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 float getMaxPTMsize()
const;
123 void setMaxPTMsize(
float maxptmsize);
130 float getPrecursorMassTolerance()
const;
131 void setPrecursorMassTolerance(
float precursor_mass_tolerance);
138 float getPeakMassTolerance()
const;
139 void setPeakMassTolerance(
float 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);
154 const std::map<String, std::vector<String> >& getModifications()
const;
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:160
String spectra_
Specifies a spectrum file to search.
Definition: InspectInfile.h:158
UInt blind_
Definition: InspectInfile.h:166
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Int modifications_per_peptide_
allowed number of modifications per peptide
Definition: InspectInfile.h:164
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
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
Int tag_count_
Number of tags to generate. <0 is not set.
Definition: InspectInfile.h:180
Inspect input file adapter.
Definition: InspectInfile.h:50
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
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
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
float 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:102