{"action":"created","comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/pulls/comments/174548937","pull_request_review_id":103922219,"id":174548937,"diff_hunk":"@@ -0,0 +1,270 @@\n+// --------------------------------------------------------------------------\n+//                   OpenMS -- Open-Source Mass Spectrometry\n+// --------------------------------------------------------------------------\n+// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,\n+// ETH Zurich, and Freie Universitaet Berlin 2002-2017.\n+//\n+// This software is released under a three-clause BSD license:\n+//  * Redistributions of source code must retain the above copyright\n+//    notice, this list of conditions and the following disclaimer.\n+//  * Redistributions in binary form must reproduce the above copyright\n+//    notice, this list of conditions and the following disclaimer in the\n+//    documentation and/or other materials provided with the distribution.\n+//  * Neither the name of any author or any participating institution\n+//    may be used to endorse or promote products derived from this software\n+//    without specific prior written permission.\n+// For a full list of authors, refer to the file AUTHORS.\n+// --------------------------------------------------------------------------\n+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\n+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\n+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE\n+// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING\n+// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,\n+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,\n+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;\n+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,\n+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR\n+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF\n+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n+//\n+// --------------------------------------------------------------------------\n+// $Maintainer: Timo Sachsenberg $\n+// $Authors: Hendrik Weisser $\n+// --------------------------------------------------------------------------\n+\n+#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERIDENTIFICATIONALGORITHM_H\n+#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERIDENTIFICATIONALGORITHM_H\n+\n+#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>\n+#include <OpenMS/ANALYSIS/SVM/SimpleSVM.h>\n+#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h>\n+#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/ElutionModelFitter.h>\n+#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPickedHelperStructs.h>\n+#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/EGHTraceFitter.h>\n+#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/GaussTraceFitter.h>\n+#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>\n+#include <OpenMS/KERNEL/MSExperiment.h>\n+#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>\n+#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>\n+#include <OpenMS/CONCEPT/ProgressLogger.h>\n+#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SimpleOpenMSSpectraAccessFactory.h>\n+\n+#include <vector>\n+#include <fstream>\n+#include <map>\n+\n+namespace OpenMS\n+{\n+\n+class OPENMS_DLLAPI FeatureFinderIdentificationAlgorithm :\n+  public DefaultParamHandler\n+{\n+public:\n+  /// default constructor\n+  FeatureFinderIdentificationAlgorithm(); \n+\n+  /// Main method for actual FeatureFinder\n+  /// External ids may be empty and greatly speed up the detectin process\n+  void run(\n+    std::vector<PeptideIdentification> peptides,\n+    std::vector<ProteinIdentification> proteins,\n+    std::vector<PeptideIdentification> peptides_ext,\n+    std::vector<ProteinIdentification> proteins_ext,\n+    FeatureMap & features\n+    );\n+\n+  void runOnCandidates(FeatureMap & features);\n+\n+  PeakMap& getMSData() { return ms_data_; }\n+  const PeakMap& getMSData() const { return ms_data_; }\n+\n+  PeakMap& getChromatograms() { return chrom_data_; }\n+  const PeakMap& getChromatograms() const { return chrom_data_; }\n+\n+  ProgressLogger& getProgressLogger() { return prog_log_; }\n+  ProgressLogger const & getProgressLogger() const { return prog_log_; }\n+\n+  TargetedExperiment& getLibrary() { return library_; }\n+  const TargetedExperiment& getLibrary() const { return library_; }\n+\n+protected:\n+  typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace;\n+  typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces;\n+\n+  // mapping: RT (not necessarily unique) -> pointer to peptide\n+  typedef std::multimap<double, PeptideIdentification*> RTMap;\n+  // mapping: charge -> internal/external: (RT -> pointer to peptide)\n+  typedef std::map<Int, std::pair<RTMap, RTMap> > ChargeMap;\n+  // mapping: sequence -> charge -> internal/external ID information\n+  typedef std::map<AASequence, ChargeMap> PeptideMap;\n+  // mapping: peptide ref. -> int./ext.: (RT -> pointer to peptide)\n+  typedef std::map<String, std::pair<RTMap, RTMap> > PeptideRefRTMap;\n+\n+  PeptideMap peptide_map_;\n+\n+  Size n_internal_peps_;\n+  Size 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