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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: Florian Zeller $
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// $Authors: Florian Zeller $
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// --------------------------------------------------------------------------
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnParameters.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/MS2Feature.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/MSPeak.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/CentroidData.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/LCElutionPeak.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/BackgroundIntensityBin.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/BackgroundControl.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/LCMSCData.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/ProcessData.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/MS2Info.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/FeatureLCProfile.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SHFeature.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/LCMS.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/FTPeakDetectController.h>
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#include <OpenMS/DATASTRUCTURES/Param.h>
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#include <OpenMS/KERNEL/Feature.h>
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmSHCtrl.h>
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std::vector<Feature> FeatureFinderAlgorithmSHCtrl::extractPeaks(Vec datavec)
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SuperHirnParameters::instance()->initIsotopeDist_ = false; // reset this so that the IsotopeDist gets reinitalized
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FTPeakDetectController controller;
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controller.startScanParsing(datavec);
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std::vector<Feature> thefeatures;
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std::vector<SHFeature>::iterator p = controller.getLCMS()->get_feature_list_begin();
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while (p != controller.getLCMS()->get_feature_list_end())
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double mz = (*p).get_MZ();
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int charge = (*p).get_charge_state();
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double rt = (*p).get_retention_time();
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rt *= 60.0; // convert back
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double darea = (*p).get_peak_area();
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float area = (float) darea;
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// ------------------------------------------------------------------------------
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// Convex hull -- needs to be calculated differently according to Markus Mueller
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// ------------------------------------------------------------------------------
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// FeatureLCProfile* profile = (*p).getLCelutionProfile();
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// ConvexHull2D::PointArrayType hull_points(profile->getNbLCelutionSignals());
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// unsigned int j = 0;
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// std::map<int, MS1Signal>::iterator lcit;
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// for (lcit = profile->getLCelutionSignalsStart(); lcit != profile->getLCelutionSignalsEnd(); lcit++) {
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// //int scan = lcit->first;
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// MS1Signal signal = lcit->second;
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// hull_points[j][0] = signal.TR * 60.0; // convert back
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// hull_points[j][1] = signal.mass;
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// ConvexHull2D hull;
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// hull.addPoints(hull_points);
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// f.getConvexHulls().push_back(hull);
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// ------------------------------------------------------------------------------
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thefeatures.push_back(f);
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void FeatureFinderAlgorithmSHCtrl::initParams(Param param)
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// MS1 data centroid data
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// Key: ms1:data_is_centroided_already
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// 1 == data is centroided already
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SuperHirnParameters::instance()->centroidDataModus_ = !(param.getValue("centroiding:active").toBool());
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//def->search_tag("Precursor detection scan levels", &vInt);
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// Key: ms1:precursor_detection_scan_levels
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IntList list = (IntList)(param.getValue("ms1:precursor_detection_scan_levels"));
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for (unsigned int i = 0; i < list.size(); i++)
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FTPeakDetecMzXmlReader::PEAK_EXTRACTION_SCAN_LEVELS.push_back(list.at(i));
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// belongs to SPECIFIC MS2 PEAK DETECTION PARAMETERS:
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//def->search_tag("Fragment Mass Scan levels", &vInt);
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FTPeakDetecMzXmlReader::FRAGMENT_MASS_SCAN_LEVELS.push_back(2);
