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OpenMS
2.4.0
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107 use_ms1_traces_(use_ms1_traces)
114 void MS1Extraction_(
const std::vector< OpenSwath::SwathMap > & swath_maps,
115 std::map< std::string, OpenSwath::ChromatogramPtr >& ms1_chromatograms,
120 bool load_into_memory,
121 bool ms1only =
false);
140 void prepareExtractionCoordinates_(std::vector< OpenSwath::ChromatogramPtr > & chrom_list,
141 std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > & coordinates,
201 std::vector< OpenSwath::SwathMap > & swath_maps,
204 const Param & feature_finder_param,
206 const Param & irt_detection_param,
207 const String & mz_correction_function,
208 const String& irt_mzml_out,
211 bool load_into_memory =
false);
231 const std::vector< OpenMS::MSChromatogram >& chromatograms,
234 const Param& default_ffparam,
235 const Param& irt_detection_param,
236 std::vector< OpenSwath::SwathMap > & swath_maps,
237 const String & mz_correction_function,
238 double mz_extraction_window,
242 void simpleExtractChromatograms(
const std::vector< OpenSwath::SwathMap > & swath_maps,
244 std::vector< OpenMS::MSChromatogram > & chromatograms,
248 bool load_into_memory);
297 void performExtraction(
const std::vector< OpenSwath::SwathMap > & swath_maps,
300 const Param & feature_finder_param,
308 bool load_into_memory);
316 void writeOutFeaturesAndChroms_(std::vector< OpenMS::MSChromatogram > & chromatograms,
339 void scoreAllChromatograms(
341 const std::map< std::string, OpenSwath::ChromatogramPtr > & ms1_chromatograms,
342 const std::vector< OpenSwath::SwathMap >& swath_maps,
344 const Param& feature_finder_param,
346 const double rt_extraction_window,
350 bool ms1only =
false);
379 void copyBatchTransitions_(
const std::vector<OpenSwath::LightCompound>& used_compounds,
380 const std::vector<OpenSwath::LightTransition>& all_transitions,
381 std::vector<OpenSwath::LightTransition>& output);
429 void performExtractionSonar(
const std::vector< OpenSwath::SwathMap > & swath_maps,
432 const Param & feature_finder_param,
440 bool load_into_memory);
445 void computeSonarWindows_(
const std::vector< OpenSwath::SwathMap > & swath_maps,
446 double & sonar_winsize,
447 double & sonar_start,
449 int & sonar_total_win);
454 void performSonarExtraction_(
const std::vector< OpenSwath::SwathMap > & used_maps,
455 const std::vector< ChromatogramExtractor::ExtractionCoordinates > & coordinates,
456 std::vector< OpenSwath::ChromatogramPtr > & chrom_list,
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
This class supports reading and writing of PQP files.
Definition: TransitionPQPFile.h:57
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
@ SQMASS
SqLite format for mass and chromatograms.
Definition: FileTypes.h:103
std::vector< OpenSwath::SwathMap > loadSplit(StringList file_list, String tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, String readoptions="normal")
Loads a Swath run from a list of split mzML files.
TransformationDescription performRTNormalization(const OpenSwath::LightTargetedExperiment &irt_transitions, std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const String &mz_correction_function, const String &irt_mzml_out, Size debug_level, bool sonar=false, bool load_into_memory=false)
Perform RT and m/z correction of the input data using RT-normalization peptides.
double linear_fp_mass_acc
whether to estimate the fixed point or use the one proved with numpressFixedPoint
Definition: MSNumpressCoder.h:76
void setMinFloat(const String &key, double min)
Sets the minimum value for the floating point or floating point list parameter key.
void setCompression(const std::string &compression)
set compression using a string mapping to enum NumpressCompression.
Definition: MSNumpressCoder.h:94
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:67
Invalid value exception.
Definition: Exception.h:335
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:93
@ MZML
MzML file (.mzML)
Definition: FileTypes.h:72
@ MZXML
MzXML file (.mzXML)
Definition: FileTypes.h:64
bool estimate_fixed_point
which compression schema to use
Definition: MSNumpressCoder.h:75
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
Class to write out an OpenSwath TSV output (mProphet input)
Definition: OpenSwathTSVWriter.h:56
Description of the experimental settings.
Definition: ExperimentalSettings.h:58
A more convenient string class.
Definition: String.h:57
Class to write out an OpenSwath OSW SQLite output (PyProphet input)
Definition: OpenSwathOSWWriter.h:58
Class to execute an OpenSwath Workflow.
Definition: OpenSwathWorkflow.h:261
void setValidStrings(const String &key, const std::vector< String > &strings)
Sets the valid strings for the parameter key.
