OpenMS  2.4.0
OpenSwathWorkflow.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 // Interfaces
42 
43 #include <OpenMS/FORMAT/MzMLFile.h> // debug file store only
44 
45 // Kernel and implementations
51 
52 // Helpers
54 // #include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/DataAccessHelper.h>
58 
59 // Algorithms
66 
67 #include <cassert>
68 #include <limits>
69 
70 // #define OPENSWATH_WORKFLOW_DEBUG
71 
72 // The workflow class
73 namespace OpenMS
74 {
75 
83  {
91  bool ppm;
98  };
99 
100  class OPENMS_DLLAPI OpenSwathWorkflowBase :
101  public ProgressLogger
102  {
103 
104 protected:
105 
106  explicit OpenSwathWorkflowBase(bool use_ms1_traces) :
107  use_ms1_traces_(use_ms1_traces)
108  {
109  }
110 
114  void MS1Extraction_(const std::vector< OpenSwath::SwathMap > & swath_maps,
115  std::map< std::string, OpenSwath::ChromatogramPtr >& ms1_chromatograms,
116  Interfaces::IMSDataConsumer * chromConsumer,
117  const ChromExtractParams & cp,
118  const OpenSwath::LightTargetedExperiment& transition_exp,
119  const TransformationDescription& trafo_inverse,
120  bool load_into_memory,
121  bool ms1only = false);
122 
140  void prepareExtractionCoordinates_(std::vector< OpenSwath::ChromatogramPtr > & chrom_list,
141  std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > & coordinates,
142  const OpenSwath::LightTargetedExperiment & transition_exp_used,
143  const bool ms1, const TransformationDescription trafo_inverse,
144  const ChromExtractParams & cp) const;
145 
146 
155 
158 
159 
160  };
161 
166  public OpenSwathWorkflowBase
167  {
168  public:
169 
171  OpenSwathWorkflowBase(false)
172  {
173  }
174 
175  explicit OpenSwathRetentionTimeNormalization(bool use_ms1_traces) :
176  OpenSwathWorkflowBase(use_ms1_traces)
177  {
178  }
179 
200  TransformationDescription performRTNormalization(const OpenSwath::LightTargetedExperiment & irt_transitions,
201  std::vector< OpenSwath::SwathMap > & swath_maps,
202  double min_rsq,
203  double min_coverage,
204  const Param & feature_finder_param,
205  const ChromExtractParams & cp_irt,
206  const Param & irt_detection_param,
207  const String & mz_correction_function,
208  const String& irt_mzml_out,
209  Size debug_level,
210  bool sonar = false,
211  bool load_into_memory = false);
212 
213  public:
214 
230  TransformationDescription RTNormalization(const OpenSwath::LightTargetedExperiment& transition_exp_,
231  const std::vector< OpenMS::MSChromatogram >& chromatograms,
232  double min_rsq,
233  double min_coverage,
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,
239  bool ppm);
240 
242  void simpleExtractChromatograms(const std::vector< OpenSwath::SwathMap > & swath_maps,
243  const OpenSwath::LightTargetedExperiment & irt_transitions,
244  std::vector< OpenMS::MSChromatogram > & chromatograms,
245  const TransformationDescription& trafo,
246  const ChromExtractParams & cp,
247  bool sonar,
248  bool load_into_memory);
249 
250  static void addChromatograms(MSChromatogram& base_chrom, const MSChromatogram& newchrom);
251  };
252 
261  class OPENMS_DLLAPI OpenSwathWorkflow :
262  public OpenSwathWorkflowBase
263  {
266 
267  public:
268 
269  explicit OpenSwathWorkflow(bool use_ms1_traces) :
270  OpenSwathWorkflowBase(use_ms1_traces)
271  {
272  }
273 
297  void performExtraction(const std::vector< OpenSwath::SwathMap > & swath_maps,
298  const TransformationDescription trafo,
299  const ChromExtractParams & cp,
300  const Param & feature_finder_param,
301  const OpenSwath::LightTargetedExperiment& transition_exp,
302  FeatureMap& out_featureFile,
303  bool store_features,
304  OpenSwathTSVWriter & tsv_writer,
305  OpenSwathOSWWriter & osw_writer,
