114 INCOMPATIBLE_INPUT_DATA
135 ExitCodes run(
PeakMap& unprocessed_spectra, std::vector<FASTAFile::FASTAEntry>& fasta_db, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms,
PeakMap& spectra);
138 void updateMembers_()
override;
double fragment_mass_tolerance_xlinks_
Definition: OpenPepXLLFAlgorithm.h:150
Size missed_cleavages_
Definition: OpenPepXLLFAlgorithm.h:163
Definition: OpenPepXLLFAlgorithm.h:111
bool fragment_mass_tolerance_unit_ppm_
Definition: OpenPepXLLFAlgorithm.h:151
StringList cross_link_residue1_
Definition: OpenPepXLLFAlgorithm.h:153
Int max_precursor_charge_
Definition: OpenPepXLLFAlgorithm.h:144
Int min_precursor_charge_
Definition: OpenPepXLLFAlgorithm.h:143
double cross_link_mass_
Definition: OpenPepXLLFAlgorithm.h:155
bool use_sequence_tags_
Definition: OpenPepXLLFAlgorithm.h:168
IntList precursor_correction_steps_
Definition: OpenPepXLLFAlgorithm.h:147
String add_b_ions_
Definition: OpenPepXLLFAlgorithm.h:172
Search for cross-linked peptide pairs in tandem MS spectra.
Definition: OpenPepXLLFAlgorithm.h:103
String add_z_ions_
Definition: OpenPepXLLFAlgorithm.h:176
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Size max_variable_mods_per_peptide_
Definition: OpenPepXLLFAlgorithm.h:161
String enzyme_name_
Definition: OpenPepXLLFAlgorithm.h:164
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
String add_x_ions_
Definition: OpenPepXLLFAlgorithm.h:173
String add_c_ions_
Definition: OpenPepXLLFAlgorithm.h:175
StringList fixedModNames_
Definition: OpenPepXLLFAlgorithm.h:159
String deisotope_mode_
Definition: OpenPepXLLFAlgorithm.h:167
Int number_top_hits_
Definition: OpenPepXLLFAlgorithm.h:166
double precursor_mass_tolerance_
Definition: OpenPepXLLFAlgorithm.h:145
ExitCodes
Exit codes.
Definition: OpenPepXLLFAlgorithm.h:109
StringList varModNames_
Definition: OpenPepXLLFAlgorithm.h:160
Definition: OpenPepXLLFAlgorithm.h:112
String cross_link_name_
Definition: OpenPepXLLFAlgorithm.h:157
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
StringList cross_link_residue2_
Definition: OpenPepXLLFAlgorithm.h:154
Size sequence_tag_min_length_
Definition: OpenPepXLLFAlgorithm.h:169
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
String decoy_string_
Definition: OpenPepXLLFAlgorithm.h:140
Definition: OpenPepXLLFAlgorithm.h:113
Size peptide_min_size_
Definition: OpenPepXLLFAlgorithm.h:162
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
double fragment_mass_tolerance_
Definition: OpenPepXLLFAlgorithm.h:149
A more convenient string class.
Definition: String.h:58
String add_y_ions_
Definition: OpenPepXLLFAlgorithm.h:171
bool precursor_mass_tolerance_unit_ppm_
Definition: OpenPepXLLFAlgorithm.h:146
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
DoubleList cross_link_mass_mono_link_
Definition: OpenPepXLLFAlgorithm.h:156
bool decoy_prefix_
Definition: OpenPepXLLFAlgorithm.h:141
String add_losses_
Definition: OpenPepXLLFAlgorithm.h:177
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
String add_a_ions_
Definition: OpenPepXLLFAlgorithm.h:174