 |
OpenMS
2.4.0
|
Go to the documentation of this file.
58 return transition_group_id +
"_Precursor_i" +
String(isotope);
74 double min_upper_edge_dist,
75 double lower,
double upper);
90 double min_upper_edge_dist,
91 double lower,
double upper);
111 double& lower,
double& upper);
124 template <
class TargetedExperimentT>
126 const TargetedExperimentT& targeted_exp,
127 TargetedExperimentT& selected_transitions,
128 double min_upper_edge_dist)
130 if (exp.
size() == 0 || exp[0].getPrecursors().
size() == 0)
133 <<
" does not have any experiments or any precursors. Is it a SWATH map? "
134 <<
"I will move to the next map."
141 if (selected_transitions.getTransitions().size() == 0)
144 <<
" no transition were within the precursor window of " << lower <<
" to " << upper
168 bool useQualCutoff =
false,
169 double qualCutoff = 0.0);
Definition: OpenMSInfo.cpp:68
double percTIC
Definition: OPXLDataStructs.h:130
Integer data array class.
Definition: DataArrays.h:51
void validateTargetedExperiment(const OpenMS::TargetedExperiment &targeted_exp)
Validate a TargetedExperiment (check that all ids are unique)
double total_current
Definition: OPXLDataStructs.h:136
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:118
void registerOptionsAndFlags_() override
Sets the valid command line options (with argument) and flags (without argument).
Definition: OpenPepXLLF.cpp:161
int main(int argc, const char **argv)
Definition: OpenPepXL.cpp:1464
Size ensureUniqueId()
Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was cha...
Definition: UniqueIdInterface.h:158
This class supports reading and writing of OpenSWATH transition lists.
Definition: TransitionTSVFile.h:142
Base class for TOPP applications.
Definition: TOPPBase.h:150
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a MzIdentML file.
This class supports reading and writing of PQP files.
Definition: TransitionPQPFile.h:57
double xcorrx_max
Definition: OPXLDataStructs.h:145
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
void store(const String &filename, const TargetedExperiment &id) const
Stores a map in a TraML file.
const std::vector< Peptide > & getPeptides() const
Size matched_linear_alpha
Definition: OPXLDataStructs.h:147
MSExperiment spectra_xlink_peaks
Definition: OPXLDataStructs.h:298
PeakMap MapType
Definition: PeakPickerIterative.cpp:84
const Map< String, std::vector< CVTerm > > & getCVTerms() const
returns the accession string of the term
ProteinProteinCrossLink cross_link
structure of the cross-link
Definition: OPXLDataStructs.h:115
virtual void getLinearIonSpectrum(PeakSpectrum &spectrum, AASequence &peptide, Size link_pos, bool frag_alpha, int charge=1, Size link_pos_2=0) const
Generates fragment ions not containing the cross-linker for one peptide.
double wTIC
Definition: OPXLDataStructs.h:131
void registerOptionsAndFlags_() override
Sets the valid command line options (with argument) and flags (without argument).
Definition: OpenPepXL.cpp:169
String getOSAsString() const
Definition: OpenMSInfo.cpp:80
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
@ DATA_PROCESSING
General data processing (if no other term applies)
Definition: DataProcessing.h:60
int precursor_correction
Definition: OPXLDataStructs.h:81
void setEnzyme(const String &name)
Sets the enzyme for the digestion (by name)
Comparator to sort CrossLinkSpectrumMatches by the main score.
Definition: OPXLDataStructs.h:179
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:451
void generateDecoys(const OpenMS::TargetedExperiment &exp, OpenMS::TargetedExperiment &dec, const String &method, const double aim_decoy_fraction, const bool switchKR, const String &decoy_tag, const int max_attempts, const double identity_threshold, const double precursor_mz_shift, const double product_mz_shift, const double product_mz_threshold, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, const bool enable_specific_losses, const bool enable_unspecific_losses, const int round_decPow=-4) const
Generate decoys from a TargetedExperiment.
const String & getIdentifier() const
retrieve document identifier (e.g. an LSID)
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
static String getTime()
Return the build time of OpenMS.
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:93
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:119
@ MRM
SpectraST MRM List.
Definition: FileTypes.h:102
std::vector< String > protein_refs
Definition: TargetedExperimentHelper.h:535
@ MZML
MzML file (.mzML)
Definition: FileTypes.h:72
@ MZXML
MzXML file (.mzXML)
Definition: FileTypes.h:64
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:113
Description of the experimental settings.
