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InspectInfile.h
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34 
35 #ifndef OPENMS_FORMAT_INSPECTINFILE_H
36 #define OPENMS_FORMAT_INSPECTINFILE_H
37 
39 
40 #include <map>
41 
42 namespace OpenMS
43 {
51  class OPENMS_DLLAPI InspectInfile
52  {
53 public:
54 
56  InspectInfile();
57 
59  InspectInfile(const InspectInfile& inspect_infile);
60 
62  virtual ~InspectInfile();
63 
65  InspectInfile& operator=(const InspectInfile& inspect_infile);
66 
68  bool operator==(const InspectInfile& inspect_infile) const;
69 
74  void store(const String& filename);
75 
84  void handlePTMs(const String& modification_line, const String& modifications_filename, const bool monoisotopic);
85 
91  const String& getSpectra() const;
92  void setSpectra(const String& spectra);
93 
99  const String& getDb() const;
100  void setDb(const String& db);
101 
103  const String& getEnzyme() const;
104  void setEnzyme(const String& enzyme);
105 
107  Int getModificationsPerPeptide() const;
108  void setModificationsPerPeptide(Int modifications_per_peptide);
109 
115  UInt getBlind() const;
116  void setBlind(UInt blind);
117 
123  float getMaxPTMsize() const;
124  void setMaxPTMsize(float maxptmsize);
125 
131  float getPrecursorMassTolerance() const;
132  void setPrecursorMassTolerance(float precursor_mass_tolerance);
133 
139  float getPeakMassTolerance() const;
140  void setPeakMassTolerance(float peak_mass_tolerance);
141 
143  UInt getMulticharge() const;
144  void setMulticharge(UInt multicharge);
145 
147  const String& getInstrument() const;
148  void setInstrument(const String& instrument);
149 
151  Int getTagCount() const;
152  void setTagCount(Int TagCount);
153 
155  const std::map<String, std::vector<String> >& getModifications() const;
156 
157 private:
158 
160 
162 
164 
166 
168 
170  float maxptmsize_;
171 
173 
175 
177 
180 
182 
183  std::map<String, std::vector<String> > PTMname_residues_mass_type_;
184 
185  };
186 
187 } // namespace OpenMS
188 
189 #endif // OPENMS_FORMAT_INSPECTINFILE_H
A more convenient string class.
Definition: String.h:57
String db_
Specifies the name of a database (.trie file) to search. The .trie file contains one or more protein ...
Definition: InspectInfile.h:161
String spectra_
Specifies a spectrum file to search.
Definition: InspectInfile.h:159
UInt blind_
Definition: InspectInfile.h:167
unsigned int UInt
Unsigned integer type.
Definition: Types.h:95
Int modifications_per_peptide_
allowed number of modifications per peptide
Definition: InspectInfile.h:165
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
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:174
Int tag_count_
Number of tags to generate. <0 is not set.
Definition: InspectInfile.h:181
Inspect input file adapter.
Definition: InspectInfile.h:51
float precursor_mass_tolerance_
Specifies the parent mass tolerance, in Daltons. A candidate&#39;s flanking mass can differ from the tag&#39;...
Definition: InspectInfile.h:172
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:183
String instrument_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:179
String enzyme_
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values...
Definition: InspectInfile.h:163
float maxptmsize_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:170
UInt multicharge_
Definition: InspectInfile.h:176
int Int
Signed integer type.
Definition: Types.h:103

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:01 using doxygen 1.8.13