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