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