OpenMS  3.0.0
NucleicAcidSpectrumGenerator.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2022.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
41 
42 namespace OpenMS
43 {
44  class NASequence;
45 
53  class OPENMS_DLLAPI NucleicAcidSpectrumGenerator :
54  public DefaultParamHandler
55  {
56  public:
57 
63 
66 
68  ~NucleicAcidSpectrumGenerator() override;
70 
73 
77  void getSpectrum(MSSpectrum& spectrum, const NASequence& oligo, Int min_charge, Int max_charge) const;
79 
94  void getMultipleSpectra(std::map<Int, MSSpectrum>& spectra, const NASequence& oligo, const std::set<Int>& charges, Int base_charge = 1) const;
95 
97  void updateMembers_() override;
99 
100  protected:
101 
103  void addFragmentPeaks_(MSSpectrum& spectrum, const std::vector<double>& fragment_masses, const String& ion_type, double offset, double intensity, Size start = 0) const;
104 
106  void addAMinusBPeaks_(MSSpectrum& spectrum, const std::vector<double>& fragment_masses, const NASequence& oligo, Size start = 0) const;
107 
109  MSSpectrum getUnchargedSpectrum_(const NASequence& oligo) const;
110 
112  void addChargedSpectrum_(MSSpectrum& spectrum, const MSSpectrum& uncharged_spectrum, Int charge, bool add_precursor) const;
113 
127  double a_intensity_;
128  double b_intensity_;
129  double c_intensity_;
130  double d_intensity_;
131  double w_intensity_;
132  double x_intensity_;
133  double y_intensity_;
134  double z_intensity_;
137  };
138 }
MSDataTransformingConsumer.h
DefaultParamHandler.h
OpenMS::NucleicAcidSpectrumGenerator::aB_intensity_
double aB_intensity_
Definition: NucleicAcidSpectrumGenerator.h:135
OpenMS::ProteinIdentification::SearchParameters::digestion_enzyme
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:273
NucleicAcidSearchEngine::AnnotatedHit::sequence
NASequence sequence
Definition: NucleicAcidSearchEngine.cpp:283
OpenMS::ProgressLogger::setProgress
void setProgress(SignedSize value) const
Sets the current progress.
MzTabFile.h
OpenMS::IdentificationData::registerParentSequence
ParentSequenceRef registerParentSequence(const ParentSequence &parent)
Register a parent sequence (e.g. protein or intact RNA)
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::StringUtils::toInt
static Int toInt(const String &this_s)
Definition: StringUtils.h:206
DataArrays.h
FileHandler.h
OpenMS::MzTabFile
File adapter for MzTab files.
Definition: MzTabFile.h:55
OpenMS::IdentificationDataInternal::DBSearchParam::fragment_mass_tolerance
double fragment_mass_tolerance
Definition: DBSearchParam.h:62
OpenMS::NucleicAcidSpectrumGenerator::getMultipleSpectra
void getMultipleSpectra(std::map< Int, MSSpectrum > &spectra, const NASequence &oligo, const std::set< Int > &charges, Int base_charge=1) const
Generates spectra in multiple charge states for an oligonucleotide sequence.
NucleicAcidSearchEngine::PrecursorInfo
Definition: NucleicAcidSearchEngine.cpp:265
Size
OpenMS::IdentificationData::ScoreType
IdentificationDataInternal::ScoreType ScoreType
Definition: IdentificationData.h:125
OpenMS::Normalizer
Normalizes the peak intensities spectrum-wise.
Definition: Normalizer.h:57
NucleicAcidSearchEngine::PrecursorInfo::PrecursorInfo
PrecursorInfo(Size scan_index, Int charge, Size isotope, const IdentificationData::AdductOpt &adduct=std::nullopt)
Definition: NucleicAcidSearchEngine.cpp:272
OpenMS::NucleicAcidSpectrumGenerator::add_z_ions_
bool add_z_ions_
Definition: NucleicAcidSpectrumGenerator.h:121
OpenMS::OMSFile
This class supports reading and writing of OMS files.
Definition: OMSFile.h:48
OpenMS::NucleicAcidSpectrumGenerator::z_intensity_
double z_intensity_
Definition: NucleicAcidSpectrumGenerator.h:134
OpenMS::IdentificationData::findScoreType
ScoreTypeRef findScoreType(const String &score_name) const
Look up a score type by name.
OpenMS::NucleicAcidSpectrumGenerator::d_intensity_
double d_intensity_
Definition: NucleicAcidSpectrumGenerator.h:130
IdentificationDataConverter.h
OpenMS::Param::setValue
void setValue(const std::string &key, const ParamValue &value, const std::string &description="", const std::vector< std::string > &tags=std::vector< std::string >())
Sets a value.
