OpenMS  3.0.0
InspectInfile.h
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34 
35 #pragma once
36 
38 
39 #include <map>
40 
41 namespace OpenMS
42 {
50  class OPENMS_DLLAPI InspectInfile
51  {
52 public:
53 
55  InspectInfile();
56 
58  InspectInfile(const InspectInfile& inspect_infile);
59 
61  virtual ~InspectInfile();
62 
64  InspectInfile& operator=(const InspectInfile& inspect_infile);
65 
67  bool operator==(const InspectInfile& inspect_infile) const;
68 
73  void store(const String& filename);
74 
83  void handlePTMs(const String& modification_line, const String& modifications_filename, const bool monoisotopic);
84 
90  const String& getSpectra() const;
91  void setSpectra(const String& spectra);
92 
98  const String& getDb() const;
99  void setDb(const String& db);
100 
102  const String& getEnzyme() const;
103  void setEnzyme(const String& enzyme);
104 
106  Int getModificationsPerPeptide() const;
107  void setModificationsPerPeptide(Int modifications_per_peptide);
108 
114  UInt getBlind() const;
115  void setBlind(UInt blind);
116 
122  float getMaxPTMsize() const;
123  void setMaxPTMsize(float maxptmsize);
124 
130  float getPrecursorMassTolerance() const;
131  void setPrecursorMassTolerance(float precursor_mass_tolerance);
132 
138  float getPeakMassTolerance() const;
139  void setPeakMassTolerance(float peak_mass_tolerance);
140 
142  UInt getMulticharge() const;
143  void setMulticharge(UInt multicharge);
144 
146  const String& getInstrument() const;
147  void setInstrument(const String& instrument);
148 
150  Int getTagCount() const;
151  void setTagCount(Int TagCount);
152 
154  const std::map<String, std::vector<String> >& getModifications() const;
155 
156 private:
157 
159 
161 
163 
165 
167 
169  float maxptmsize_;
170 
172 
174 
176 
179 
181 
182  std::map<String, std::vector<String> > PTMname_residues_mass_type_;
183 
184  };
185 
186 } // namespace OpenMS
187 
OpenMS::InspectInfile::PTMname_residues_mass_type_
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:182
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::InspectInfile::maxptmsize_
float maxptmsize_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:169
OpenMS::InspectInfile::modifications_per_peptide_
Int modifications_per_peptide_
allowed number of modifications per peptide
Definition: InspectInfile.h:164
OpenMS::InspectInfile::blind_
UInt blind_
Definition: InspectInfile.h:166
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::InspectInfile::spectra_
String spectra_
Specifies a spectrum file to search.
Definition: InspectInfile.h:158
OpenMS::InspectInfile::multicharge_
UInt multicharge_
Definition: InspectInfile.h:175
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::InspectInfile::enzyme_
String enzyme_
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
Definition: InspectInfile.h:162
OpenMS::InspectInfile::peak_mass_tolerance_
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:173
OpenMS::InspectInfile::tag_count_
Int tag_count_
Number of tags to generate. <0 is not set.
Definition: InspectInfile.h:180
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::InspectInfile::precursor_mass_tolerance_
float precursor_mass_tolerance_
Specifies the parent mass tolerance, in Daltons. A candidate's flanking mass can differ from the tag'...
Definition: InspectInfile.h:171
String.h
OpenMS::InspectInfile::db_
String db_
Specifies the name of a database (.trie file) to search. The .trie file contains one or more protein ...
Definition: InspectInfile.h:160
OpenMS::InspectInfile::instrument_
String instrument_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:178
OpenMS::InspectInfile
Inspect input file adapter.
Definition: InspectInfile.h:50