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InspectInfile.h
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34 
35 #ifndef OPENMS_FORMAT_INSPECTINFILE_H
36 #define OPENMS_FORMAT_INSPECTINFILE_H
37 
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  Real getMaxPTMsize() const;
123  void setMaxPTMsize(Real maxptmsize);
124 
130  Real getPrecursorMassTolerance() const;
131  void setPrecursorMassTolerance(Real precursor_mass_tolerance);
132 
138  Real getPeakMassTolerance() const;
139  void setPeakMassTolerance(Real 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 Map<String, std::vector<String> > & getModifications() const;
155 
156 private:
157 
159 
161 
163 
165 
167 
170 
172 
174 
176 
179 
181 
183 
184  };
185 
186 } // namespace OpenMS
187 
188 #endif // OPENMS_FORMAT_INSPECTINFILE_H
float Real
Real type.
Definition: Types.h:109
A more convenient string class.
Definition: String.h:56
String db_
Specifies the name of a database (.trie file) to search. The .trie file contains one or more protein ...
Definition: InspectInfile.h:160
String spectra_
Specifies a spectrum file to search.
Definition: InspectInfile.h:158
UInt blind_
Definition: InspectInfile.h:166
Int modifications_per_peptide_
allowed number of modifications per peptide
Definition: InspectInfile.h:164
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
Real 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
Int tag_count_
Number of tags to generate. &lt;0 is not set.
Definition: InspectInfile.h:180
Inspect input file adapter.
Definition: InspectInfile.h:50
Real 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:171
String instrument_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:178
String enzyme_
Specifies the name of a enzyme. &quot;Trypsin&quot;, &quot;None&quot;, and &quot;Chymotrypsin&quot; are the available values...
Definition: InspectInfile.h:162
Real maxptmsize_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:169
UInt multicharge_
Definition: InspectInfile.h:175
int Int
Signed integer type.
Definition: Types.h:100
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:15 using doxygen 1.8.5