OpenMS::Math::median
static double median(IteratorType begin, IteratorType end, bool sorted=false)
Calculates the median of a range of values.
Definition: StatisticFunctions.h:138
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::IdentificationData::registerAdduct
AdductRef registerAdduct(const AdductInfo &adduct)
Register an adduct.
OpenMS::MSSpectrum::findNearest
Size findNearest(CoordinateType mz) const
Binary search for the peak nearest to a specific m/z.
NucleicAcidSearchEngine::PrecursorInfo::scan_index
Size scan_index
Definition: NucleicAcidSearchEngine.cpp:267
OpenMS::NASequence
Representation of a nucleic acid sequence.
Definition: NASequence.h:61
OpenMS::Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM
const std::string PRECURSOR_ERROR_PPM_USERPARAM
Definition: Constants.h:275
OpenMS::SVOutStream::modifyStrings
bool modifyStrings(bool modify)
Switch modification of strings (quoting/replacing of separators) on/off.
OpenMS::DigestionEnzymeDB::getInstance
static InstanceType * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
OpenMS::NucleicAcidSpectrumGenerator::a_intensity_
double a_intensity_
Definition: NucleicAcidSpectrumGenerator.h:127
ModifiedNASequenceGenerator.h
OpenMS::File::basename
static String basename(const String &file)
OpenMS::Exception::InvalidValue
Invalid value exception.
Definition: Exception.h:327
OpenMS::MSExperiment::sortSpectra
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
OpenMS::String::substitute
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
OpenMS::FASTAFile
This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusua...
Definition: FASTAFile.h:60
OpenMS::IdentificationDataInternal::DBSearchParam::fragment_tolerance_ppm
bool fragment_tolerance_ppm
Definition: DBSearchParam.h:64
OpenMS::StringUtils::toQString
static QString toQString(const String &this_s)
Definition: StringUtils.h:201
OpenMS::WindowMower
WindowMower augments the highest peaks in a sliding or jumping window.
Definition: WindowMower.h:54
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::Ribonucleotide
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:51
OpenMS::Peak1D::setMZ
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:119
OpenMS::IdentificationData::registerProcessingSoftware
ProcessingSoftwareRef registerProcessingSoftware(const ProcessingSoftware &software)
Register data processing software.
NucleicAcidSearchEngine::preprocessSpectra_
void preprocessSpectra_(PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool single_charge_spectra, bool negative_mode, Int min_charge, Int max_charge, bool include_unknown_charge)
Definition: NucleicAcidSearchEngine.cpp:532
OpenMS::IDFilter::filterObservationMatchesByScore
static void filterObservationMatchesByScore(IdentificationData &id_data, IdentificationData::ScoreTypeRef score_ref, double cutoff)
Filter observation matches (e.g. PSMs) in IdentificationData by score.
OpenMS::MzTab::getNucleicAcidSectionRows
const MzTabNucleicAcidSectionRows & getNucleicAcidSectionRows() const
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
JavaInfo.h
OpenMS::ModifiedNASequenceGenerator::applyVariableModifications
static void applyVariableModifications(const std::set< ConstRibonucleotidePtr > &var_mods, const NASequence &seq, Size max_variable_mods_per_NASequence, std::vector< NASequence > &all_modified_NASequences, bool keep_original=true)
Applies variable modifications to a single NASequence. If keep_original is set the original (e....
OpenMS::MSExperiment::begin
Iterator begin()
Definition: MSExperiment.h:150
NucleicAcidSearchEngine::deisotopeAndSingleChargeMSSpectrum_
void deisotopeAndSingleChargeMSSpectrum_(MSSpectrum &in, Int min_charge, Int max_charge, double fragment_tolerance, bool fragment_unit_ppm, bool keep_only_deisotoped=false, Size min_isopeaks=3, Size max_isopeaks=10, bool make_single_charged=true)
Definition: NucleicAcidSearchEngine.cpp:376
NucleicAcidSearchEngine::AnnotatedHit::oligo_ref
IdentificationData::IdentifiedOligoRef oligo_ref
Definition: NucleicAcidSearchEngine.cpp:282
OpenMS::RNaseDigestion::digest
void digest(const NASequence &rna, std::vector< NASequence > &output, Size min_length=0, Size max_length=0) const
Performs the enzymatic digestion of a (potentially modified) RNA.
