OpenMS
InspectInfile.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg $
6 // $Authors: $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
12 
13 #include <map>
14 
15 namespace OpenMS
16 {
24  class OPENMS_DLLAPI InspectInfile
25  {
26 public:
27 
30 
32  InspectInfile(const InspectInfile& inspect_infile);
33 
35  virtual ~InspectInfile();
36 
38  InspectInfile& operator=(const InspectInfile& inspect_infile);
39 
41  bool operator==(const InspectInfile& inspect_infile) const;
42 
47  void store(const String& filename);
48 
57  void handlePTMs(const String& modification_line, const String& modifications_filename, const bool monoisotopic);
58 
64  const String& getSpectra() const;
65  void setSpectra(const String& spectra);
66 
72  const String& getDb() const;
73  void setDb(const String& db);
74 
76  const String& getEnzyme() const;
77  void setEnzyme(const String& enzyme);
78 
81  void setModificationsPerPeptide(Int modifications_per_peptide);
82 
88  UInt getBlind() const;
89  void setBlind(UInt blind);
90 
96  float getMaxPTMsize() const;
97  void setMaxPTMsize(float maxptmsize);
98 
105  void setPrecursorMassTolerance(float precursor_mass_tolerance);
106 
112  float getPeakMassTolerance() const;
113  void setPeakMassTolerance(float peak_mass_tolerance);
114 
117  void setMulticharge(UInt multicharge);
118 
120  const String& getInstrument() const;
121  void setInstrument(const String& instrument);
122 
124  Int getTagCount() const;
125  void setTagCount(Int TagCount);
126 
128  const std::map<String, std::vector<String> >& getModifications() const;
129 
130 private:
131 
133 
135 
137 
139 
142 
143  float maxptmsize_;
144 
146 
148 
151 
153 
155 
156  std::map<String, std::vector<String> > PTMname_residues_mass_type_;
157 
158  };
159 
160 } // namespace OpenMS
161 
Inspect input file adapter.
Definition: InspectInfile.h:25
Int getTagCount() const
Number of tags to generate.
void setBlind(UInt blind)
String instrument_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:152
void handlePTMs(const String &modification_line, const String &modifications_filename, const bool monoisotopic)
void setDb(const String &db)
InspectInfile()
default constructor
Int modifications_per_peptide_
allowed number of modifications per peptide
Definition: InspectInfile.h:138
InspectInfile(const InspectInfile &inspect_infile)
copy constructor
void setPeakMassTolerance(float peak_mass_tolerance)
UInt blind_
Definition: InspectInfile.h:140
UInt getBlind() const
run Inspect in a blind mode
void setMaxPTMsize(float maxptmsize)
const std::map< String, std::vector< String > > & getModifications() const
return the modifications (the modification names map to the affected residues, the mass change and th...
float getPrecursorMassTolerance() const
Specifies the parent mass tolerance, in Daltons.
float getMaxPTMsize() const
the maximum modification size (in Da) to consider in a blind search
float precursor_mass_tolerance_
Specifies the parent mass tolerance, in Daltons. A candidate's flanking mass can differ from the tag'...
Definition: InspectInfile.h:145
String db_
Specifies the name of a database (.trie file) to search. The .trie file contains one or more protein ...
Definition: InspectInfile.h:134
void store(const String &filename)
Int tag_count_
Number of tags to generate. <0 is not set.
Definition: InspectInfile.h:154
void setSpectra(const String &spectra)
String enzyme_
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
Definition: InspectInfile.h:136
float peak_mass_tolerance_
How far b and y peaks can be shifted from their expected masses. Default is 0.5. Higher values produc...
Definition: InspectInfile.h:147
Int getModificationsPerPeptide() const
Number of PTMs permitted in a single peptide.
const String & getInstrument() const
If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent m...
void setEnzyme(const String &enzyme)
float maxptmsize_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:143
InspectInfile & operator=(const InspectInfile &inspect_infile)
assignment operator
const String & getSpectra() const
Specifies a spectrum file to search.
void setMulticharge(UInt multicharge)
void setTagCount(Int TagCount)
UInt multicharge_
Definition: InspectInfile.h:149
const String & getEnzyme() const
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
void setPrecursorMassTolerance(float precursor_mass_tolerance)
UInt getMulticharge() const
If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states i...
std::map< String, std::vector< String > > PTMname_residues_mass_type_
the modification names map to the affected residues, the mass change and the type
Definition: InspectInfile.h:156
virtual ~InspectInfile()
destructor
float getPeakMassTolerance() const
How far b and y peaks can be shifted from their expected masses.
void setModificationsPerPeptide(Int modifications_per_peptide)
bool operator==(const InspectInfile &inspect_infile) const
equality operator
String spectra_
Specifies a spectrum file to search.
Definition: InspectInfile.h:132
void setInstrument(const String &instrument)
const String & getDb() const
Specifies the name of a database (.trie file) to search.
A more convenient string class.
Definition: String.h:34
int Int
Signed integer type.
Definition: Types.h:72
unsigned int UInt
Unsigned integer type.
Definition: Types.h:64
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19