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OpenPepXLLFAlgorithm.h
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1
2 // --------------------------------------------------------------------------
3 // OpenMS -- Open-Source Mass Spectrometry
4 // --------------------------------------------------------------------------
5 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
6 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
7 //
8 // This software is released under a three-clause BSD license:
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12 // notice, this list of conditions and the following disclaimer in the
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31 // --------------------------------------------------------------------------
32 // $Maintainer: Eugen Netz $
33 // $Authors: Eugen Netz $
34 // --------------------------------------------------------------------------
35
36 #pragma once
37
38 #include <OpenMS/CONCEPT/ProgressLogger.h>
39 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
40 #include <OpenMS/KERNEL/StandardTypes.h>
41 #include <OpenMS/FORMAT/FASTAFile.h>
42 #include <OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h>
43
44 namespace OpenMS
45 {
46
47 //-------------------------------------------------------------
48 //Doxygen docu
49 //-------------------------------------------------------------
50
103 class OPENMS_DLLAPI OpenPepXLLFAlgorithm :
104 public DefaultParamHandler, public ProgressLogger
105 {
106 public:
107
109 enum ExitCodes
110 {
111 EXECUTION_OK,
112 ILLEGAL_PARAMETERS,
113 UNEXPECTED_RESULT,
114 INCOMPATIBLE_INPUT_DATA
115 };
116
118 OpenPepXLLFAlgorithm();
119
121 ~OpenPepXLLFAlgorithm() override;
122
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);
136
137 private:
138 void updateMembers_() override;
139
140 String decoy_string_;
141 bool decoy_prefix_;
142
143 Int min_precursor_charge_;
144 Int max_precursor_charge_;
145 double precursor_mass_tolerance_;
146 bool precursor_mass_tolerance_unit_ppm_;
147 IntList precursor_correction_steps_;
148
149 double fragment_mass_tolerance_;
150 double fragment_mass_tolerance_xlinks_;
151 bool fragment_mass_tolerance_unit_ppm_;
152
153 StringList cross_link_residue1_;
154 StringList cross_link_residue2_;
155 double cross_link_mass_;
156 DoubleList cross_link_mass_mono_link_;
157 String cross_link_name_;
158
159 StringList fixedModNames_;
160 StringList varModNames_;
161 Size max_variable_mods_per_peptide_;
162 Size peptide_min_size_;
163 Size missed_cleavages_;
164 String enzyme_name_;
165
166 Int number_top_hits_;
167 String deisotope_mode_;
168 bool use_sequence_tags_;
169 Size sequence_tag_min_length_;
170
171 String add_y_ions_;
172 String add_b_ions_;
173 String add_x_ions_;
174 String add_a_ions_;
175 String add_c_ions_;
176 String add_z_ions_;
177 String add_losses_;
178 };
179 }
OpenMS::OpenPepXLLFAlgorithm::fragment_mass_tolerance_unit_ppm_
bool fragment_mass_tolerance_unit_ppm_
Definition: OpenPepXLLFAlgorithm.h:151
OpenMS::OpenPepXLLFAlgorithm::EXECUTION_OK
Definition: OpenPepXLLFAlgorithm.h:111
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::OpenPepXLLFAlgorithm::decoy_prefix_
bool decoy_prefix_
Definition: OpenPepXLLFAlgorithm.h:141
OpenMS::OpenPepXLLFAlgorithm::cross_link_mass_
double cross_link_mass_
Definition: OpenPepXLLFAlgorithm.h:155
OpenMS::OpenPepXLLFAlgorithm::fragment_mass_tolerance_
double fragment_mass_tolerance_
Definition: OpenPepXLLFAlgorithm.h:149
OpenMS::OpenPepXLLFAlgorithm::add_x_ions_
String add_x_ions_
Definition: OpenPepXLLFAlgorithm.h:173
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::OpenPepXLLFAlgorithm::precursor_mass_tolerance_
double precursor_mass_tolerance_
Definition: OpenPepXLLFAlgorithm.h:145
OpenMS::OpenPepXLLFAlgorithm::cross_link_residue2_
StringList cross_link_residue2_
Definition: OpenPepXLLFAlgorithm.h:154
OpenMS::OpenPepXLLFAlgorithm::precursor_mass_tolerance_unit_ppm_
bool precursor_mass_tolerance_unit_ppm_
Definition: OpenPepXLLFAlgorithm.h:146
OpenMS::OpenPepXLLFAlgorithm
Search for cross-linked peptide pairs in tandem MS spectra.