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//def->search_tag("MS1 max inter scan distance", &INT);
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// Key: ms1:max_inter_scan_distance
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FTPeakDetecMzXmlReader::MS1_base_inter_scan_distance = param.getValue("ms1:max_inter_scan_distance");
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//def->search_tag("MS1 LC retention time resolution", &DB);
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// Key: ms1:tr_resolution
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SuperHirnParameters::instance()->ms1TRResolution_ = param.getValue("ms1:tr_resolution"); //0.01;
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// Key: ms1:intensity_threshold
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// float thresh = 1000;
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// def->search_tag("FT peak detect MS1 intensity min threshold", &DB);
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// LCMSCData::intensity_min_threshold = param.getValue("ms1:intensity_threshold");;
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// NOTE: Was hardcoded to 1000, however:
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// - def->search_tag("FT peak detect MS2 intensity min threshold", &INTENSITY_THRESHOLD);
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// - but the above is probably something different
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SuperHirnParameters::instance()->intensityThreshold_ = param.getValue("ms1:intensity_threshold");
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// MS1 max inter scan distance
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// Key: ms1:max_inter_scan_rt_distance
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SuperHirnParameters::instance()->maxInterScanRetentionTimeDistance_ = param.getValue(
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"ms1:max_inter_scan_rt_distance"); // 0.1;
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// def->search_tag("FT peak detect MS1 min nb peak members", &min_nb_cluster_members);
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// Key: ms1:min_nb_cluster_members
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SuperHirnParameters::instance()->minNbClusterMembers_ = param.getValue("ms1:min_nb_cluster_members"); // 4
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//def->search_tag("Detectable isotope factor",&DB);
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// Key: ms1:detectable_isotope_factor
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SuperHirnParameters::instance()->detectableIsotopeFactor_ = param.getValue("ms1:detectable_isotope_factor"); // 0.05;
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// def->search_tag("IntensityCV",&DB);
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// Key: ms1:intensity_cv
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SuperHirnParameters::instance()->intensityCV_ = param.getValue("ms1:intensity_cv"); // 0.9;
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// ----------------------------------------------------------------------
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// from void FT_PEAK_DETECT_initializer::init_all(){
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// ----------------------------------------------------------------------
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//def->search_tag("Centroid window width",&INT);
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// Key: centroiding:window_width
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SuperHirnParameters::instance()->centroidWindowWidth_ = param.getValue("centroiding:window_width"); // 5;
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//def->search_tag("Absolute isotope mass precision",&DB);
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// Key: centroiding:absolute_isotope_mass_precision
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SuperHirnParameters::instance()->massTolDa_ = param.getValue("centroiding:absolute_isotope_mass_precision"); // 0.01;
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//def->search_tag("Relative isotope mass precision",&DB);
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// Key: centroiding:relative_isotope_mass_precision
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SuperHirnParameters::instance()->massTolPpm_ = param.getValue("centroiding:relative_isotope_mass_precision"); // 10;
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//def->search_tag("Minimal peak height",&DB);
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// Key: centroiding:minimal_peak_height
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SuperHirnParameters::instance()->minIntensity_ = param.getValue("centroiding:minimal_peak_height"); // 0.0;
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//def->search_tag("Min. Centroid MS Signal Intensity",&DB);
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// Key: centroiding:min_ms_signal_intensity
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SuperHirnParameters::instance()->intensityFloor_ = param.getValue("centroiding:min_ms_signal_intensity"); // 50; //in config its 50, but in CentroidData it's 1;
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//def->search_tag("Report mono peaks",&INT);
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// NO OpenMS equivalent
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FTPeakDetecMzXmlReader::sfReportMonoPeaks = 0;
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//def->search_tag("Report scan number",&INT);
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// NO OpenMS equivalent
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FTPeakDetecMzXmlReader::sfReportScanNumber = 0;
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// ----------------------------------------------------------------------
