35 #ifndef OPENMS_FORMAT_XTANDEMINFILE_H 
   36 #define OPENMS_FORMAT_XTANDEMINFILE_H 
   90     void setFragmentMassTolerance(
double tolerance);
 
   93     double getFragmentMassTolerance() 
const;
 
   96     void setPrecursorMassTolerancePlus(
double tol);
 
   99     double getPrecursorMassTolerancePlus() 
const;
 
  102     void setPrecursorMassToleranceMinus(
double tol);
 
  105     double getPrecursorMassToleranceMinus() 
const;
 
  108     void setPrecursorErrorType(MassType mono_isotopic);
 
  111     MassType getPrecursorErrorType() 
const;
 
  114     void setFragmentMassErrorUnit(ErrorUnit unit);
 
  117     ErrorUnit getFragmentMassErrorUnit() 
const;
 
  120     void setPrecursorMassErrorUnit(ErrorUnit unit);
 
  123     ErrorUnit getPrecursorMassErrorUnit() 
const;
 
  126     void setNumberOfThreads(
UInt threads);
 
  129     UInt getNumberOfThreads() 
const;
 
  138     void setOutputFilename(
const String& output);
 
  141     const String& getOutputFilename() 
const;
 
  144     void setInputFilename(
const String& input_file);
 
  147     const String& getInputFilename() 
const;
 
  150     void setTaxonomyFilename(
const String& filename);
 
  153     const String& getTaxonomyFilename() 
const;
 
  156     void setDefaultParametersFilename(
const String& filename);
 
  159     const String& getDefaultParametersFilename() 
const;
 
  162     void setTaxon(
const String& taxon);
 
  165     const String& getTaxon() 
const;
 
  168     void setMaxPrecursorCharge(
Int max_charge);
 
  171     Int getMaxPrecursorCharge() 
const;
 
  174     void setNumberOfMissedCleavages(
UInt missed_cleavages);
 
  177     UInt getNumberOfMissedCleavages() 
const;
 
  180     void setMaxValidEValue(
double value);
 
  183     double getMaxValidEValue() 
const;
 
  186     bool isRefining() 
const;
 
  189     void setSemiCleavage(
const bool semi_cleavage);
 
  192     void setRefine(
const bool refine);
 
  200     void write(
const String& filename);
 
  209     void load(
const String& filename);
 
  217     void writeTo_(std::ostream& os);
 
  219     void writeNote_(std::ostream& os, 
const String& type, 
const String& label, 
const String& value);
 
  221     void writeNote_(std::ostream& os, 
const String& type, 
const String& label, 
const char* value);
 
  223     void writeNote_(std::ostream& os, 
const String& type, 
const String& label, 
bool value);
 
  231     String convertModificationSet_(
const std::set<ModificationDefinition>& mods) 
const;
 
  289     std::vector<Internal::XTandemInfileNote> 
notes_;
 
  294 #endif // OPENMS_FORMAT_XTANDEMINFILE_H 
MassType fragment_mass_type_
Definition: XTandemInfile.h:245
A more convenient string class. 
Definition: String.h:56
UInt max_precursor_charge_
Definition: XTandemInfile.h:247
XTandem input file. 
Definition: XTandemInfile.h:52
ErrorUnit
error unit, either Da or ppm 
Definition: XTandemInfile.h:58
UInt batch_size_
Definition: XTandemInfile.h:255
ErrorUnit precursor_mass_error_unit_
Definition: XTandemInfile.h:241
String default_parameters_file_
Definition: XTandemInfile.h:280
UInt number_of_threads_
Definition: XTandemInfile.h:253
ErrorUnit fragment_mass_error_unit_
Definition: XTandemInfile.h:243
MassType
Mass type of the precursor, either monoisotopic or average. 
Definition: XTandemInfile.h:65
String input_filename_
Definition: XTandemInfile.h:259
MassType precursor_mass_type_
Definition: XTandemInfile.h:239
String taxonomy_file_
Definition: XTandemInfile.h:263
Representation of a set of modification definitions. 
Definition: ModificationDefinitionsSet.h:57
UInt number_of_missed_cleavages_
Definition: XTandemInfile.h:278
String output_filename_
Definition: XTandemInfile.h:261
double refine_max_valid_evalue_
Definition: XTandemInfile.h:275
double precursor_mass_tolerance_plus_
Definition: XTandemInfile.h:235
double fragment_mass_tolerance_
Definition: XTandemInfile.h:233
double precursor_lower_mz_
Definition: XTandemInfile.h:249
String cleavage_site_
Definition: XTandemInfile.h:267
Base class for loading/storing XML files that have a handler derived from XMLHandler. 
Definition: XMLFile.h:51
bool semi_cleavage_
semi cleavage 
Definition: XTandemInfile.h:273
String taxon_
Definition: XTandemInfile.h:265
double max_valid_evalue_
Definition: XTandemInfile.h:283
int Int
Signed integer type. 
Definition: Types.h:100
ModificationDefinitionsSet modifications_
Definition: XTandemInfile.h:257
std::vector< Internal::XTandemInfileNote > notes_
Definition: XTandemInfile.h:289
double precursor_mass_tolerance_minus_
Definition: XTandemInfile.h:237
double fragment_lower_mz_
Definition: XTandemInfile.h:251
bool refine_
Enable/disable xtandem refinement. 
Definition: XTandemInfile.h:270