RNaseDigestion.h
Peak1D.h
OpenMS::WindowMower::filterPeakSpectrum
void filterPeakSpectrum(PeakSpectrum &spectrum)
MzMLFile.h
OpenMS::NASequence::size
size_t size() const
Int
OpenMS::PeptideIdentification::setRT
void setRT(double rt)
sets the RT of the MS2 spectrum where the identification occurred
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
OpenMS::IDFilter::removeDecoys
static void removeDecoys(IdentificationData &id_data)
Filter IdentificationData to remove parent sequences annotated as decoys.
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::NucleicAcidSpectrumGenerator::add_c_ions_
bool add_c_ions_
Definition: NucleicAcidSpectrumGenerator.h:116
OpenMS::Constants::c
const double c
Definition: Constants.h:209
OpenMS::MSSpectrum::getRT
double getRT() const
OpenMS::RNaseDigestion::setEnzyme
void setEnzyme(const DigestionEnzyme *enzyme) override
Sets the enzyme for the digestion.
OpenMS::RibonucleotideDB::getInstance
static RibonucleotideDB * getInstance()
replacement for constructor (singleton pattern)
OpenMS::IdentificationDataInternal::ObservationMatch::peak_annotations
PeakAnnotationSteps peak_annotations
Definition: ObservationMatch.h:85
NucleicAcidSearchEngine::PrecursorInfo::charge
Int charge
Definition: NucleicAcidSearchEngine.cpp:268
OpenMS::IdentificationDataInternal::DBSearchParam::mass_type
enum MassType mass_type
Definition: DBSearchParam.h:50
OpenMS::MzTab
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:477
OpenMS::ProteinIdentification::MONOISOTOPIC
Definition: ProteinIdentification.h:249
OpenMS::IdentificationData::getObservationMatches
const ObservationMatches & getObservationMatches() const
Return the registered observation matches (immutable)
Definition: IdentificationData.h:479
StatisticFunctions.h
NucleicAcidSearchEngine::parseAdduct_
AdductInfo parseAdduct_(const String &adduct)
Definition: NucleicAcidSearchEngine.cpp:348
OpenMS::IdentificationDataInternal::DBSearchParam::precursor_tolerance_ppm
bool precursor_tolerance_ppm
Definition: DBSearchParam.h:63
OpenMS::ProgressLogger::startProgress
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
NucleicAcidSearchEngine::HasInvalidLength::max_size_
Size max_size_
Definition: NucleicAcidSearchEngine.cpp:337
NASequence.h
OpenMS::IdentificationDataInternal::ScoreType
Information about a score type.
Definition: ScoreType.h:45
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OpenMS::IdentificationData::getInputFiles
const InputFiles & getInputFiles() const
Return the registered input files (immutable)
Definition: IdentificationData.h:401
OpenMS::NucleicAcidSpectrumGenerator::add_first_prefix_ion_
bool add_first_prefix_ion_
Definition: NucleicAcidSpectrumGenerator.h:123
OPENMS_PRECONDITION
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:120
NucleicAcidSearchEngine::getModifications_
set< ConstRibonucleotidePtr > getModifications_(const set< String > &mod_names)
Definition: NucleicAcidSearchEngine.cpp:292
SpectrumSettings.h
OpenMS::Constants::PROTON_MASS_U
const double PROTON_MASS_U
Definition: Constants.h:116
OPENMS_LOG_WARN
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
OpenMS::MascotGenericFile::writeSpectrum
void writeSpectrum(std::ostream &os, const PeakSpectrum &spec, const String &filename, const String &native_id_type_accession)
writes a spectrum in MGF format to an ostream
OpenMS::ProgressLogger::endProgress
void endProgress() const
Ends the progress display.
OpenMS::IdentificationData::registerIdentifiedOligo
IdentifiedOligoRef registerIdentifiedOligo(const IdentifiedOligo &oligo)
Register an identified RNA oligonucleotide.
OpenMS::IdentificationDataInternal::DBSearchParam::database
String database
Definition: DBSearchParam.h:52
OpenMS::EnzymaticDigestion::setMissedCleavages
void setMissedCleavages(Size missed_cleavages)
Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when lo...
OpenMS::MzTab::getOligonucleotideSectionRows
const MzTabOligonucleotideSectionRows & getOligonucleotideSectionRows() const
OpenMS::Software::setVersion
void setVersion(const String &version)
Sets the software version.
ListUtils.h
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:120
OpenMS::NLargest
NLargest removes all but the n largest peaks.
Definition: NLargest.h:54
OpenMS::IdentificationData::getParentSequences
const ParentSequences & getParentSequences() const
Return the registered parent sequences (immutable)
Definition: IdentificationData.h:443
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::PeptideIdentification::getHits
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance_ppm
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:270
OpenMS::DateTime::now
static DateTime now()
Returns the current date and time.
