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OpenMS
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112 use_ms1_traces_(false),
113 use_ms1_ion_mobility_(false),
115 threads_outer_loop_(-1)
132 use_ms1_traces_(use_ms1_traces),
133 use_ms1_ion_mobility_(use_ms1_ion_mobility),
135 threads_outer_loop_(threads_outer_loop)
153 const std::vector< OpenSwath::SwathMap > & swath_maps,
154 std::vector< MSChromatogram >& ms1_chromatograms,
159 bool ms1only =
false,
160 int ms1_isotopes = 0);
179 void prepareExtractionCoordinates_(std::vector< OpenSwath::ChromatogramPtr > & chrom_list,
180 std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > & coordinates,
184 const bool ms1 =
false,
185 const int ms1_isotopes = -1)
const;
275 std::vector< OpenSwath::SwathMap > & swath_maps,
279 const Param & feature_finder_param,
281 const Param& irt_detection_param,
282 const Param& calibration_param,
283 const String& irt_mzml_out,
286 bool load_into_memory =
false);
320 const std::vector< OpenMS::MSChromatogram >& chromatograms,
322 std::vector< OpenSwath::SwathMap > & swath_maps,
325 const Param& default_ffparam,
326 const Param& irt_detection_param,
327 const Param& calibration_param);
340 void simpleExtractChromatograms_(
const std::vector< OpenSwath::SwathMap > & swath_maps,
342 std::vector< OpenMS::MSChromatogram > & chromatograms,
346 bool load_into_memory);
404 OpenSwathWorkflow(
bool use_ms1_traces,
bool use_ms1_ion_mobility,
bool prm,
int threads_outer_loop) :
434 void performExtraction(
const std::vector< OpenSwath::SwathMap > & swath_maps,
438 const Param & feature_finder_param,
441 bool store_features_in_featureFile,
447 bool load_into_memory);
466 void writeOutFeaturesAndChroms_(std::vector< OpenMS::MSChromatogram > & chromatograms,
508 void scoreAllChromatograms_(
509 const std::vector< OpenMS::MSChromatogram > & ms2_chromatograms,
510 const std::vector< OpenMS::MSChromatogram > & ms1_chromatograms,
511 const std::vector< OpenSwath::SwathMap >& swath_maps,
513 const Param& feature_finder_param,
515 const double rt_extraction_window,
519 int nr_ms1_isotopes = 0,
520 bool ms1only =
false)
const;
550 void copyBatchTransitions_(
const std::vector<OpenSwath::LightCompound>& used_compounds,
551 const std::vector<OpenSwath::LightTransition>& all_transitions,
552 std::vector<OpenSwath::LightTransition>& output);
612 void performExtractionSonar(
const std::vector< OpenSwath::SwathMap > & swath_maps,
616 const Param & feature_finder_param,
624 bool load_into_memory);
629 void computeSonarWindows_(
const std::vector< OpenSwath::SwathMap > & swath_maps,
630 double & sonar_winsize,
631 double & sonar_start,
633 int & sonar_total_win);
638 void performSonarExtraction_(
const std::vector< OpenSwath::SwathMap > & used_maps,
639 const std::vector< ChromatogramExtractor::ExtractionCoordinates > & coordinates,
640 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:154
This class supports reading and writing of OpenSWATH transition lists.
Definition: TransitionTSVFile.h:144
String extraction_function
The extraction function in mass space.
Definition: OpenSwathWorkflow.h:93
double extra_rt_extract
Whether to extract some extra in the retention time (can be useful if one wants to look at the chroma...
Definition: OpenSwathWorkflow.h:97
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
SqLite format for mass and chromatograms, see SqMassFile.
Definition: FileTypes.h:103
void simpleExtractChromatograms_(const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::LightTargetedExperiment &irt_transitions, std::vector< OpenMS::MSChromatogram > &chromatograms, const TransformationDescription &trafo, const ChromExtractParams &cp, bool sonar, bool load_into_memory)
Simple method to extract chromatograms (for the RT-normalization peptides)
void setMinFloat(const String &key, double min)
Sets the minimum value for the floating point or floating point list parameter key.
bool prm_
Whether data is acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows.