Definition: ExperimentalSettings.h:58
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
double score
final score
Definition: OPXLDataStructs.h:122
This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object.
Definition: MRMDecoy.h:88
Precondition failed exception.
Definition: Exception.h:166
static ModificationsDB * getInstance(OpenMS::String unimod_file="CHEMISTRY/unimod.xml", OpenMS::String psimod_file="CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file="CHEMISTRY/XLMOD.obo")
Returns a pointer to the modifications DB (singleton)
Definition: ModificationsDB.h:77
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:65
@ OS_WINDOWS
Definition: OpenMSInfo.cpp:58
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
void pickExperiment(PeakMap &chromatograms, FeatureMap &output, TargetedExperiment &transition_exp, TransformationDescription trafo, PeakMap &swath_map)
Picker and prepare functions.
void addMSLevel(int level)
adds a desired MS level for peaks to load
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double getMonoWeight(Residue::ResidueType type=Residue::Full, Int charge=0) const
static bool contains(const std::vector< T > &container, const E &elem)
Checks whether the element elem is contained in the given container.
Definition: ListUtils.h:149
static String removeExtension(const String &file)
static bool checkSwathMapAndSelectTransitions(const OpenMS::PeakMap &exp, const TargetedExperimentT &targeted_exp, TargetedExperimentT &selected_transitions, double min_upper_edge_dist)
Check the map and select transition in one function.
Definition: OpenSwathHelper.h:125
OPXLDataStructs::PreprocessedPairSpectra preprocessPairs_(const PeakMap &spectra, const vector< 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)
Definition: OpenPepXL.cpp:277
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
void reannotateTransitions(OpenMS::TargetedExperiment &exp, double precursor_mz_threshold, double product_mz_threshold, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, int round_decPow=-4)
Annotates and filters transitions in a TargetedExperiment.
void load(const String &filename, TargetedExperiment &id)
Loads a map from a TraML file.
@ TSV
msInspect file (.tsv)
Definition: FileTypes.h:87
void convertTargetedExperimentToTSV(const char *filename, OpenMS::TargetedExperiment &targeted_exp)
Write out a targeted experiment (TraML structure) into a tsv file.
IntensityType getIntensity() const
Definition: Peak2D.h:166
database which holds all residue modifications from UniMod
Definition: ModificationsDB.h:72
String toString() const
returns the peptide as string with modifications embedded in brackets
Size matched_xlink_beta
Definition: OPXLDataStructs.h:150
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
ExitCodes run(std::vector< FASTAFile::FASTAEntry > &proteins, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)
forward for old interface and pyOpenMS; use run<T>() for more control
Definition: PeptideIndexing.h:147
TOPPOpenPepXLLF()
Definition: OpenPepXLLF.cpp:155
@ ARCH_32BIT
Definition: OpenMSInfo.cpp:60
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:58
@ OS_MACOS
Definition: OpenMSInfo.cpp:58
double ppm_error_abs_sum_xlinks_alpha
Definition: OPXLDataStructs.h:160
std::string OpenMS_OSNames[]
Definition: OpenMSInfo.cpp:59
@ UNKNOWN
Unknown file extension.
Definition: FileTypes.h:60
const double PROTON_MASS_U
Definition: TransitionExperiment.h:206
int main(int argc, const char **argv)
Definition: OpenPepXLLF.cpp:1262
void uisTransitions(OpenMS::TargetedExperiment &exp, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, double mz_threshold, const std::vector< std::pair< double, double > > &swathes, int round_decPow=-4, size_t max_num_alternative_localizations=20, int shuffle_seed=-1, bool disable_decoy_transitions=false)
Annotate UIS / site-specific transitions.
void endProgress() const
Ends the progress display.
static OpenMSOSInfo getOSInfo()
Definition: OpenMSInfo.cpp:92
virtual void getXLinkIonSpectrum(PeakSpectrum &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, bool frag_alpha, int mincharge, int maxcharge, Size link_pos_2=0) const
Generates fragment ions containing the cross-linker for one peptide.
@ DECOY
Decoy transition.
Definition: ReactionMonitoringTransition.h:71
double log_occupancy_beta
Definition: OPXLDataStructs.h:144
void setMissedCleavages(Size missed_cleavages)
Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when lo...
Size size() const
Definition: MSExperiment.h:127
NLargest removes all but the n largest peaks.
Definition: NLargest.h:54
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:109
double ppm_error_abs_sum
Definition: OPXLDataStructs.h:166
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:115
static String computePrecursorId(const String &transition_group_id, int isotope)
Compute unique precursor identifier.