306  Interfaces::IMSDataConsumer * chromConsumer,
307  int batchSize,
308  bool load_into_memory);
309 
310  protected:
311 
312 
316  void writeOutFeaturesAndChroms_(std::vector< OpenMS::MSChromatogram > & chromatograms,
317  const FeatureMap & featureFile,
318  FeatureMap& out_featureFile,
319  bool store_features,
320  Interfaces::IMSDataConsumer * chromConsumer);
321 
339  void scoreAllChromatograms(
340  const OpenSwath::SpectrumAccessPtr input,
341  const std::map< std::string, OpenSwath::ChromatogramPtr > & ms1_chromatograms,
342  const std::vector< OpenSwath::SwathMap >& swath_maps,
343  OpenSwath::LightTargetedExperiment& transition_exp,
344  const Param& feature_finder_param,
346  const double rt_extraction_window,
347  FeatureMap& output,
348  OpenSwathTSVWriter & tsv_writer,
349  OpenSwathOSWWriter & osw_writer,
350  bool ms1only = false);
351 
366  void selectCompoundsForBatch_(const OpenSwath::LightTargetedExperiment& transition_exp_used_all,
367  OpenSwath::LightTargetedExperiment& transition_exp_used, int batch_size, size_t j);
368 
379  void copyBatchTransitions_(const std::vector<OpenSwath::LightCompound>& used_compounds,
380  const std::vector<OpenSwath::LightTransition>& all_transitions,
381  std::vector<OpenSwath::LightTransition>& output);
382 
383  };
384 
394  class OPENMS_DLLAPI OpenSwathWorkflowSonar :
395  public OpenSwathWorkflow
396  {
397 
398  public:
399  explicit OpenSwathWorkflowSonar(bool use_ms1_traces) :
400  OpenSwathWorkflow(use_ms1_traces)
401  {}
402 
429  void performExtractionSonar(const std::vector< OpenSwath::SwathMap > & swath_maps,
430  const TransformationDescription trafo,
431  const ChromExtractParams & cp,
432  const Param & feature_finder_param,
433  const OpenSwath::LightTargetedExperiment& transition_exp,
434  FeatureMap& out_featureFile,
435  bool store_features,
436  OpenSwathTSVWriter & tsv_writer,
437  OpenSwathOSWWriter & osw_writer,
438  Interfaces::IMSDataConsumer * chromConsumer,
439  int batchSize,
440  bool load_into_memory);
441 
445  void computeSonarWindows_(const std::vector< OpenSwath::SwathMap > & swath_maps,
446  double & sonar_winsize,
447  double & sonar_start,
448  double & sonar_end,
449  int & sonar_total_win);
450 
454  void performSonarExtraction_(const std::vector< OpenSwath::SwathMap > & used_maps,
455  const std::vector< ChromatogramExtractor::ExtractionCoordinates > & coordinates,
456  std::vector< OpenSwath::ChromatogramPtr > & chrom_list,
457  const ChromExtractParams & cp);
458 
466  };
467 
468 }
469 
470 
OpenMS::UniqueIdInterface::ensureUniqueId
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
OpenMS::TransitionTSVFile
This class supports reading and writing of OpenSWATH transition lists.
Definition: TransitionTSVFile.h:142
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:150
OpenMS::TransitionPQPFile
This class supports reading and writing of PQP files.
Definition: TransitionPQPFile.h:57
LinearResamplerAlign.h
OpenMS::Param::copy
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::FileTypes::SQMASS
@ SQMASS
SqLite format for mass and chromatograms.
Definition: FileTypes.h:103
FileHandler.h
FileTypes.h
OpenMS::SwathFile::loadSplit
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.
OpenMS::OpenSwathRetentionTimeNormalization::performRTNormalization
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.
OpenMS::MSNumpressCoder::NumpressConfig::linear_fp_mass_acc
double linear_fp_mass_acc
whether to estimate the fixed point or use the one proved with numpressFixedPoint
Definition: MSNumpressCoder.h:76
OpenMS::Param::setMinFloat
void setMinFloat(const String &key, double min)
Sets the minimum value for the floating point or floating point list parameter key.