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// ----------------------------------------------------------------------
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// feature parameters:
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//def->search_tag("MS1 retention time tolerance", &TMP);
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// Key: ms1:retention_time_tolerance
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SuperHirnParameters::instance()->trTol_ = param.getValue("ms1:retention_time_tolerance"); // 0.5;
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// def->search_tag("MS1 m/z tolerance", &TMP);
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// Key: ms1:mz_tolerance
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SuperHirnParameters::instance()->mzTolPpm_ = param.getValue("ms1:mz_tolerance"); // 0.0;
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// ConsensusIsotopePattern::FT_MZ_TOLERANCE = SHFeature::PPM_MZ_TOL;
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// MS2_M2_matcher parameters:
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//def->search_tag("MS2 mass matching modus", &TMP_B);
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// Key: general:ms2_mass_matching_modus
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// Unit: define which modus used to match ms2 assignments to ms1 peaks
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// - theoretical mass [1] : use theoretical mass calculated from sequence
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// - MS1 precursor mass [0]: use measured ms1 mass of precursor ion
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// MS2Info::THEO_MATCH_MODUS = 1;
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// MS2 matching PPM parameters:
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//def->search_tag("MS2 PPM m/z tolerance", &TMP);
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// Key: general:ms2_ppm_mz_tolerance
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// MS2Info::MS2_MZ_PPM_TOLERANCE = 30;
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// MS2 retention time tolerance:
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//def->search_tag("MS2 retention time tolerance", &TMP);
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// Key: general:ms2_retention_time_tolerance
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// Unit: retention time tolerance with which MS2 identifications will be associated
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// to a defined MS1 LC elution peak [min]
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// (if set to -1, then the MS1 retention time tolerance will be used
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// MS2Info::MS2_TR_TOL = TMP;
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// MS2Info::MS2_TR_TOL = SHFeature::TR_TOL;
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// def->search_tag("Peptide Prophet Threshold", &TMP);
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// Key: general:peptide_prophet_threshold
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//double d = param.getValue("general:peptide_prophet_threshold"); // 0.9;
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// ------ peptide_DELTA_group::PEPTIDE_PROBABILITY_THRESHOLD = d;
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// SHFeature::PEPTIDE_PROBABILITY_THRESHOLD = d;
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// PKUNSZT: commented out: the default is 0.9 already.
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// SuperHirnParameters::instance()->peptideProbabilityThreshold_ = d;
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// ------ interact_parser::PEPTIDE_PROBABILITY_THRESHOLD = d;
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// LCMS::PEP_PROPHET_THERSHOLD = d; // THIS IS NEVER USED
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//def->search_tag("Create monoisotopic LC profile", &TMP_B);
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// ------- LCMSDataImporter::CREATE_FEATURE_ELUTION_PROFILES = 1;
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// FTPeakDetectController::CREATE_FEATURE_ELUTION_PROFILES = 1;
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SuperHirnParameters::instance()->createFeatureElutionProfiles_ = true;
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// ------- LC_MS_XML_writer::STORE_FEATURE_ELUTION_PROFILES = 1;
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/////////////////////////////////////////////////
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// Parameters for the peak merging:
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//def->search_tag("Activation of MS1 feature merging post processing", &TMP_B);
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// Key: ms1_feature_merger:active
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// MS1FeatureMerger::MS1_FEATURE_CLUSTERING = param.getValue("ms1_feature_merger:active").toBool(); //1;
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SuperHirnParameters::instance()->ms1FeatureClustering_ = param.getValue("ms1_feature_merger:active").toBool(); //1;
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//def->search_tag("MS1 LC retention time resolution", &TMP); // belongs to MS1 PEAK DETECTION PARAMETERS FOR THE DIFFERENT FILTER METHODS:
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// Key: ms1_feature_merger:tr_resolution
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// MS1FeatureMerger::MS1_PEAK_AREA_TR_RESOLUTION = param.getValue("ms1_feature_merger:tr_resolution"); //0.01;
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SuperHirnParameters::instance()->ms1PeakAreaTrResolution_ = param.getValue("ms1_feature_merger:tr_resolution"); //0.01;
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//def->search_tag("Initial Apex Tr tolerance", &TMP);