OpenMS::NucleicAcidSpectrumGenerator::add_x_ions_
bool add_x_ions_
Definition: NucleicAcidSpectrumGenerator.h:119
OpenMS::IdentificationDataInternal::DBSearchParam
Parameters specific to a database search step.
Definition: DBSearchParam.h:47
NucleicAcidSearchEngine::AnnotatedHit::precursor_error_ppm
double precursor_error_ppm
Definition: NucleicAcidSearchEngine.cpp:284
OpenMS::IdentificationDataInternal::ProcessingSoftware::assigned_scores
std::vector< ScoreTypeRef > assigned_scores
Definition: ProcessingSoftware.h:56
OpenMS::ListUtils::concatenate
static String concatenate(const std::vector< T > &container, const String &glue="")
Concatenates all elements of the container and puts the glue string between elements.
Definition: ListUtils.h:209
WindowMower.h
OpenMS::Precursor
Precursor meta information.
Definition: Precursor.h:58
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::File::exists
static bool exists(const String &file)
Method used to test if a file exists.
NucleicAcidSearchEngine::calculateAndFilterFDR_
void calculateAndFilterFDR_(IdentificationData &id_data, bool only_top_hits)
Definition: NucleicAcidSearchEngine.cpp:804
OMSFile.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::IdentificationData::getDBSearchParams
const DBSearchParams & getDBSearchParams() const
Return the registered database search parameters (immutable)
Definition: IdentificationData.h:419
NucleicAcidSearchEngine::HasInvalidLength::HasInvalidLength
HasInvalidLength(Size min_size, Size max_size)
Definition: NucleicAcidSearchEngine.cpp:339
OpenMS::AdductInfo::getMassShift
double getMassShift(bool use_avg_mass=false) const
returns the mass shift caused by this adduct if charges are compensated with protons
PeptideHit.h
OpenMS::IdentificationDataInternal::ProcessingSoftware
Information about software used for data processing.
Definition: ProcessingSoftware.h:48
RNaseDB.h
NucleicAcidSearchEngine::postProcessHits_
void postProcessHits_(const PeakMap &exp, vector< HitsByScore > &annotated_hits, IdentificationData &id_data, bool negative_mode)
Definition: NucleicAcidSearchEngine.cpp:739
OpenMS::Normalizer::filterPeakMap
void filterPeakMap(PeakMap &exp) const
OpenMS::ProteinIdentification::SearchParameters::variable_modifications
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:267
NucleicAcidSearchEngine::calculatePrecursorMass_
double calculatePrecursorMass_(double mz, Int charge, Int isotope, double adduct_mass, bool negative_mode)
Definition: NucleicAcidSearchEngine.cpp:657
OpenMS::IdentificationDataInternal::DBSearchParam::digestion_enzyme
const DigestionEnzyme * digestion_enzyme
Definition: DBSearchParam.h:67
OpenMS::ProteinIdentification::SearchParameters::mass_type
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:265
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProteaseDB.h
OpenMS::NucleicAcidSpectrumGenerator::add_metainfo_
bool add_metainfo_
Definition: NucleicAcidSpectrumGenerator.h:124
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
OpenMS::IdentificationData::registerScoreType
ScoreTypeRef registerScoreType(const ScoreType &score)
Register a score type.
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...
OpenMS::IdentificationData::registerInputFile
InputFileRef registerInputFile(const InputFile &file)
Register an input file.
OpenMS::IdentificationDataInternal::Observation
Representation of an observation, e.g. a spectrum or feature, in an input data file.
Definition: Observation.h:53
OpenMS::NucleicAcidSpectrumGenerator::add_b_ions_
bool add_b_ions_
Definition: NucleicAcidSpectrumGenerator.h:115
FASTAFile.h
OpenMS::SVOutStream
Stream class for writing to comma/tab/...-separated values files.
Definition: SVOutStream.h:56
NucleicAcidSearchEngine::fragment_ion_codes_
vector< String > fragment_ion_codes_
Definition: NucleicAcidSearchEngine.cpp:155
NucleicAcidSearchEngine::generateLFQInput_
void generateLFQInput_(IdentificationData &id_data, const String &out_file)
Definition: NucleicAcidSearchEngine.cpp:831
OpenMS::ProteinIdentification::SearchParameters::db
String db
The used database.
Definition: ProteinIdentification.h:261
OpenMS::SpectrumLookup
Helper class for looking up spectra based on different attributes.
