature_set, const std::string &enz, int min_charge, int max_charge)
static bool isEnz_(const char &n, const char &c, const std::string &enz)
static Size countEnzymatic_(const String &peptide, const std::string &enz)
static void store(const String &pin_file, const std::vector< PeptideIdentification > &peptide_ids, const StringList &feature_set, const std::string &enz, int min_charge, int max_charge)
static Int getScanNumber_(const String &scan_identifier)
A more convenient string class.
Definition: String.h:60
This class provides some basic file handling methods for text files.
Definition: TextFile.h:47
int Int
Signed integer type.
Definition: Types.h:102
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
const double c
Definition: Constants.h:209
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47