Definition: OpenSwathHelper.h:56
static void convertTargetedExp(const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)
convert from the OpenMS TargetedExperiment to the LightTargetedExperiment
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
TOPPOpenPepXL()
Definition: OpenPepXL.cpp:163
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:109
double wTICold
Definition: OPXLDataStructs.h:132
bool hasPeptide(const String &ref) const
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:294
A helper class that is used by several OpenSWATH tools.
Definition: OpenSwathHelper.h:48
static bool isInstantiated()
Check whether ModificationsDB was instantiated before.
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
double xcorrc_max
Definition: OPXLDataStructs.h:146
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
ProteinProteinCrossLinkType getType() const
Definition: OPXLDataStructs.h:83
Used to load and store xQuest result files.
Definition: XQuestResultXMLFile.h:55
String sequence
Definition: TargetedExperimentHelper.h:537
Scoring of an spectrum given library intensities of a transition group.
Definition: DIAPrescoring.h:64
double num_iso_peaks_mean_linear_beta
Definition: OPXLDataStructs.h:154
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:218
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:112
double ppm_error_abs_sum_linear
Definition: OPXLDataStructs.h:162
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:110
double ppm_error_abs_sum_xlinks
Definition: OPXLDataStructs.h:163
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
#define LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:450
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
@ ARCH_64BIT
Definition: OpenMSInfo.cpp:60
double intsum_beta
Definition: OPXLDataStructs.h:135
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...
double num_iso_peaks_mean
Definition: OPXLDataStructs.h:152
std::vector< DataProcessingPtr > & getDataProcessing()
returns a mutable reference to the description of the applied processing
double ppm_error_abs_sum_linear_beta
Definition: OPXLDataStructs.h:159
std::vector< PeptideHit::PeakAnnotation > frag_annotations
Definition: OPXLDataStructs.h:170
String db
The used database.
Definition: ProteinIdentification.h:106
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
double log_occupancy_alpha
Definition: OPXLDataStructs.h:143
double ppm_error_abs_sum_beta
Definition: OPXLDataStructs.h:165
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
@ OS_LINUX
Definition: OpenMSInfo.cpp:58
void setStrictFlag(bool f)
Set the flag for strict mapping.
Definition: MRMFeatureFinderScoring.h:193
Type
Actual file types enum.
Definition: FileTypes.h:58
Unable to create file exception.
Definition: Exception.h:636
@ ARCH_UNKNOWN
Definition: OpenMSInfo.cpp:60
DecoyTransitionType getDecoyTransitionType() const
Returns the type of transition (target or decoy)
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
double num_iso_peaks_mean_linear_alpha
Definition: OPXLDataStructs.h:153
void setChromatograms(const std::vector< MSChromatogram > &chromatograms)
sets the chromatogram list
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:113
Size size() const
returns the number of residues
void detectingTransitions(OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions)
Select detecting fragment ions.
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
double match_odds
Definition: OPXLDataStructs.h:139
bool hasCharge() const
Whether peptide or compound has set charge state.
Definition: TargetedExperimentHelper.h:314
T round(T x)
Rounds the value.
Definition: MathFunctions.h:138
double ppm_error_abs_sum_alpha
Definition: OPXLDataStructs.h:164
void setPrecursors(const std::vector< Precursor > &precursors)
sets the precursors
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL.
Definition: OPXLDataStructs.h:72
void setParameters(const Param ¶m)
Sets the parameters.
double num_iso_peaks_mean_xlinks_alpha
Definition: OPXLDataStructs.h:155
double xquest_score
counts, scores and other data for xQuest-like output
Definition: OPXLDataStructs.h:128
@ OS_UNKNOWN
Definition: OpenMSInfo.cpp:58
const Param & getDefaults() const
Non-mutable access to the default parameters.
double match_odds_beta
Definition: OPXLDataStructs.h:141
@ UNKNOWN
Unknown type.
Definition: ReactionMonitoringTransition.h:69
OpenMS_Architecture arch
Definition: OpenMSInfo.cpp:78
std::string OpenMS_ArchNames[]
Definition: OpenMSInfo.cpp:61
int precursor_correction
Definition: OPXLDataStructs.h:168
static String getVersion()
Return the version number of OpenMS.
const Param & getParameters() const
Non-mutable access to the parameters.
static OpenSwath::SpectrumAccessPtr getSpectrumAccessOpenMSPtr(boost::shared_ptr< OpenMS::PeakMap > exp)
Simple Factory method to get a SpectrumAccess Ptr from an MSExperiment.