Definition: SpectrumLookup.h:67
OpenMS::IdentificationDataInternal::IteratorWrapper
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:45
NucleicAcidSearchEngine::PrecursorInfo::adduct
IdentificationData::AdductOpt adduct
Definition: NucleicAcidSearchEngine.cpp:270
OpenMS::AdductInfo
Definition: AdductInfo.h:42
ProteinIdentification.h
OpenMS::MzTab::getOSMSectionRows
const MzTabOSMSectionRows & getOSMSectionRows() const
Param.h
NucleicAcidSearchEngine::ambiguous_mods_
map< String, String > ambiguous_mods_
Definition: NucleicAcidSearchEngine.cpp:156
OpenMS::SpectrumLookup::readSpectra
void readSpectra(const SpectrumContainer &spectra, const String &scan_regexp=default_scan_regexp)
Read and index spectra for later look-up.
Definition: SpectrumLookup.h:103
OpenMS::Peak1D::getMZ
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:113
OpenMS::NucleicAcidSpectrumGenerator::add_precursor_peaks_
bool add_precursor_peaks_
Definition: NucleicAcidSpectrumGenerator.h:125
OpenMS::IdentificationData::getObservations
const Observations & getObservations() const
Return the registered observations (immutable)
Definition: IdentificationData.h:437
SpectrumLookup.h
OpenMS::Ribonucleotide::isAmbiguous
bool isAmbiguous() const
Return whether this is an "ambiguous" modification (representing isobaric modifications on the base/r...
OPENMS_LOG_DEBUG
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
OpenMS::IdentificationData::registerObservation
ObservationRef registerObservation(const Observation &obs)
Register an observation (e.g. MS2 spectrum or feature)
OpenMS::PeptideIdentification::setHigherScoreBetter
void setHigherScoreBetter(bool value)
sets the peptide score orientation
OpenMS::MzTabFile::store
void store(const String &filename, const MzTab &mz_tab) const
OpenMS::IdentificationData::setCurrentProcessingStep
void setCurrentProcessingStep(ProcessingStepRef step_ref)
Set a data processing step that will apply to all subsequent "register..." calls.
RibonucleotideDB.h
OpenMS::OMSFile::store
void store(const String &filename, const IdentificationData &id_data)
Write out an IdentificationData object to SQL-based OMS file.
OpenMS::IdentificationDataInternal::ScoredProcessingResult::addProcessingStep
void addProcessingStep(const AppliedProcessingStep &step)
Add an applied processing step.
Definition: ScoredProcessingResult.h:66
OpenMS::IdentificationData::registerDBSearchParam
SearchParamRef registerDBSearchParam(const DBSearchParam &param)
Register database search parameters.
OpenMS::MSDataTransformingConsumer
Transforming consumer of MS data.
Definition: MSDataTransformingConsumer.h:58
OpenMS::IdentificationDataInternal::DBSearchParam::variable_mods
std::set< String > variable_mods
Definition: DBSearchParam.h:59
OpenMS::SpectrumSettings::setPrecursors
void setPrecursors(const std::vector< Precursor > &precursors)
sets the precursors
OpenMS::String::split
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
NucleicAcidSearchEngine::AnnotatedHit
Definition: NucleicAcidSearchEngine.cpp:280
OpenMS::MSSpectrum::clear
void clear(bool clear_meta_data)
Clears all data and meta data.
OpenMS::IdentificationDataInternal::ParentSequence
Representation of a parent sequence that is identified only indirectly (e.g. a protein).
Definition: ParentSequence.h:49
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
NucleicAcidSearchEngine::HasInvalidLength::min_size_
Size min_size_
Definition: NucleicAcidSearchEngine.cpp:336
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::NucleicAcidSpectrumGenerator::add_a_ions_
bool add_a_ions_
Definition: NucleicAcidSpectrumGenerator.h:114
OpenMS::File::path
static String path(const String &file)
Normalizer.h
MascotGenericFile.h
OpenMS::PeptideHit::setCharge
void setCharge(Int charge)
sets the charge of the peptide
CsvFile.h
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to the parameters.
OpenMS::IdentificationDataInternal::DBSearchParam::max_length
Size max_length
Definition: DBSearchParam.h:71
OpenMS::MascotGenericFile
Read/write Mascot generic files (MGF).
Definition: MascotGenericFile.h:62
OpenMS::PeakFileOptions::setFillData
void setFillData(bool only)
sets whether to fill the actual data into the container (spectrum/chromatogram)
OpenMS::IdentificationDataInternal::DBSearchParam::charges
std::set< Int > charges
Definition: DBSearchParam.h:56
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:269
NucleicAcidSearchEngine::HasInvalidLength::operator()
bool operator()(const NASequence &s) const
Definition: NucleicAcidSearchEngine.cpp:343
OpenMS::NucleicAcidSpectrumGenerator::add_aB_ions_
bool add_aB_ions_
Definition: NucleicAcidSpectrumGenerator.h:122
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:53
OpenMS::Citation
Stores Citations for individual TOPP tools.