Definition: OpenSwathWorkflow.h:204
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
OpenSwathWorkflowBase(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, int threads_outer_loop)
Constructor.
Definition: OpenSwathWorkflow.h:131
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
OpenSwathCalibrationWorkflow(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:245
double min_upper_edge_dist
Whether to not extract anything closer than this (in Da) from the upper edge.
Definition: OpenSwathWorkflow.h:85
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:129
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
A more convenient string class.
Definition: String.h:59
Class to write out an OpenSwath OSW SQLite output (PyProphet input).
Definition: OpenSwathOSWWriter.h:115
Execute all steps in an OpenSwath analysis.
Definition: OpenSwathWorkflow.h:382
void setValidStrings(const String &key, const std::vector< String > &strings)
Sets the valid strings for the parameter key.
OpenSwathWorkflowBase()
Default constructor.
Definition: OpenSwathWorkflow.h:111
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double mz_extraction_window
Extraction window in Da or ppm (e.g. 50ppm means extraction +/- 25ppm)
Definition: OpenSwathWorkflow.h:87
Definition: OpenSwathBase.h:84
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
double rt_extraction_window
The retention time extraction window.
Definition: OpenSwathWorkflow.h:95
Unknown file extension.
Definition: FileTypes.h:60
Definition: TransitionExperiment.h:207
Quality Control function for OpenSwath.
Definition: SwathQC.h:63
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.
std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:239
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::vector< LightCompound > & getCompounds()
Definition: TransitionExperiment.h:229
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:219
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
bool use_ms1_ion_mobility_
Whether to use ion mobility extraction on MS1 traces.
Definition: OpenSwathWorkflow.h:201
OpenSwathWorkflowSonar(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:586
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
TransformationDescription doDataNormalization_(const OpenSwath::LightTargetedExperiment &transition_exp_, const std::vector< OpenMS::MSChromatogram > &chromatograms, TransformationDescription &im_trafo, std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &default_ffparam, const Param &irt_detection_param, const Param &calibration_param)
Perform retention time and m/z calibration.
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
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)
bool ppm
Whether the extraction window is given in ppm or Da.
Definition: OpenSwathWorkflow.h:91
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenSwath::LightTransition TransitionType
Definition: OpenSwathWorkflow.h:385
Execute all steps for retention time and m/z calibration of SWATH-MS data.
Definition: OpenSwathWorkflow.h:235
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenSwathCalibrationWorkflow()
Definition: OpenSwathWorkflow.h:240
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
bool use_ms1_traces_
Whether to use the MS1 traces.
Definition: OpenSwathWorkflow.h:198
A class containing correction functions for Swath MS maps.
Definition: SwathMapMassCorrection.h:52
A container for features.
Definition: FeatureMap.h:97
OpenSWATH Peptide Query Parameter (PQP) SQLite DB, see TransitionPQPFile.
Definition: FileTypes.h:104
void remove(const String &key)
Remove the entry key or a section key (when suffix is ':')
Definition: OpenSwathWorkflow.h:100
MRMTransitionGroup< MSChromatogram, TransitionType > MRMTransitionGroupType
Definition: OpenSwathWorkflow.h:386
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.
Definition: DataProcessing.h:72
static Type nameToType(const String &name)
Converts a file type name into a Type.
The representation of a chromatogram.
Definition: MSChromatogram.h:54
double im_extraction_window
Extraction window in ion mobility.
Definition: OpenSwathWorkflow.h:89
int threads_outer_loop_
How many threads should be used for the outer loop.
Definition: OpenSwathWorkflow.h:215
Execute all steps in an OpenEcho analysis (OpenSwath for SONAR data)
Definition: OpenSwathWorkflow.h:580
OpenSwathWorkflow(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, int threads_outer_loop)
Constructor.
Definition: OpenSwathWorkflow.h:404
Management and storage of parameters / INI files.
Definition: Param.h:73
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:172
String & ensureLastChar(char end)
Makes sure the string ends with the character end.
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
Definition: TransitionExperiment.h:46
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
static String typeToName(Type type)
Returns the name/extension of the type.