OpenMS::MSNumpressCoder::NumpressConfig::setCompression
void setCompression(const std::string &compression)
set compression using a string mapping to enum NumpressCompression.
Definition: MSNumpressCoder.h:94
OpenMS::Exception::IllegalArgument
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
OpenMS::ChromExtractParams::mz_extraction_window
double mz_extraction_window
Extraction window in Da or ppm (e.g. 50ppm means extraction +/- 25ppm)
Definition: OpenSwathWorkflow.h:87
OpenMS::ChromExtractParams::im_extraction_window
double im_extraction_window
Extraction window in ion mobility.
Definition: OpenSwathWorkflow.h:89
TransitionTSVFile.h
OpenSwathWorkflow.h
OpenMS::ChromExtractParams
ChromatogramExtractor parameters.
Definition: OpenSwathWorkflow.h:82
SwathMap.h
OpenMS::Interfaces::IMSDataConsumer
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:67
OpenMS::Exception::InvalidValue
Invalid value exception.
Definition: Exception.h:335
OpenMS::FileHandler::getTypeByFileName
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
OpenMS::MRMFeatureFinderScoring
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:93
SwathMapMassCorrection.h
OpenMS::FileTypes::MZML
@ MZML
MzML file (.mzML)
Definition: FileTypes.h:72
OpenMS::FileTypes::MZXML
@ MZXML
MzXML file (.mzXML)
Definition: FileTypes.h:64
OpenMS::MSNumpressCoder::NumpressConfig::estimate_fixed_point
bool estimate_fixed_point
which compression schema to use
Definition: MSNumpressCoder.h:75
OpenMS::Param::setValue
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
OpenMS::OpenSwathTSVWriter
Class to write out an OpenSwath TSV output (mProphet input)
Definition: OpenSwathTSVWriter.h:56
OpenMS::ExperimentalSettings
Description of the experimental settings.
Definition: ExperimentalSettings.h:58
OpenMS::String
A more convenient string class.
Definition: String.h:57
MSDataSqlConsumer.h
OpenMS::OpenSwathOSWWriter
Class to write out an OpenSwath OSW SQLite output (PyProphet input)
Definition: OpenSwathOSWWriter.h:58
MzMLFile.h
TransitionExperiment.h
ISpectrumAccess.h
OpenMS::OpenSwathWorkflow
Class to execute an OpenSwath Workflow.
Definition: OpenSwathWorkflow.h:261
OpenMS::Param::setValidStrings
void setValidStrings(const String &key, const std::vector< String > &strings)
Sets the valid strings for the parameter key.
SimpleOpenMSSpectraAccessFactory.h
LOG_ERROR
#define LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:446
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
FeatureXMLFile.h
OpenMS::PeakFileOptions::setNumpressConfigurationMassTime
void setNumpressConfigurationMassTime(MSNumpressCoder::NumpressConfig config)
Get numpress configuration options for m/z or rt dimension.
OpenMS::ChromExtractParams::rt_extraction_window
double rt_extraction_window
The retention time extraction window.
Definition: OpenSwathWorkflow.h:95
DataStructures.h
LOG_INFO
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
IMSDataConsumer.h
OpenMS::TraMLFile::load
void load(const String &filename, TargetedExperiment &id)
Loads a map from a TraML file.
OpenMS::FileTypes::TSV
@ TSV
msInspect file (.tsv)
Definition: FileTypes.h:87
OpenMS::NoopMSDataWritingConsumer
Consumer class that perform no operation.
Definition: MSDataWritingConsumer.h:258
OpenMS::Internal::MzMLHandler::getOptions
PeakFileOptions & getOptions()
Get the peak file options.
OpenMS::Param::getValue
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
OpenMS::ProgressLogger::startProgress
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
ChromatogramExtractor.h
SpectrumAccessOpenMS.h
OpenMS::FileTypes::UNKNOWN
@ UNKNOWN
Unknown file extension.
Definition: FileTypes.h:60
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:206
OpenMS::ProgressLogger::endProgress
void endProgress() const
Ends the progress display.
OpenMS::MSDataWritingConsumer::setExperimentalSettings
void setExperimentalSettings(const ExperimentalSettings &exp) override
Set experimental settings for the whole file.
