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 setOutputResults(
String result);
183 String getOutputResults()
const;
186 void setMaxValidEValue(
double value);
189 double getMaxValidEValue()
const;
192 bool isRefining()
const;
195 void setSemiCleavage(
const bool semi_cleavage);
198 void setAllowIsotopeError(
const bool allow_isotope_error);
201 void setRefine(
const bool refine);
204 void setCleavageSite(
const String& cleavage_site);
207 const String& getCleavageSite()
const;
215 void write(
const String& filename);
224 void load(
const String& filename);
232 void writeTo_(std::ostream& os);
234 void writeNote_(std::ostream& os,
const String& type,
const String& label,
const String& value);
236 void writeNote_(std::ostream& os,
const String& type,
const String& label,
const char* value);
238 void writeNote_(std::ostream& os,
const String& type,
const String& label,
bool value);
246 String convertModificationSet_(
const std::set<ModificationDefinition>& mods)
const;
308 std::vector<Internal::XTandemInfileNote>
notes_;
313 #endif // OPENMS_FORMAT_XTANDEMINFILE_H
MassType fragment_mass_type_
Definition: XTandemInfile.h:260
A more convenient string class.
Definition: String.h:57
UInt max_precursor_charge_
Definition: XTandemInfile.h:262
XTandem input file.
Definition: XTandemInfile.h:52
ErrorUnit
error unit, either Da or ppm
Definition: XTandemInfile.h:58
UInt batch_size_
Definition: XTandemInfile.h:270
ErrorUnit precursor_mass_error_unit_
Definition: XTandemInfile.h:256
String default_parameters_file_
Definition: XTandemInfile.h:297
bool allow_isotope_error_
Definition: XTandemInfile.h:290
UInt number_of_threads_
Definition: XTandemInfile.h:268
ErrorUnit fragment_mass_error_unit_
Definition: XTandemInfile.h:258
MassType
Mass type of the precursor, either monoisotopic or average.
Definition: XTandemInfile.h:65
String input_filename_
Definition: XTandemInfile.h:274
MassType precursor_mass_type_
Definition: XTandemInfile.h:254
String taxonomy_file_
Definition: XTandemInfile.h:278
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
UInt number_of_missed_cleavages_
Definition: XTandemInfile.h:295
String output_filename_
Definition: XTandemInfile.h:276
double refine_max_valid_evalue_
Definition: XTandemInfile.h:292
double precursor_mass_tolerance_plus_
Definition: XTandemInfile.h:250
double fragment_mass_tolerance_
Definition: XTandemInfile.h:248
String output_results_
Definition: XTandemInfile.h:300
double precursor_lower_mz_
Definition: XTandemInfile.h:264
String cleavage_site_
Definition: XTandemInfile.h:282
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:53
bool semi_cleavage_
semi cleavage
Definition: XTandemInfile.h:288
String taxon_
Definition: XTandemInfile.h:280
double max_valid_evalue_
Definition: XTandemInfile.h:302
int Int
Signed integer type.
Definition: Types.h:96
ModificationDefinitionsSet modifications_
Definition: XTandemInfile.h:272
std::vector< Internal::XTandemInfileNote > notes_
Definition: XTandemInfile.h:308
double precursor_mass_tolerance_minus_
Definition: XTandemInfile.h:252
double fragment_lower_mz_
Definition: XTandemInfile.h:266
bool refine_
Enable/disable xtandem refinement.
Definition: XTandemInfile.h:285