References MSDataWritingConsumer::addDataProcessing(), SwathWindowLoader::annotateSwathMapsFromFile(), TransitionPQPReader::convertPQPToTargetedExperiment(), OpenSwathDataAccessHelper::convertTargetedExp(), TransitionTSVReader::convertTSVToTargetedExperiment(), Param::copy(), ProgressLogger::endProgress(), UniqueIdInterface::ensureUniqueId(), MSNumpressCoder::NumpressConfig::estimate_fixed_point, ChromExtractParams::extra_rt_extract, ChromExtractParams::extraction_function, TransformationDescription::fitModel(), LightTargetedExperiment::getCompounds(), DefaultParamHandler::getDefaults(), MzMLHandler::getOptions(), LightTargetedExperiment::getProteins(), LightTargetedExperiment::getTransitions(), FileHandler::getType(), Param::getValue(), String::hasSuffix(), MSNumpressCoder::NumpressConfig::linear_fp_mass_acc, TraMLFile::load(), TransformationXMLFile::load(), SwathFile::loadMzML(), SwathFile::loadMzXML(), SwathFile::loadSplit(), LOG_DEBUG, LOG_ERROR, LOG_INFO, LOG_WARN, main(), ChromExtractParams::min_upper_edge_dist, ChromExtractParams::mz_extraction_window, FileTypes::MZML, FileTypes::MZXML, FileTypes::nameToType(), MSNumpressCoder::NumpressConfig::numpressErrorTolerance, OpenSwathWorkflow::performExtraction(), OpenSwathWorkflowSonar::performExtractionSonar(), OpenSwathRetentionTimeNormalization::performRTNormalization(), ChromExtractParams::ppm, FileTypes::PQP, DataProcessing::QUANTITATION, SwathWindowLoader::readSwathWindows(), Param::remove(), ChromExtractParams::rt_extraction_window, MSNumpressCoder::NumpressConfig::setCompression(), PeakFileOptions::setCompression(), MSDataWritingConsumer::setExpectedSize(), MSDataWritingConsumer::setExperimentalSettings(), ProgressLogger::setLogType(), Param::setMaxFloat(), Param::setMinFloat(), Param::setMinInt(), PeakFileOptions::setNumpressConfigurationIntensity(), PeakFileOptions::setNumpressConfigurationMassTime(), DefaultParamHandler::setParameters(), Param::setValidStrings(), Param::setValue(), PeakFileOptions::setWriteIndex(), DataProcessing::SMOOTHING, ProgressLogger::startProgress(), FeatureXMLFile::store(), String::suffix(), String::toLower(), FileTypes::TRAML, LightTargetedExperiment::transitions, FileTypes::TSV, FileTypes::typeToName(), and FileTypes::UNKNOWN.