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// --------------------------------------------------------------------------
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// OpenMS -- Open-Source Mass Spectrometry
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// --------------------------------------------------------------------------
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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// This software is released under a three-clause BSD license:
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above copyright
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// notice, this list of conditions and the following disclaimer in the
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// documentation and/or other materials provided with the distribution.
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// * Neither the name of any author or any participating institution
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// may be used to endorse or promote products derived from this software
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// without specific prior written permission.
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// For a full list of authors, refer to the file AUTHORS.
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// --------------------------------------------------------------------------
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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// --------------------------------------------------------------------------
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// $Maintainer: Hannes Roest $
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// $Authors: Hannes Roest $
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// --------------------------------------------------------------------------
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#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
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#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/DataAccessHelper.h>
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bool SortDoubleDoublePairFirst(const std::pair<double, double>& left, const std::pair<double, double>& right)
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return left.first < right.first;
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MRMFeatureFinderScoring::MRMFeatureFinderScoring() :
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DefaultParamHandler("MRMFeatureFinderScoring"),
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defaults_.setValue("stop_report_after_feature", -1, "Stop reporting after feature (ordered by quality; -1 means do not stop).");
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defaults_.setValue("rt_extraction_window", -1.0, "Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution). For this to work, the TraML input file needs to contain normalized RT values.");
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defaults_.setValue("rt_normalization_factor", 1.0, "The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)");
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defaults_.setValue("quantification_cutoff", 0.0, "Cutoff below which peaks should not be used for quantification any more", StringList::create("advanced"));
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defaults_.setMinFloat("quantification_cutoff", 0.0);
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defaults_.setValue("write_convex_hull", "false", "Whether to write out all points of all features into the featureXML", StringList::create("advanced"));
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defaults_.setValidStrings("write_convex_hull", StringList::create("true,false"));
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defaults_.setValue("add_up_spectra", 1, "Add up spectra around the peak apex (needs to be a non-even integer)", StringList::create("advanced"));
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defaults_.setMinInt("add_up_spectra", 1);
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defaults_.setValue("spacing_for_spectra_resampling", 0.005, "If spectra are to be added, use this spacing to add them up", StringList::create("advanced"));
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defaults_.setMinFloat("spacing_for_spectra_resampling", 0.0);
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defaults_.insert("TransitionGroupPicker:", MRMTransitionGroupPicker().getDefaults());
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defaults_.insert("DIAScoring:", DIAScoring().getDefaults());
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defaults_.insert("EMGScoring:", EmgScoring().getDefaults());
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// One can turn on / off each score individually
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scores_to_use.setValue("use_shape_score", "true", "Use the shape score", StringList::create("advanced"));
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scores_to_use.setValidStrings("use_shape_score", StringList::create("true,false"));
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scores_to_use.setValue("use_coelution_score", "true", "Use the coelution score", StringList::create("advanced"));
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scores_to_use.setValidStrings("use_coelution_score", StringList::create("true,false"));
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scores_to_use.setValue("use_rt_score", "true", "Use the retention time score", StringList::create("advanced"));
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scores_to_use.setValidStrings("use_rt_score", StringList::create("true,false"));
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scores_to_use.setValue("use_library_score", "true", "Use the library score", StringList::create("advanced"));
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scores_to_use.setValidStrings("use_library_score", StringList::create("true,false"));
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scores_to_use.setValue("use_elution_model_score", "true", "Use the elution model (EMG) score", StringList::create("advanced"));
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scores_to_use.setValidStrings("use_elution_model_score", StringList::create("true,false"));
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scores_to_use.setValue("use_intensity_score", "true", "Use the intensity score", StringList::create("advanced"));
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scores_to_use.setValidStrings("use_intensity_score", StringList::create("true,false"));
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scores_to_use.setValue("use_nr_peaks_score", "true", "Use the number of peaks score", StringList::create("advanced"));
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scores_to_use.setValidStrings("use_nr_peaks_score", StringList::create("true,false"));
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scores_to_use.setValue("use_total_xic_score", "true", "Use the total XIC score", StringList::create("advanced"));
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scores_to_use.setValidStrings("use_total_xic_score", StringList::create("true,false"));
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scores_to_use.setValue("use_sn_score", "true", "Use the SN (signal to noise) score", StringList::create("advanced"));
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scores_to_use.setValidStrings("use_sn_score", StringList::create("true,false"));
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defaults_.insert("Scores:", scores_to_use);
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// write defaults into Param object param_
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MRMFeatureFinderScoring::~MRMFeatureFinderScoring()
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void MRMFeatureFinderScoring::updateMembers_()
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void MRMFeatureFinderScoring::handle_params()
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stop_report_after_feature_ = (int)param_.getValue("stop_report_after_feature");
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rt_extraction_window_ = (DoubleReal)param_.getValue("rt_extraction_window");
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rt_normalization_factor_ = (DoubleReal)param_.getValue("rt_normalization_factor");
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quantification_cutoff_ = (DoubleReal)param_.getValue("quantification_cutoff");
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write_convex_hull_ = param_.getValue("write_convex_hull").toBool();
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add_up_spectra_ = param_.getValue("add_up_spectra");
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spacing_for_spectra_resampling_ = param_.getValue("spacing_for_spectra_resampling");
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diascoring_.setParameters(param_.copy("DIAScoring:", true));