Definition: TOPPBase.h:73
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::MSSpectrum::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position.
OpenMS::IdentificationDataInternal::DBSearchParam::min_length
Size min_length
Definition: DBSearchParam.h:70
NucleicAcidSpectrumGenerator.h
OpenMS::NucleicAcidSpectrumGenerator::b_intensity_
double b_intensity_
Definition: NucleicAcidSpectrumGenerator.h:128
OpenMS::IdentificationDataInternal::IdentifiedSequence::sequence
SeqType sequence
Definition: IdentifiedSequence.h:54
OpenMS::NucleicAcidSpectrumGenerator::add_w_ions_
bool add_w_ions_
Definition: NucleicAcidSpectrumGenerator.h:118
OpenMS::PeptideHit::setSequence
void setSequence(const AASequence &sequence)
sets the peptide sequence
OpenMS::ProteinIdentification::SearchParameters::fixed_modifications
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:266
OpenMS::IdentificationDataInternal::RNA
Definition: MetaData.h:69
OpenMS::IdentificationData::getScoreTypes
const ScoreTypes & getScoreTypes() const
Return the registered score types (immutable)
Definition: IdentificationData.h:431
NucleicAcidSearchEngine::AnnotatedHit::annotations
vector< PeptideHit::PeakAnnotation > annotations
Definition: NucleicAcidSearchEngine.cpp:285
SVOutStream.h
OpenMS::IdentificationData::registerObservationMatch
ObservationMatchRef registerObservationMatch(const ObservationMatch &match)
Register an observation match (e.g. peptide-spectrum match)
OpenMS::CsvFile
This class handles csv files. Currently only loading is implemented.
Definition: CsvFile.h:49
NLargest.h
OpenMS::SpectrumSettings::getNativeID
const String & getNativeID() const
returns the native identifier for the spectrum, used by the acquisition software.
OpenMS::FalseDiscoveryRate
Calculates false discovery rates (FDR) from identifications.
Definition: FalseDiscoveryRate.h:77
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::NucleicAcidSpectrumGenerator::x_intensity_
double x_intensity_
Definition: NucleicAcidSpectrumGenerator.h:132
main
int main(int argc, const char **argv)
Definition: NucleicAcidSearchEngine.cpp:1450
MSExperiment.h
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:271
OpenMS::IdentificationDataInternal::InputFile::primary_files
std::set< String > primary_files
Definition: include/OpenMS/METADATA/ID/InputFile.h:56
OpenMS::IdentificationDataInternal::DBSearchParam::missed_cleavages
Size missed_cleavages
Definition: DBSearchParam.h:69
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::IdentificationDataConverter::exportIDs
static void exportIDs(const IdentificationData &id_data, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, bool export_ids_wo_scores=false)
Export to legacy peptide/protein identifications.
OpenMS::IdentificationData
Representation of spectrum identification results and associated data.
Definition: IdentificationData.h:94
OpenMS::StringUtils::toDouble
static double toDouble(const String &this_s)
Definition: StringUtils.h:216
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::NucleicAcidSpectrumGenerator::add_d_ions_
bool add_d_ions_
Definition: NucleicAcidSpectrumGenerator.h:117
OpenMS::NucleicAcidSpectrumGenerator::c_intensity_
double c_intensity_
Definition: NucleicAcidSpectrumGenerator.h:129
OpenMS::File::TempDir
Class representing a temporary directory.
Definition: File.h:64
OpenMS::IdentificationDataInternal::DBSearchParam::precursor_mass_tolerance
double precursor_mass_tolerance
Definition: DBSearchParam.h:61
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::String::substr
String substr(size_t pos=0, size_t n=npos) const
Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...
OpenMS::IdentificationData::getCurrentProcessingStep
ProcessingStepRef getCurrentProcessingStep()
Return the current processing step (set via setCurrentProcessingStep()).
OpenMS::ThresholdMower::filterPeakMap
void filterPeakMap(PeakMap &exp)
OpenMS::MSExperiment::end
Iterator end()
Definition: MSExperiment.h:160
OpenMS::CVTerm
Representation of controlled vocabulary term.