OpenMS::MSNumpressCoder::NumpressConfig::numpressErrorTolerance
double numpressErrorTolerance
fixed point for numpress algorithms
Definition: MSNumpressCoder.h:73
OpenMS::ChromExtractParams::ppm
bool ppm
Whether the extraction window is given in ppm or Da.
Definition: OpenSwathWorkflow.h:91
OpenMS::TransformationDescription::fitModel
void fitModel(const String &model_type, const Param &params=Param())
Fits a model to the data.
OpenMS::OpenSwathDataAccessHelper::convertTargetedExp
static void convertTargetedExp(const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)
convert from the OpenMS TargetedExperiment to the LightTargetedExperiment
SwathWindowLoader.h
OpenSwathHelper.h
SwathFile.h
OpenSwath::LightTargetedExperiment::getProteins
std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:238
SpectrumAccessOpenMSInMemory.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
LOG_DEBUG
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
OpenMS::TraMLFile
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
OpenSwath::LightTargetedExperiment::getCompounds
std::vector< LightCompound > & getCompounds()
Definition: TransitionExperiment.h:228
OpenMS::PeakFileOptions::setNumpressConfigurationIntensity
void setNumpressConfigurationIntensity(MSNumpressCoder::NumpressConfig config)
Get numpress configuration options for intensity dimension.
MRMRTNormalizer.h
OpenSwath::LightTargetedExperiment::getTransitions
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:218
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
LOG_WARN
#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
ProgressLogger.h
MRMFeatureFinderScoring.h
TransformationXMLFile.h
OpenMS::MSDataSqlConsumer
A data consumer that inserts MS data into a SQLite database.
Definition: MSDataSqlConsumer.h:60
OpenMS::OpenSwathWorkflowSonar::OpenSwathWorkflowSonar
OpenSwathWorkflowSonar(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:399
OpenMS::Param::setMinInt
void setMinInt(const String &key, Int min)
Sets the minimum value for the integer or integer list parameter key.
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:58
OpenMS::OpenSwathWorkflow::OpenSwathWorkflow
OpenSwathWorkflow(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:269
SpectrumAccessTransforming.h
OpenMS::Param::setMaxFloat
void setMaxFloat(const String &key, double max)
Sets the maximum value for the floating point or floating point list parameter key.
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::ChromExtractParams::min_upper_edge_dist
double min_upper_edge_dist
Whether to not extract anything closer than this (in Da) from the upper edge.
Definition: OpenSwathWorkflow.h:85
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenMS::OpenSwathWorkflow::TransitionType
OpenSwath::LightTransition TransitionType
Definition: OpenSwathWorkflow.h:264
OpenMS::String::hasSuffix
bool hasSuffix(const String &string) const
true if String ends with string, false otherwise
OpenMS::TransitionPQPFile::convertPQPToTargetedExperiment
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)
OpenSwath::LightTargetedExperiment::transitions
std::vector< LightTransition > transitions
Definition: TransitionExperiment.h:215
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::TransitionTSVFile::convertTSVToTargetedExperiment
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)
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::DataProcessing::SMOOTHING
@ SMOOTHING
Smoothing of the signal to reduce noise.
Definition: DataProcessing.h:63
MSExperiment.h
OpenMS::OpenSwathWorkflowBase::use_ms1_traces_
bool use_ms1_traces_
Whether to use the MS1 traces.
Definition: OpenSwathWorkflow.h:157
DataAccessHelper.h
OpenMS::OpenSwathRetentionTimeNormalization::OpenSwathRetentionTimeNormalization
OpenSwathRetentionTimeNormalization(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:175
OpenMS::MSDataWritingConsumer::setExpectedSize
void setExpectedSize(Size expectedSpectra, Size expectedChromatograms) override
Set expected size of spectra and chromatograms to be written.
OpenMS::TransformationXMLFile::load
void load(const String &filename, TransformationDescription &transformation, bool fit_model=true)
Loads the transformation from an TransformationXML file.
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:93
OpenMS::FileTypes::PQP
@ PQP
OpenSWATH Peptide Query Parameter (PQP) SQLite DB.
