OpenMS  3.0.0
OpenPepXLAlgorithm.h
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34 
35 #pragma once
36 
43 
44 namespace OpenMS
45 {
46 
47 //-------------------------------------------------------------
48 //Doxygen docu
49 //-------------------------------------------------------------
50 
113  class OPENMS_DLLAPI OpenPepXLAlgorithm :
114  public DefaultParamHandler, public ProgressLogger
115  {
116 public:
117 
120  {
124  INCOMPATIBLE_INPUT_DATA
125  };
126 
129 
131  ~OpenPepXLAlgorithm() override;
132 
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);
146 
147 private:
148  void updateMembers_() override;
149 
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);
151 
154 
160 
164 
171 
178 
181 
189  };
190 }
OpenMS::OpenPepXLAlgorithm::EXECUTION_OK
Definition: OpenPepXLAlgorithm.h:121
DefaultParamHandler.h
OpenMS::OpenPepXLAlgorithm::fragment_mass_tolerance_
double fragment_mass_tolerance_
Definition: OpenPepXLAlgorithm.h:161
OpenMS::Internal::OpenMSBuildInfo::getOpenMPMaxNumThreads
static Size getOpenMPMaxNumThreads()
Get the maximum number of threads that OpenMP will use (including hyperthreads) Note: This could also...
Definition: BuildInfo.h:155
ConsensusXMLFile.h
OpenMS::OpenPepXLAlgorithm::run
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)
Performs the main function of this class, the search for cross-linked peptides.
BuildInfo.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::MzIdentMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a MzIdentML file.
OpenMS::OpenPepXLAlgorithm::enzyme_name_
String enzyme_name_
Definition: OpenPepXLAlgorithm.h:177
XQuestResultXMLFile.h
VersionInfo.h
OpenMS::OpenPepXLAlgorithm::cross_link_mass_iso_shift_
double cross_link_mass_iso_shift_
Definition: OpenPepXLAlgorithm.h:168
OpenMS::IdXMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
OpenMS::OpenPepXLAlgorithm::add_y_ions_
String add_y_ions_
Definition: OpenPepXLAlgorithm.h:182
OpenMS::OpenPepXLAlgorithm::add_b_ions_
String add_b_ions_
Definition: OpenPepXLAlgorithm.h:183
OpenMS::OpenPepXLAlgorithm::varModNames_
StringList varModNames_
Definition: OpenPepXLAlgorithm.h:173
OpenMS::DigestionEnzymeDB::getInstance
static InstanceType * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
OpenMS::FASTAFile
This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusua...
Definition: FASTAFile.h:60
OpenMS::VersionInfo::getTime
static String getTime()
Return the build time of OpenMS.
OpenMS::OpenPepXLAlgorithm::deisotope_mode_
String deisotope_mode_
Definition: OpenPepXLAlgorithm.h:180
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::OpenPepXLAlgorithm::cross_link_residue2_
StringList cross_link_residue2_
Definition: OpenPepXLAlgorithm.h:166
MzMLFile.h
OpenMS::DoubleList
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
ConsensusMap.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::OpenPepXLAlgorithm::UNEXPECTED_RESULT
Definition: OpenPepXLAlgorithm.h:123
OpenMS::PeakFileOptions::addMSLevel
void addMSLevel(int level)
adds a desired MS level for peaks to load
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IdXMLFile.h
OpenMS::OpenPepXLAlgorithm::precursor_mass_tolerance_unit_ppm_
bool precursor_mass_tolerance_unit_ppm_
Definition: OpenPepXLAlgorithm.h:158
OpenMS::OpenPepXLAlgorithm::add_losses_
String add_losses_
Definition: OpenPepXLAlgorithm.h:188
OpenMS::OpenPepXLAlgorithm::fragment_mass_tolerance_xlinks_
double fragment_mass_tolerance_xlinks_
Definition: OpenPepXLAlgorithm.h:162
OpenMS::OpenPepXLAlgorithm::ILLEGAL_PARAMETERS
Definition: OpenPepXLAlgorithm.h:122
OpenMS::ProgressLogger::startProgress
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
OpenMS::OpenPepXLAlgorithm::peptide_min_size_
Size peptide_min_size_
Definition: OpenPepXLAlgorithm.h:175
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OpenMS::Internal::OpenMSOSInfo::getBinaryArchitecture
static String getBinaryArchitecture()
Get Architecture of this binary (simply by looking at size of a pointer, i.e. size_t).
Definition: BuildInfo.h:87
OpenMS::OpenPepXLAlgorithm::add_c_ions_
String add_c_ions_
Definition: OpenPepXLAlgorithm.h:186
OpenMS::OpenPepXLAlgorithm::fixedModNames_
StringList fixedModNames_
Definition: OpenPepXLAlgorithm.h:172
OpenMS::OpenPepXLAlgorithm::cross_link_residue1_
StringList cross_link_residue1_
Definition: OpenPepXLAlgorithm.h:165
OpenMS::ProgressLogger::endProgress
void endProgress() const
Ends the progress display.
OpenMS::OpenPepXLAlgorithm::cross_link_mass_light_
double cross_link_mass_light_
Definition: OpenPepXLAlgorithm.h:167
OpenMS::OpenPepXLAlgorithm::decoy_prefix_
bool decoy_prefix_
Definition: OpenPepXLAlgorithm.h:153
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::Internal::OpenMSBuildInfo::getBuildType
static String getBuildType()
Get the build type used during building the OpenMS library.