Definition: DataFrameWriter.h:71
double intsum_alpha
Definition: OPXLDataStructs.h:134
void setIdentifier(const String &id)
set document identifier (e.g. an LSID)
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
double int_sum
Definition: OPXLDataStructs.h:133
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:114
void convertPQPToTargetedExperiment(const char *filename, OpenMS::TargetedExperiment &targeted_exp, bool legacy_traml_id=false)
Read in a PQP file and construct a targeted experiment (TraML structure)
std::vector< LightTransition > transitions
Definition: TransitionExperiment.h:215
vector< ResidueModification > getModifications_(StringList modNames)
Definition: OpenPepXLLF.cpp:264
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
Size matched_linear_beta
Definition: OPXLDataStructs.h:148
A container for consensus elements.
Definition: ConsensusMap.h:75
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
MSExperiment spectra_linear_peaks
Definition: OPXLDataStructs.h:297
void sortByPosition()
Lexicographically sorts the peaks by their position.
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
std::pair< SignedSize, SignedSize > cross_link_position
Definition: OPXLDataStructs.h:76
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:111
void convertTSVToTargetedExperiment(const char *filename, FileTypes::Type filetype, OpenMS::TargetedExperiment &targeted_exp)
Read in a tsv/mrm file and construct a targeted experiment (TraML structure)
MSExperiment spectra_all_peaks
Definition: OPXLDataStructs.h:299
void restrictTransitions(OpenMS::TargetedExperiment &exp, double lower_mz_limit, double upper_mz_limit, const std::vector< std::pair< double, double > > &swathes)
Restrict and filter transitions in a TargetedExperiment.
static String getRevision()
Return the revision number from revision control system, e.g. git.
static void checkSwathMap(const OpenMS::PeakMap &swath_map, double &lower, double &upper)
Get the lower / upper offset for this SWATH map and do some sanity checks.
bool hasCVTerm(const String &accession) const
checks whether the term has a value
ExitCodes main_(int, const char **) override
The actual "main" method. main_() is invoked by main().
Definition: OpenPepXLLF.cpp:278
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:116
static String getUserDirectory()
Size scan_index_heavy
Definition: OPXLDataStructs.h:119
double log_occupancy
Definition: OPXLDataStructs.h:142
void store(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.
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
A container for features.
Definition: FeatureMap.h:93
@ PQP
OpenSWATH Peptide Query Parameter (PQP) SQLite DB.
Definition: FileTypes.h:104
Definition: OpenPepXL.cpp:159
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
double ppm_error_abs_sum_xlinks_beta
Definition: OPXLDataStructs.h:161
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...
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
An LC-MS feature.
Definition: Feature.h:70
static double mean(IteratorType begin, IteratorType end)
Calculates the mean of a range of values.
Definition: StatisticFunctions.h:134
Class for the enzymatic digestion of proteins.
Definition: ProteaseDigestion.h:60
double cross_linker_mass
Definition: OPXLDataStructs.h:77
DataArrayT::iterator getDataArrayByName(DataArrayT &a, const String &name)
Helper functions for MSSpectrum and MSChromatogram.
Definition: SpectrumHelper.h:49
const std::vector< Protein > & getProteins() const
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:89
Definition: OpenPepXLLF.cpp:151
Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds ...
Definition: PeptideIndexing.h:123
static String getOpenMSDataPath()
Returns the OpenMS data path (environment variable overwrites the default installation path)
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
const Peptide & getPeptideByRef(const String &ref) const
String os_version
Definition: OpenMSInfo.cpp:77
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
void getPrimaryMSRunPath(StringList &toFill) const
get the file path to the first MS run
@ QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
ExitCodes
Exit codes.
Definition: TOPPBase.h:155
Int writtenDigits(const FloatingPointType &=FloatingPointType())
Number of digits commonly used for writing a floating point type (a.k.a. precision)....
Definition: Types.h:294
File adapter for Swath files.
Definition: SwathFile.h:62
static Type nameToType(const String &name)
Converts a file type name into a Type.
const std::vector< ReactionMonitoringTransition > & getTransitions() const
returns the transition list
String toString() const
Conversion to String.
const char * OpenMS_locale
void convertTargetedExperimentToPQP(const char *filename, OpenMS::TargetedExperiment &targeted_exp)
Write out a targeted experiment (TraML structure) into a PQP file.