Definition: FileTypes.h:104
OpenMS::TransformationXMLFile
Used to load and store TransformationXML files.
Definition: TransformationXMLFile.h:56
OpenMS::MSDataWritingConsumer::addDataProcessing
virtual void addDataProcessing(DataProcessing d)
Optionally add a data processing method to each chromatogram and spectrum.
OpenMS::Param::remove
void remove(const String &key)
Remove the entry key or a section key (when suffix is ':')
OpenMS::PlainMSDataWritingConsumer
Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:240
OpenMS::OpenSwathRetentionTimeNormalization::OpenSwathRetentionTimeNormalization
OpenSwathRetentionTimeNormalization()
Definition: OpenSwathWorkflow.h:170
OpenMS::OpenSwathWorkflowBase
Definition: OpenSwathWorkflow.h:100
OpenMS::OpenSwathWorkflow::MRMTransitionGroupType
MRMTransitionGroup< MSChromatogram, TransitionType > MRMTransitionGroupType
Definition: OpenSwathWorkflow.h:265
OpenSwath::SpectrumAccessPtr
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:89
OpenMS::MRMTransitionGroup
The representation of a group of transitions in a targeted proteomics experiment.
Definition: MRMTransitionGroup.h:67
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::DataProcessing::QUANTITATION
@ QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
OpenMS::PeakFileOptions::setCompression
void setCompression(bool compress)
MRMTransitionGroupPicker.h
OpenMS::SwathFile
File adapter for Swath files.
Definition: SwathFile.h:62
OpenMS::FileTypes::nameToType
static Type nameToType(const String &name)
Converts a file type name into a Type.
OpenSwathOSWWriter.h
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:54
OpenMS::MSNumpressCoder::NumpressConfig
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:70
OpenMS::ChromExtractParams::extraction_function
String extraction_function
The extraction function in mass space.
Definition: OpenSwathWorkflow.h:93
SortPairDoubleByFirst
static bool SortPairDoubleByFirst(const std::pair< double, double > &left, const std::pair< double, double > &right)
Definition: OpenSwathWorkflow.cpp:81
OpenMS::FileTypes::TRAML
@ TRAML
TraML (HUPO PSI format) for transitions (.traML)
Definition: FileTypes.h:81
OpenMS::OpenSwathWorkflowSonar
Class to execute an OpenSwath Workflow for SONAR data.
Definition: OpenSwathWorkflow.h:394
OpenMS::SwathFile::loadMzXML
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.
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:74
OpenMS::OpenSwathRetentionTimeNormalization
Simple OpenSwathWorkflow to perform RT and m/z correction based on a set of known peptides.
Definition: OpenSwathWorkflow.h:165
OpenMS::SwathFile::loadMzML
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.
OpenSwath::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:170
OpenMS::TransformationXMLFile::store
void store(String filename, const TransformationDescription &transformation)
Stores the data in an TransformationXML file.
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
TransitionPQPFile.h
OpenMS::PeakFileOptions::setWriteIndex
void setWriteIndex(bool write_index)
Whether to write an index at the end of the file (e.g. indexedmzML file format)
OpenMS::SwathWindowLoader::annotateSwathMapsFromFile
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.
MSDataWritingConsumer.h
OpenMS::OpenSwathWorkflowBase::OpenSwathWorkflowBase
OpenSwathWorkflowBase(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:106
OpenMS::SwathFile::loadSqMass
std::vector< OpenSwath::SwathMap > loadSqMass(String file, boost::shared_ptr< ExperimentalSettings > &)
Loads a Swath run from a single sqMass file.
OpenSwath::LightTransition
Definition: TransitionExperiment.h:46
OpenSwathTSVWriter.h
TraMLFile.h
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:60
OpenMS::OpenSwathWorkflowBase::ms1_map_
OpenSwath::SpectrumAccessPtr ms1_map_
Spectrum Access to the MS1 map (note that this is *not* threadsafe!)
Definition: OpenSwathWorkflow.h:154
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::SwathWindowLoader::readSwathWindows
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.
OpenMS::FileTypes::typeToName
static String typeToName(Type type)
Returns the name/extension of the type.
OpenMS::ChromExtractParams::extra_rt_extract
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