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// Key: ms1_feature_merger:initial_apex_tr_tolerance
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// MS1FeatureMerger::INITIAL_TR_TOLERANCE = param.getValue("ms1_feature_merger:initial_apex_tr_tolerance"); //5.0;
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SuperHirnParameters::instance()->initialTrTolerance_ = param.getValue(
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"ms1_feature_merger:initial_apex_tr_tolerance"); //5.0;
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//def->search_tag("MS1 feature Tr merging tolerance", &TMP);
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// Key: ms1_feature_merger:feature_merging_tr_tolerance
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// MS1FeatureMerger::MS1_FEATURE_MERGING_TR_TOLERANCE = param.getValue(
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// "ms1_feature_merger:feature_merging_tr_tolerance"); //1.0;
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SuperHirnParameters::instance()->ms1FeatureMergingTrTolerance_ = param.getValue(
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"ms1_feature_merger:feature_merging_tr_tolerance"); //1.0;
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//def->search_tag("Percentage of intensity variation between LC border peaks", &TMP);
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// Key: ms1_feature_merger:intensity_variation_percentage
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// MS1FeatureMerger::PERCENTAGE_INTENSITY_ELUTION_BORDER_VARIATION = param.getValue(
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// "ms1_feature_merger:intensity_variation_percentage"); //25;
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SuperHirnParameters::instance()->percentageIntensityElutionBorderVariation_ = param.getValue(
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"ms1_feature_merger:intensity_variation_percentage"); //25;
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//def->search_tag("PPM value for the m/z clustering of merging candidates", &TMP);
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// Key: ms1_feature_merger:ppm_tolerance_for_mz_clustering
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SuperHirnParameters::instance()->ppmToleranceForMZClustering_ = param.getValue(
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"ms1_feature_merger:ppm_tolerance_for_mz_clustering"); //10;
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/////////////////////////////////////////////////
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// what information is extracted from the LC/MS or mastermap:
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// def->search_tag("start elution window", &TMP);
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// Key: ms1_feature_selection_options:start_elution_window
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SuperHirnParameters::instance()->minTR_ = param.getValue("ms1_feature_selection_options:start_elution_window"); //0;
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// def->search_tag("end elution window", &TMP);
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// Key: ms1_feature_selection_options:end_elution_window
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SuperHirnParameters::instance()->maxTR_ = param.getValue("ms1_feature_selection_options:end_elution_window"); //180;
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//def->search_tag("MS1 feature mz range min", &TMP);
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// Key: ms1_feature_selection_options:mz_range_min
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SuperHirnParameters::instance()->minFeatureMZ_ = param.getValue("ms1_feature_selection_options:mz_range_min"); //0;
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//def->search_tag("MS1 feature mz range max", &TMP );
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// Key: ms1_feature_selection_options:mz_range_max
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SuperHirnParameters::instance()->maxFeatureMZ_ = param.getValue("ms1_feature_selection_options:mz_range_max"); //2000;
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//def->search_tag("MS1 feature CHRG range min", &TMP_I );
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// Key: ms1_feature_selection_options:chrg_range_min
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SuperHirnParameters::instance()->minFeatureChrg_ = param.getValue("ms1_feature_selection_options:chrg_range_min"); //1;
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//Deisotoper::sfMinCharge = param.getValue("ms1_feature_selection_options:chrg_range_min"); //1;
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//def->search_tag("MS1 feature CHRG range max", &TMP_I );
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// Key: ms1_feature_selection_options:chrg_range_max
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SuperHirnParameters::instance()->maxFeatureChrg_ = param.getValue("ms1_feature_selection_options:chrg_range_max"); //5;
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//Deisotoper::sfMaxCharge = param.getValue("ms1_feature_selection_options:chrg_range_max"); //5;
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/////////////////////////////////////////////////
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// what and how data is stored during superhirn processing:
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// ms2 information of a feature:
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// only the best ms2 info / feature stored:
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//def->search_tag("progress all low probability ms2 info in MS1 feature", &TMP_B);
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// SHFeature::STORE_ALL_LOW_PROBABILITY_MS2_SCANS = 0;
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removed
source/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmSHCtrl.C