#define LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:446
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
void setNumpressConfigurationMassTime(MSNumpressCoder::NumpressConfig config)
Get numpress configuration options for m/z or rt dimension.
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
void load(const String &filename, TargetedExperiment &id)
Loads a map from a TraML file.
@ TSV
msInspect file (.tsv)
Definition: FileTypes.h:87
Consumer class that perform no operation.
Definition: MSDataWritingConsumer.h:258
PeakFileOptions & getOptions()
Get the peak file options.
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
@ UNKNOWN
Unknown file extension.
Definition: FileTypes.h:60
Definition: TransitionExperiment.h:206
void endProgress() const
Ends the progress display.
void setExperimentalSettings(const ExperimentalSettings &exp) override
Set experimental settings for the whole file.
double numpressErrorTolerance
fixed point for numpress algorithms
Definition: MSNumpressCoder.h:73
static void convertTargetedExp(const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)
convert from the OpenMS TargetedExperiment to the LightTargetedExperiment
std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:238
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
std::vector< LightCompound > & getCompounds()
Definition: TransitionExperiment.h:228
void setNumpressConfigurationIntensity(MSNumpressCoder::NumpressConfig config)
Get numpress configuration options for intensity dimension.
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:218
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
A data consumer that inserts MS data into a SQLite database.
Definition: MSDataSqlConsumer.h:60
OpenSwathWorkflowSonar(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:399
void setMinInt(const String &key, Int min)
Sets the minimum value for the integer or integer list parameter key.
Type
Actual file types enum.
Definition: FileTypes.h:58
OpenSwathWorkflow(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:269
void setMaxFloat(const String &key, double max)
Sets the maximum value for the floating point or floating point list parameter key.
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenSwath::LightTransition TransitionType
Definition: OpenSwathWorkflow.h:264
bool hasSuffix(const String &string) const
true if String ends with string, false otherwise
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
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.
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)
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
@ SMOOTHING
Smoothing of the signal to reduce noise.
Definition: DataProcessing.h:63
bool use_ms1_traces_
Whether to use the MS1 traces.
Definition: OpenSwathWorkflow.h:157
OpenSwathRetentionTimeNormalization(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:175
void setExpectedSize(Size expectedSpectra, Size expectedChromatograms) override
Set expected size of spectra and chromatograms to be written.
A container for features.
Definition: FeatureMap.h:93
@ PQP
OpenSWATH Peptide Query Parameter (PQP) SQLite DB.
Definition: FileTypes.h:104
virtual void addDataProcessing(DataProcessing d)
Optionally add a data processing method to each chromatogram and spectrum.
void remove(const String &key)
Remove the entry key or a section key (when suffix is ':')
Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:240
OpenSwathRetentionTimeNormalization()
Definition: OpenSwathWorkflow.h:170
Definition: OpenSwathWorkflow.h:100
MRMTransitionGroup< MSChromatogram, TransitionType > MRMTransitionGroupType
Definition: OpenSwathWorkflow.h:265
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:89
The representation of a group of transitions in a targeted proteomics experiment.
Definition: MRMTransitionGroup.h:67
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
@ QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
void setCompression(bool compress)
File adapter for Swath files.
Definition: SwathFile.h:62
static Type nameToType(const String &name)
Converts a file type name into a Type.
The representation of a chromatogram.
Definition: MSChromatogram.h:54
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:70
static bool SortPairDoubleByFirst(const std::pair< double, double > &left, const std::pair< double, double > &right)
Definition: OpenSwathWorkflow.cpp:81
@ TRAML
TraML (HUPO PSI format) for transitions (.traML)
Definition: FileTypes.h:81
Class to execute an OpenSwath Workflow for SONAR data.
Definition: OpenSwathWorkflow.h:394
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
Simple OpenSwathWorkflow to perform RT and m/z correction based on a set of known peptides.
Definition: OpenSwathWorkflow.h:165
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.
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:170
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
void setWriteIndex(bool write_index)
Whether to write an index at the end of the file (e.g. indexedmzML file format)
static void annotateSwathMapsFromFile(const std::string &filename, std::vector< OpenSwath::SwathMap > &swath_maps, bool doSort)
Annotate a Swath map using a Swath window file specifying the individual windows.
OpenSwathWorkflowBase(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:106
std::vector< OpenSwath::SwathMap > loadSqMass(String file, boost::shared_ptr< ExperimentalSettings > &)
Loads a Swath run from a single sqMass file.
Definition: TransitionExperiment.h:46
OpenSwath::SpectrumAccessPtr ms1_map_
Spectrum Access to the MS1 map (note that this is *not* threadsafe!)
Definition: OpenSwathWorkflow.h:154
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
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.
static String typeToName(Type type)
Returns the name/extension of the type.