Definition: CVTerm.h:52
NucleicAcidSearchEngine::AnnotatedHit::precursor_ref
const PrecursorInfo * precursor_ref
Definition: NucleicAcidSearchEngine.cpp:286
OpenMS::IdentificationData::cleanup
void cleanup(bool require_observation_match=true, bool require_identified_sequence=true, bool require_parent_match=true, bool require_parent_group=false, bool require_match_group=false)
Clean up the data structure after filtering parts of it.
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::IdentificationDataInternal::IdentifiedSequence
Representation of an identified sequence (peptide or oligonucleotide)
Definition: IdentifiedSequence.h:52
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:84
OpenMS::IdentificationData::registerProcessingStep
ProcessingStepRef registerProcessingStep(const ProcessingStep &step)
Register a data processing step.
ElementDB.h
OpenMS::IdentificationDataInternal::ObservationMatch::adduct_opt
AdductOpt adduct_opt
optional reference to adduct
Definition: ObservationMatch.h:81
OpenMS::IdentificationDataInternal::InputFile
Information about input files that were processed.
Definition: include/OpenMS/METADATA/ID/InputFile.h:50
OpenMS::MzMLFile::transform
void transform(const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false, bool skip_first_pass=false)
Transforms a map while loading using the supplied MSDataConsumer.
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
float
OpenMS::MSExperiment::getPrimaryMSRunPath
void getPrimaryMSRunPath(StringList &toFill) const
get the file path to the first MS run
OpenMS::IdentificationDataInternal::MONOISOTOPIC
Definition: MetaData.h:75
OpenMS::ThresholdMower
ThresholdMower removes all peaks below a threshold.
Definition: ThresholdMower.h:51
OpenMS::IdentificationDataConverter::exportMzTab
static MzTab exportMzTab(const IdentificationData &id_data)
Export to mzTab format.
OpenMS::NASequence::empty
bool empty() const
OpenMS::StringUtils::number
static String number(double d, UInt n)
Definition: StringUtils.h:196
OpenMS::TOPPBase::ExitCodes
ExitCodes
Exit codes.
Definition: TOPPBase.h:152
OpenMS::IdentificationDataInternal::ProcessingStep
Data processing step that is applied to the data (e.g. database search, PEP calculation,...
Definition: ProcessingStep.h:47
OpenMS::IdentificationDataInternal::ScoredProcessingResult::addScore
void addScore(ScoreTypeRef score_type, double score, const std::optional< ProcessingStepRef > &processing_step_opt=std::nullopt)
Add a score (possibly connected to a processing step)
Definition: ScoredProcessingResult.h:97
OpenMS::MSSpectrum::setName
void setName(const String &name)
Sets the name.
String.h
OpenMS::NASequence::toString
std::string toString() const
OpenMS::IdentificationDataInternal::AVERAGE
Definition: MetaData.h:76
OpenMS::IdentificationData::AdductOpt
IdentificationDataInternal::AdductOpt AdductOpt
Definition: IdentificationData.h:168
NucleicAcidSearchEngine::main_
ExitCodes main_(int, const char **) override
The actual "main" method. main_() is invoked by main().
Definition: NucleicAcidSearchEngine.cpp:886
OpenMS::PeakFileOptions::clearMSLevels
void clearMSLevels()
clears the MS levels
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance_ppm
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:272
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::String::remove
String & remove(char what)
Remove all occurrences of the character what.
IdentificationData.h
OpenMS::NucleicAcidSpectrumGenerator
Generates theoretical spectra for nucleic acid sequences.
Definition: NucleicAcidSpectrumGenerator.h:53
OpenMS::FalseDiscoveryRate::applyToObservationMatches
IdentificationData::ScoreTypeRef applyToObservationMatches(IdentificationData &id_data, IdentificationData::ScoreTypeRef score_ref) const
Calculate FDR on the level of observation matches (e.g. peptide-spectrum matches) for "general" ident...
OpenMS::IdentificationData::getIdentifiedOligos
const IdentifiedOligos & getIdentifiedOligos() const
Return the registered identified oligonucleotides (immutable)
Definition: IdentificationData.h:467
OpenMS::IdentificationDataConverter::importSequences
static void importSequences(IdentificationData &id_data, const std::vector< FASTAFile::FASTAEntry > &fasta, IdentificationData::MoleculeType type=IdentificationData::MoleculeType::PROTEIN, const String &decoy_pattern="")
Import FASTA sequences as parent sequences.
