124 INCOMPATIBLE_INPUT_DATA
145 ExitCodes run(
PeakMap& unprocessed_spectra,
ConsensusMap& cfeatures, std::vector<FASTAFile::FASTAEntry>& fasta_db, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids,
OPXLDataStructs::PreprocessedPairSpectra& preprocessed_pair_spectra, std::vector< std::pair<Size, Size> >& spectrum_pairs, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms,
PeakMap& spectra);
148 void updateMembers_()
override;
150 static OPXLDataStructs::PreprocessedPairSpectra preprocessPairs_(
const PeakMap& spectra,
const std::vector< std::pair<Size, Size> >& spectrum_pairs,
const double cross_link_mass_iso_shift,
double fragment_mass_tolerance,
double fragment_mass_tolerance_xlinks,
bool fragment_mass_tolerance_unit_ppm,
bool deisotope);
String add_a_ions_
Definition: OpenPepXLAlgorithm.h:185
Size missed_cleavages_
Definition: OpenPepXLAlgorithm.h:176
A more convenient string class.
Definition: String.h:58
String cross_link_name_
Definition: OpenPepXLAlgorithm.h:170
Definition: OpenPepXLAlgorithm.h:122
double fragment_mass_tolerance_xlinks_
Definition: OpenPepXLAlgorithm.h:162
Int number_top_hits_
Definition: OpenPepXLAlgorithm.h:179
String enzyme_name_
Definition: OpenPepXLAlgorithm.h:177
String add_y_ions_
Definition: OpenPepXLAlgorithm.h:182
String add_b_ions_
Definition: OpenPepXLAlgorithm.h:183
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
String deisotope_mode_
Definition: OpenPepXLAlgorithm.h:180
String decoy_string_
Definition: OpenPepXLAlgorithm.h:152
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Definition: OpenPepXLAlgorithm.h:121
String add_c_ions_
Definition: OpenPepXLAlgorithm.h:186
Search for peptide pairs linked with a labeled cross-linker.
Definition: OpenPepXLAlgorithm.h:113
StringList varModNames_
Definition: OpenPepXLAlgorithm.h:173
Size max_variable_mods_per_peptide_
Definition: OpenPepXLAlgorithm.h:174
ExitCodes
Exit codes.
Definition: OpenPepXLAlgorithm.h:119
double fragment_mass_tolerance_
Definition: OpenPepXLAlgorithm.h:161
String add_x_ions_
Definition: OpenPepXLAlgorithm.h:184
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:303
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
double cross_link_mass_light_
Definition: OpenPepXLAlgorithm.h:167
double precursor_mass_tolerance_
Definition: OpenPepXLAlgorithm.h:157
StringList cross_link_residue2_
Definition: OpenPepXLAlgorithm.h:166
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
Int max_precursor_charge_
Definition: OpenPepXLAlgorithm.h:156
String add_z_ions_
Definition: OpenPepXLAlgorithm.h:187
String add_losses_
Definition: OpenPepXLAlgorithm.h:188
bool fragment_mass_tolerance_unit_ppm_
Definition: OpenPepXLAlgorithm.h:163
IntList precursor_correction_steps_
Definition: OpenPepXLAlgorithm.h:159
Size peptide_min_size_
Definition: OpenPepXLAlgorithm.h:175
StringList cross_link_residue1_
Definition: OpenPepXLAlgorithm.h:165
Int min_precursor_charge_
Definition: OpenPepXLAlgorithm.h:155
bool decoy_prefix_
Definition: OpenPepXLAlgorithm.h:153
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
A container for consensus elements.
Definition: ConsensusMap.h:79
DoubleList cross_link_mass_mono_link_
Definition: OpenPepXLAlgorithm.h:169
bool precursor_mass_tolerance_unit_ppm_
Definition: OpenPepXLAlgorithm.h:158
StringList fixedModNames_
Definition: OpenPepXLAlgorithm.h:172
double cross_link_mass_iso_shift_
Definition: OpenPepXLAlgorithm.h:168
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Definition: OpenPepXLAlgorithm.h:123