Definition: OpenPepXLLFAlgorithm.h:103
OPXLDataStructs.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::OpenPepXLLFAlgorithm::ILLEGAL_PARAMETERS
Definition: OpenPepXLLFAlgorithm.h:112
OpenMS::OpenPepXLLFAlgorithm::add_losses_
String add_losses_
Definition: OpenPepXLLFAlgorithm.h:177
StandardTypes.h
OpenMS::OpenPepXLLFAlgorithm::precursor_correction_steps_
IntList precursor_correction_steps_
Definition: OpenPepXLLFAlgorithm.h:147
OpenMS::OpenPepXLLFAlgorithm::peptide_min_size_
Size peptide_min_size_
Definition: OpenPepXLLFAlgorithm.h:162
OpenMS::OpenPepXLLFAlgorithm::cross_link_residue1_
StringList cross_link_residue1_
Definition: OpenPepXLLFAlgorithm.h:153
OpenMS::OpenPepXLLFAlgorithm::sequence_tag_min_length_
Size sequence_tag_min_length_
Definition: OpenPepXLLFAlgorithm.h:169
OpenMS::OpenPepXLLFAlgorithm::min_precursor_charge_
Int min_precursor_charge_
Definition: OpenPepXLLFAlgorithm.h:143
OpenMS::OpenPepXLLFAlgorithm::missed_cleavages_
Size missed_cleavages_
Definition: OpenPepXLLFAlgorithm.h:163
OpenMS::OpenPepXLLFAlgorithm::cross_link_mass_mono_link_
DoubleList cross_link_mass_mono_link_
Definition: OpenPepXLLFAlgorithm.h:156
OpenMS::OpenPepXLLFAlgorithm::enzyme_name_
String enzyme_name_
Definition: OpenPepXLLFAlgorithm.h:164
OpenMS::OpenPepXLLFAlgorithm::add_y_ions_
String add_y_ions_
Definition: OpenPepXLLFAlgorithm.h:171
OpenMS::OpenPepXLLFAlgorithm::use_sequence_tags_
bool use_sequence_tags_
Definition: OpenPepXLLFAlgorithm.h:168
OpenMS::OpenPepXLLFAlgorithm::add_b_ions_
String add_b_ions_
Definition: OpenPepXLLFAlgorithm.h:172
FASTAFile.h
OpenMS::OpenPepXLLFAlgorithm::fixedModNames_
StringList fixedModNames_
Definition: OpenPepXLLFAlgorithm.h:159
ProgressLogger.h
OpenMS::DoubleList
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
OpenMS::OpenPepXLLFAlgorithm::deisotope_mode_
String deisotope_mode_
Definition: OpenPepXLLFAlgorithm.h:167
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::OpenPepXLLFAlgorithm::decoy_string_
String decoy_string_
Definition: OpenPepXLLFAlgorithm.h:140
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
DefaultParamHandler.h
OpenMS::OpenPepXLLFAlgorithm::add_c_ions_
String add_c_ions_
Definition: OpenPepXLLFAlgorithm.h:175
OpenMS::OpenPepXLLFAlgorithm::add_a_ions_
String add_a_ions_
Definition: OpenPepXLLFAlgorithm.h:174
OpenMS::OpenPepXLLFAlgorithm::cross_link_name_
String cross_link_name_
Definition: OpenPepXLLFAlgorithm.h:157
OpenMS::OpenPepXLLFAlgorithm::fragment_mass_tolerance_xlinks_
double fragment_mass_tolerance_xlinks_
Definition: OpenPepXLLFAlgorithm.h:150
OpenMS::OpenPepXLLFAlgorithm::number_top_hits_
Int number_top_hits_
Definition: OpenPepXLLFAlgorithm.h:166
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
int
OpenMS::OpenPepXLLFAlgorithm::ExitCodes
ExitCodes
Exit codes.
Definition: OpenPepXLLFAlgorithm.h:109
OpenMS::OpenPepXLLFAlgorithm::UNEXPECTED_RESULT
Definition: OpenPepXLLFAlgorithm.h:113
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::OpenPepXLLFAlgorithm::max_precursor_charge_
Int max_precursor_charge_
Definition: OpenPepXLLFAlgorithm.h:144
OpenMS::OpenPepXLLFAlgorithm::add_z_ions_
String add_z_ions_
Definition: OpenPepXLLFAlgorithm.h:176
OpenMS::OpenPepXLLFAlgorithm::varModNames_
StringList varModNames_
Definition: OpenPepXLLFAlgorithm.h:160
OpenMS::OpenPepXLLFAlgorithm::max_variable_mods_per_peptide_
Size max_variable_mods_per_peptide_
Definition: OpenPepXLLFAlgorithm.h:161