OpenMS::NucleicAcidSpectrumGenerator::add_y_ions_
bool add_y_ions_
Definition: NucleicAcidSpectrumGenerator.h:120
IDFilter.h
NucleicAcidSearchEngine::PrecursorInfo::isotope
Size isotope
Definition: NucleicAcidSearchEngine.cpp:269
OpenMS::NucleicAcidSpectrumGenerator::add_all_precursor_charges_
bool add_all_precursor_charges_
Definition: NucleicAcidSpectrumGenerator.h:126
OpenMS::MSExperiment::ConstIterator
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:106
OpenMS::AASequence::fromString
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
OpenMS::Precursor::setCharge
void setCharge(Int charge)
Mutable access to the charge.
OpenMS::IdentificationData::calculateCoverages
void calculateCoverages(bool check_molecule_length=false)
Calculate sequence coverages of parent sequences.
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::PeakFileOptions::setMSLevels
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
OpenMS::NucleicAcidSpectrumGenerator::y_intensity_
double y_intensity_
Definition: NucleicAcidSpectrumGenerator.h:133
NucleicAcidSearchEngine::resolveAmbiguousMods_
void resolveAmbiguousMods_(HitsByScore &hits)
Definition: NucleicAcidSearchEngine.cpp:678
SpectrumAlignment.h
OpenMS::MetaboliteSpectralMatching::computeHyperScore
static double computeHyperScore(double fragment_mass_error, bool fragment_mass_tolerance_unit_ppm, const MSSpectrum &exp_spectrum, const MSSpectrum &db_spectrum, double mz_lower_bound=0.0)
hyperscore computation
OpenMS::Exception::ElementNotFound
Element could not be found exception.
Definition: Exception.h:674
OpenMS::Constants::C13C12_MASSDIFF_U
const double C13C12_MASSDIFF_U
Definition: Constants.h:121
OpenMS::RNaseDigestion
Class for the enzymatic digestion of RNAs.
Definition: RNaseDigestion.h:52
PeptideIdentification.h
OpenMS::IdentificationDataInternal::ObservationMatch
Representation of a search hit (e.g. peptide-spectrum match).
Definition: ObservationMatch.h:73
OpenMS::MSExperiment::getNrSpectra
Size getNrSpectra() const
get the total number of spectra available
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
OpenMS::NucleicAcidSpectrumGenerator::w_intensity_
double w_intensity_
Definition: NucleicAcidSpectrumGenerator.h:131
OpenMS::PeptideIdentification::setMZ
void setMZ(double mz)
sets the MZ of the MS2 spectrum
FalseDiscoveryRate.h
OpenMS::MzMLFile::setOptions
void setOptions(const PeakFileOptions &)
set options for loading/storing
OpenMS::IdentificationDataInternal::DBSearchParam::molecule_type
enum MoleculeType molecule_type
Definition: DBSearchParam.h:49
OpenMS::TOPPBase::main
ExitCodes main(int argc, const char **argv)
Main routine of all TOPP applications.
StandardTypes.h
MetaboliteSpectralMatching.h
OpenMS::NucleicAcidSpectrumGenerator::precursor_intensity_
double precursor_intensity_
Definition: NucleicAcidSpectrumGenerator.h:136
OpenMS::NLargest::filterPeakSpectrum
void filterPeakSpectrum(PeakSpectrum &spectrum)
NucleicAcidSearchEngine::HitsByScore
multimap< double, AnnotatedHit, greater< double > > HitsByScore
Definition: NucleicAcidSearchEngine.cpp:289
File.h
OpenMS::OMSFile::load
void load(const String &filename, IdentificationData &id_data)
Read in a OMS file and construct an IdentificationData object.
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!
TOPPBase.h
NucleicAcidSearchEngine::HasInvalidLength
Definition: NucleicAcidSearchEngine.cpp:334
OpenMS::PeptideIdentification::setScoreType
void setScoreType(const String &type)
sets the peptide score type
MSSpectrum.h
OpenMS::SpectrumLookup::findByScanNumber
Size findByScanNumber(Size scan_number) const
Look up spectrum by scan number (extracted from the native ID).
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
ThresholdMower.h
NucleicAcidSearchEngine::resolve_ambiguous_mods_
bool resolve_ambiguous_mods_
Definition: NucleicAcidSearchEngine.cpp:157
NucleicAcidSearchEngine
Definition: NucleicAcidSearchEngine.cpp:141
NucleicAcidSearchEngine::registerOptionsAndFlags_
void registerOptionsAndFlags_() override
Sets the valid command line options (with argument) and flags (without argument).
Definition: NucleicAcidSearchEngine.cpp:160
OpenMS::PeptideHit::setScore
void setScore(double score)
sets the PSM score
NucleicAcidSearchEngine::NucleicAcidSearchEngine
NucleicAcidSearchEngine()
Definition: NucleicAcidSearchEngine.cpp:147
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55