@ TRAML
TraML (HUPO PSI format) for transitions (.traML)
Definition: FileTypes.h:81
Definition: ConfidenceScoring.h:58
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:63
void clearMSLevels()
clears the MS levels
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:117
std::vector< OpenSwath::SwathMap > loadMzXML(String file, String tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, String readoptions="normal")
Loads a Swath run from a single mzXML file.
Management and storage of parameters / INI files.
Definition: Param.h:74
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
std::vector< OpenSwath::SwathMap > loadMzML(String file, String tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, String readoptions="normal")
Loads a Swath run from a single mzML file.
Size getNumberOfModifications() const
Returns the number of modifications read from the unimod.xml file.
The CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum i...
Definition: OPXLDataStructs.h:112
void clear(bool clear_meta_data)
Clears all data and meta data.
double pre_score
Definition: OPXLDataStructs.h:129
static String getBranch()
Return the branch name from revision control system, e.g. git.
const std::vector< Feature > & getSubordinates() const
immutable access to subordinate features
void filterSpectrum(SpectrumType &spectrum)
Definition: NLargest.h:78
double num_iso_peaks_mean_xlinks_beta
Definition: OPXLDataStructs.h:156
OpenMS_Architecture
Definition: OpenMSInfo.cpp:60
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
Generates theoretical spectra for cross-linked peptides.
Definition: TheoreticalSpectrumGeneratorXLMS.h:56
const IntegerDataArrays & getIntegerDataArrays() const
Returns a const reference to the integer meta data arrays.
int getChargeState() const
Return the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:320
Generate assays from a TargetedExperiment.
Definition: MRMAssay.h:66
OpenMS_OS
Definition: OpenMSInfo.cpp:58
The AASeqWithMassComparator is a comparator for AASeqWithMass objects.
Definition: OPXLDataStructs.h:272
OpenMSOSInfo()
Definition: OpenMSInfo.cpp:70
const String & getPeptideRef() const
const double C13C12_MASSDIFF_U
double precursor_error_ppm
Definition: OPXLDataStructs.h:137
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a xQuest XML file.
static void selectSwathTransitions(const OpenMS::TargetedExperiment &targeted_exp, OpenMS::TargetedExperiment &selected_transitions, double min_upper_edge_dist, double lower, double upper)
Select transitions between lower and upper and write them into the new TargetedExperiment.
double ppm_error_abs_sum_linear_alpha
Definition: OPXLDataStructs.h:158
ExitCodes main_(int, const char **) override
The actual "main" method. main_() is invoked by main().
Definition: OpenPepXL.cpp:486
Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications.
Definition: IDMapper.h:66
AASequence alpha
Definition: OPXLDataStructs.h:74
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
@ TARGET
Target transition.
Definition: ReactionMonitoringTransition.h:70
Search parameters of the DB search.
Definition: ProteinIdentification.h:103
Float data array class.
Definition: DataArrays.h:45
String getArchAsString() const
Definition: OpenMSInfo.cpp:85
Size scan_index_light
reference to pair of spectra
Definition: OPXLDataStructs.h:118
const String & getLoadedFilePath() const
get the file_name_ which is the absolute path to the file loaded from
ExitCodes main(int argc, const char **argv)
Main routine of all TOPP applications.
UInt64 getUniqueId() const
Non-mutable access to unique id - returns the unique id.
Definition: UniqueIdInterface.h:109
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
Definition: DataFrameWriter.h:45
OpenMS_OS os
Definition: OpenMSInfo.cpp:76
static void readSwathWindows(const std::string &filename, std::vector< double > &swath_prec_lower_, std::vector< double > &swath_prec_upper_)
Reading a tab delimited file specifying the SWATH windows.
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
double match_odds_alpha
Definition: OPXLDataStructs.h:140
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
Used to load and store idXML files.
Definition: IdXMLFile.h:63
OpenMS_Architecture getBinaryArchitecture()
Definition: OpenMSInfo.cpp:191
static String typeToName(Type type)
Returns the name/extension of the type.
void annotate(PeakMap &map, const std::vector< PeptideIdentification > &peptide_ids, const std::vector< ProteinIdentification > &protein_ids, const bool clear_ids=false, const bool mapMS1=false)
Mapping method for peak maps.
Definition: IDMapper.h:96
Size matched_xlink_alpha
Definition: OPXLDataStructs.h:149
@ CMD
Command line progress.
Definition: ProgressLogger.h:72
AASequence beta
Definition: OPXLDataStructs.h:75