Definition: BuildInfo.h:147
OpenMS::OpenPepXLAlgorithm::max_variable_mods_per_peptide_
Size max_variable_mods_per_peptide_
Definition: OpenPepXLAlgorithm.h:174
OpenMS::ModificationsDB::getInstance
static ModificationsDB * getInstance()
Returns a pointer to the modifications DB (singleton)
OpenMS::OPXLDataStructs::PreprocessedPairSpectra
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:303
OPXLDataStructs.h
OpenMS::MzIdentMLFile
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::OpenPepXLAlgorithm::cross_link_mass_mono_link_
DoubleList cross_link_mass_mono_link_
Definition: OpenPepXLAlgorithm.h:169
DigestionEnzymeProtein.h
OpenPepXLAlgorithm.h
OpenMS::XQuestResultXMLFile
Used to load and store xQuest result files.
Definition: XQuestResultXMLFile.h:55
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProteaseDB.h
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
OpenMS::DataValue
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:58
ProgressLogger.h
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
FASTAFile.h
OpenMS::ProteinIdentification::SearchParameters::db
String db
The used database.
Definition: ProteinIdentification.h:261
OpenMS::OpenPepXLAlgorithm::cross_link_name_
String cross_link_name_
Definition: OpenPepXLAlgorithm.h:170
OpenMS::OpenPepXLAlgorithm::add_z_ions_
String add_z_ions_
Definition: OpenPepXLAlgorithm.h:187
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::Internal::OpenMSOSInfo::getArchAsString
String getArchAsString() const
Get the current architecture (32-bit or 64-bit)
Definition: BuildInfo.h:75
OpenMS::VersionInfo::getVersion
static String getVersion()
Return the version number of OpenMS.
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to the parameters.
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
ModificationsDB.h
OpenMS::OpenPepXLAlgorithm::add_a_ions_
String add_a_ions_
Definition: OpenPepXLAlgorithm.h:185
OpenMS::VersionInfo::getRevision
static String getRevision()
Return the revision number from revision control system, e.g. git.
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::File::getUserDirectory
static String getUserDirectory()
OpenMS::OpenPepXLAlgorithm
Search for peptide pairs linked with a labeled cross-linker.
Definition: OpenPepXLAlgorithm.h:113
OpenMS::Param::update
bool update(const Param &p_outdated, const bool add_unknown=false)
Rescue parameter values from p_outdated to current param.
OpenMS::OpenMS_Log_debug
Logger::LogStream OpenMS_Log_debug
Global static instance of a LogStream to capture messages classified as debug output....
OpenMS::OpenPepXLAlgorithm::min_precursor_charge_
Int min_precursor_charge_
Definition: OpenPepXLAlgorithm.h:155
OpenMS::FASTAFile::load
void load(const String &filename, std::vector< FASTAEntry > &data) const
loads a FASTA file given by 'filename' and stores the information in 'data' This uses more RAM than r...
OpenMS::Internal::OpenMSOSInfo::getOSAsString
String getOSAsString() const
Get the current operating system (Windows, MacOS, Linux)
Definition: BuildInfo.h:69
OpenMS::File::getOpenMSDataPath
static String getOpenMSDataPath()
Returns the OpenMS data path (environment variable overwrites the default installation path)
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
String.h
OpenMS::OpenPepXLAlgorithm::missed_cleavages_
Size missed_cleavages_
Definition: OpenPepXLAlgorithm.h:176
OpenMS::PeakFileOptions::clearMSLevels
void clearMSLevels()
clears the MS levels
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::File::getTempDirectory
static String getTempDirectory()
OpenMS::OpenPepXLAlgorithm::ExitCodes
ExitCodes
Exit codes.
Definition: OpenPepXLAlgorithm.h:119
OpenMS::Internal::OpenMSOSInfo
Definition: BuildInfo.h:55
OpenMS::VersionInfo::getBranch
static String getBranch()
Return the branch name from revision control system, e.g. git.
OpenMS::OpenPepXLAlgorithm::add_x_ions_
String add_x_ions_
Definition: OpenPepXLAlgorithm.h:184
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::Internal::OpenMSOSInfo::getOSVersionAsString
String getOSVersionAsString() const
Get the OS version (e.g. 10.15 for macOS or 10 for Windows)
Definition: BuildInfo.h:81
OpenMS::XQuestResultXMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a xQuest XML file.
OpenMS::OpenPepXLAlgorithm::precursor_correction_steps_
IntList precursor_correction_steps_
Definition: OpenPepXLAlgorithm.h:159
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
StandardTypes.h
OpenMS::Internal::OpenMSOSInfo::getOSInfo
static OpenMSOSInfo getOSInfo()
Constructs and returns an OpenMSOSInfo object.
Definition: BuildInfo.h:102
File.h
MzIdentMLFile.h
OpenMS::MzMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
OpenMS::OpenPepXLAlgorithm::precursor_mass_tolerance_
double precursor_mass_tolerance_
Definition: OpenPepXLAlgorithm.h:157
TOPPBase.h
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:58
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::OpenPepXLAlgorithm::max_precursor_charge_
Int max_precursor_charge_
Definition: OpenPepXLAlgorithm.h:156
OpenMS::OpenPepXLAlgorithm::decoy_string_
String decoy_string_
Definition: OpenPepXLAlgorithm.h:152
OpenMS::OpenPepXLAlgorithm::fragment_mass_tolerance_unit_ppm_
bool fragment_mass_tolerance_unit_ppm_
Definition: OpenPepXLAlgorithm.h:163
OpenMS::OpenPepXLAlgorithm::number_top_hits_
Int number_top_hits_
Definition: OpenPepXLAlgorithm.h:179