35 #ifndef OPENMS_FORMAT_INSPECTINFILE_H
36 #define OPENMS_FORMAT_INSPECTINFILE_H
73 void store(
const String & filename);
83 void handlePTMs(
const String & modification_line,
const String & modifications_filename,
const bool monoisotopic);
90 const String & getSpectra()
const;
91 void setSpectra(
const String & spectra);
98 const String & getDb()
const;
99 void setDb(
const String & db);
102 const String & getEnzyme()
const;
103 void setEnzyme(
const String & enzyme);
106 Int getModificationsPerPeptide()
const;
107 void setModificationsPerPeptide(
Int modifications_per_peptide);
114 UInt getBlind()
const;
115 void setBlind(
UInt blind);
122 Real getMaxPTMsize()
const;
123 void setMaxPTMsize(
Real maxptmsize);
130 Real getPrecursorMassTolerance()
const;
131 void setPrecursorMassTolerance(
Real precursor_mass_tolerance);
138 Real getPeakMassTolerance()
const;
139 void setPeakMassTolerance(
Real peak_mass_tolerance);
142 UInt getMulticharge()
const;
143 void setMulticharge(
UInt multicharge);
146 const String & getInstrument()
const;
147 void setInstrument(
const String & instrument);
150 Int getTagCount()
const;
151 void setTagCount(
Int TagCount);
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. <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's flanking mass can differ from the tag'...
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. "Trypsin", "None", and "Chymotrypsin" 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