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emgscoring_.setFitterParam(param_.copy("EmgScoring:", true));
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use_coelution_score_ = param_.getValue("Scores:use_coelution_score").toBool();
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use_shape_score_ = param_.getValue("Scores:use_shape_score").toBool();
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use_rt_score_ = param_.getValue("Scores:use_rt_score").toBool();
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use_library_score_ = param_.getValue("Scores:use_library_score").toBool();
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use_elution_model_score_ = param_.getValue("Scores:use_elution_model_score").toBool();
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use_intensity_score_ = param_.getValue("Scores:use_intensity_score").toBool();
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use_total_xic_score_ = param_.getValue("Scores:use_total_xic_score").toBool();
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use_nr_peaks_score_ = param_.getValue("Scores:use_nr_peaks_score").toBool();
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use_sn_score_ = param_.getValue("Scores:use_sn_score").toBool();
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void MRMFeatureFinderScoring::mapExperimentToTransitionList(OpenSwath::SpectrumAccessPtr input,
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TargetedExpType& transition_exp, TransitionGroupMapType& transition_group_map,
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TransformationDescription trafo, double rt_extraction_window)
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double rt_min, rt_max, expected_rt;
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std::map<String, int> chromatogram_map;
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Size nr_chromatograms = input->getNrChromatograms();
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for (Size i = 0; i < input->getNrChromatograms(); i++)
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chromatogram_map[input->getChromatogramNativeID(i)] = boost::numeric_cast<int>(i);
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// Iterate thorugh all transitions and store the transition with the
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// corresponding chromatogram in the corresponding transition group
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startProgress(0, nr_chromatograms, "Mapping transitions to chromatograms ");
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for (Size i = 0; i < transition_exp.getTransitions().size(); i++)
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// get the current transition and try to find the corresponding chromatogram
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const TransitionType* transition = &transition_exp.getTransitions()[i];
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if (chromatogram_map.find(transition->getNativeID()) == chromatogram_map.end())
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std::cerr << "Error: Transition " + transition->getNativeID() + " from group " +
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transition->getPeptideRef() + " does not have a corresponding chromatogram" << std::endl;
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throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
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"Error: Transition " + transition->getNativeID() + " from group " +
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transition->getPeptideRef() + " does not have a corresponding chromatogram");
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MSChromatogram<ChromatogramPeak> chromatogram_old;
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OpenSwath::ChromatogramPtr cptr = input->getChromatogramById(chromatogram_map[transition->getNativeID()]);
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OpenSwathDataAccessHelper::convertToOpenMSChromatogram(chromatogram_old, cptr);
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RichPeakChromatogram chromatogram;
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// Create the chromatogram information
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// Get the expected retention time, apply the RT-transformation
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// (which describes the normalization) and then take the difference.
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// Note that we inverted the transformation in the beginning because
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// we want to transform from normalized to real RTs here and not the
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expected_rt = PeptideRTMap_[transition->getPeptideRef()];
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double de_normalized_experimental_rt = trafo.apply(expected_rt);
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rt_max = de_normalized_experimental_rt + rt_extraction_window;
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rt_min = de_normalized_experimental_rt - rt_extraction_window;
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for (MSChromatogram<ChromatogramPeak>::const_iterator it = chromatogram_old.begin(); it != chromatogram_old.end(); ++it)
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if (rt_extraction_window >= 0 && (it->getRT() < rt_min || it->getRT() > rt_max))
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ChromatogramPeak peak;
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peak.setMZ(it->getRT());
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peak.setIntensity(it->getIntensity());
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chromatogram.push_back(peak);
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if (chromatogram.empty())
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std::cerr << "Error: Could not find any points for chromatogram " + transition->getNativeID() + \
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". Maybe your retention time transformation is off?" << std::endl;
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throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
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"Error: Could not find any points for chromatogram " + transition->getNativeID() + \
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". Maybe your retention time transformation is off?");
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chromatogram.setMetaValue("product_mz", transition->getProductMZ());
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chromatogram.setMetaValue("precursor_mz", transition->getPrecursorMZ());
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chromatogram.setNativeID(transition->getNativeID());
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// Create new transition group if there is none for this peptide
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if (transition_group_map.find(transition->getPeptideRef()) == transition_group_map.end())
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MRMTransitionGroupType transition_group;
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transition_group.setTransitionGroupID(transition->getPeptideRef());
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transition_group_map[transition->getPeptideRef()] = transition_group;
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// Now add the transition and the chromatogram to the group
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MRMTransitionGroupType& transition_group = transition_group_map[transition->getPeptideRef()];
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transition_group.addTransition(*transition, transition->getNativeID());
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transition_group.addChromatogram(chromatogram, chromatogram.getNativeID());
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setProgress(++progress);
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// The assumption is that for each transition that is in the TargetedExperiment we have exactly one chromatogram
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for (TransitionGroupMapType::iterator trgroup_it = transition_group_map.begin(); trgroup_it != transition_group_map.end(); trgroup_it++)
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if (trgroup_it->second.getChromatograms().size() > 0 && (trgroup_it->second.getChromatograms().size() != trgroup_it->second.getTransitions().size()))
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throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Error: Could not match all transition to all chromatograms:\nFor chromatogram " + \
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trgroup_it->second.getTransitionGroupID() + " I found " + String(trgroup_it->second.getChromatograms().size()) + \
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" chromatograms but " + String(trgroup_it->second.getTransitions().size()) + " transitions.");
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source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.C
