Merge pull request #4 from poshul/fix/FLASHDeconvOnly

Fix/flash deconv only

src/openms/include/OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h

@@ -34,9 +34,10 @@
 
 #pragma once
 
-#include <OpenMS/KERNEL/MSSpectrum.h>
 #include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
 #include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>
+#include <OpenMS/KERNEL/MSSpectrum.h>
+
 #include <iomanip>
 
 namespace OpenMS
@@ -63,7 +64,7 @@ namespace OpenMS
     /**
        @brief Constructor for DeconvolvedSpectrum. Takes the spectrum and scan number calculated from outside
        @param spectrum spectrum for which the deconvolution will be performed
-       @param scan_number scan number of the spectrum: this argument is put here for real time case where scan number should be input separately.
+       @param scan_number scan number of the spectrum
   */
     DeconvolvedSpectrum(const MSSpectrum& spectrum, const int scan_number);
 

src/openms/include/OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvAlgorithm.h

@@ -34,15 +34,16 @@
 
 #pragma once
 
-#include <OpenMS/KERNEL/MSSpectrum.h>
-#include <OpenMS/KERNEL/MSExperiment.h>
+#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
 #include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
-#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
-#include <OpenMS/DATASTRUCTURES//Matrix.h>
 #include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>
-#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
-#include <iostream>
+#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
+#include <OpenMS/DATASTRUCTURES/Matrix.h>
+#include <OpenMS/KERNEL/MSExperiment.h>
+#include <OpenMS/KERNEL/MSSpectrum.h>
+
 #include <boost/dynamic_bitset.hpp>
+#include <iostream>
 
 namespace OpenMS
 {
@@ -76,11 +77,10 @@ namespace OpenMS
     FLASHDeconvAlgorithm& operator=(const FLASHDeconvAlgorithm& fd) = default;
 
     /**
-      @brief main deconvolution function that generates the deconvolved and decoy deconvolved spectrum from the original spectrum.
+      @brief main deconvolution function that generates the deconvolved target and decoy spectrum based on the original spectrum.
       @param spec the original spectrum
       @param survey_scans the survey scans to assign precursor mass to the deconvolved spectrum.
-      @param scan_number scan number is provided from input spectrum to this function in most cases.
-      But this parameter is used for real time deconvolution where scan number may be put separately.
+      @param scan_number scan number from input spectrum.
       @param precursor_map_for_FLASHIda deconvolved precursor information from FLASHIda
  */
     void performSpectrumDeconvolution(const MSSpectrum& spec,
@@ -94,7 +94,7 @@ namespace OpenMS
     // return decoy deconvolved spectrum
     //DeconvolvedSpectrum& getDecoyDeconvolvedSpectrum();
 
-    /// get calculated averagine. This should be called after calculateAveragine is called.
+    /// get calculated averagine. Call after calculateAveragine is called.
     const PrecalculatedAveragine& getAveragine();
 
     /// set calculated averagine
@@ -132,7 +132,7 @@ namespace OpenMS
 
     /** @brief Examine intensity distribution over isotope indices. Also determines the most plausible isotope index or, monoisotopic mono_mass
         @param mono_mass monoisotopic mass
-        @param per_isotope_intensities per isotope intensity - aggregated through charges
+        @param per_isotope_intensities vector of intensities associated with each isotope - aggregated through charges
         @param offset output offset between input monoisotopic mono_mass and determined monoisotopic mono_mass
         @param avg precalculated averagine
         @param window_width isotope offset value range. If -1, set automatically.
@@ -193,7 +193,6 @@ namespace OpenMS
 
     FLASHDeconvAlgorithm* targetFD_;
 
-
     /// if it is set to 0, not a decoy run. If 1, the charge decoy run, If 2, the random noise decoy run
     int decoy_run_flag_ = 0;
 

src/openms/include/OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h

@@ -35,9 +35,9 @@
 #pragma once
 
 #include <OpenMS/APPLICATIONS/TOPPBase.h>
-#include <OpenMS/CONCEPT/Constants.h>
-#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
 #include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
+#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
+#include <OpenMS/CONCEPT/Constants.h>
 #include <OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h>
 
 namespace OpenMS
@@ -55,7 +55,7 @@ namespace OpenMS
 
   struct OPENMS_DLLAPI FLASHDeconvHelperStructs
   {
-    /// Averagine patterns pre-calculated for speed up. Other variables are also calculated for fast cosine calculation
+    /// @brief Averagine patterns pre-calculated for speed up. Other variables are also calculated for fast cosine calculation
     class OPENMS_DLLAPI PrecalculatedAveragine
     {
     private:
@@ -172,7 +172,7 @@ namespace OpenMS
       bool operator==(const TopPicItem& other) const;
     };
 
-    ///
+    /// Mass feature (Deconvolved masses in spectra are traced by Mass tracing to generate mass features - like LC-MS features).
     struct OPENMS_DLLAPI MassFeature
     {
     public:

src/openms/include/OpenMS/ANALYSIS/TOPDOWN/MassFeatureTrace.h

@@ -34,13 +34,14 @@
 
 #pragma once
 
-#include <OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h>
-#include <iostream>
-#include <iomanip>
-#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
 #include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
+#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
 #include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>
 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
+#include <OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h>
+
+#include <iostream>
+#include <iomanip>
 
 namespace OpenMS
 {
@@ -76,14 +77,14 @@ namespace OpenMS
 
     /// assignment operator
     MassFeatureTrace& operator=(const MassFeatureTrace& fd) = default;
+    MassFeatureTrace& operator=(MassFeatureTrace&& fd) = default;
 
     /// Obtain and store information from deconvolved_spectrum (necessary information for mass tracing afterwards)
     void storeInformationFromDeconvolvedSpectrum(DeconvolvedSpectrum& deconvolved_spectrum);
 
     /**
        @brief Find mass features.
        @param averagine precalculated averagine for cosine calculation
-       @param fst file streams for topfd output tsv, feature files
        */
     std::vector<FLASHDeconvHelperStructs::MassFeature> findFeatures(const PrecalculatedAveragine& averagine);
 

src/openms/include/OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h

@@ -88,6 +88,11 @@ namespace OpenMS
       */
     void updateMonomassAndIsotopeIntensities();
 
+    /**
+           @brief Update isotope cosine sore and qscore
+           @param avg precalculated averagine
+           @param min_cos the peak groups with cosine score less than this will have QScore 0.
+      */
     void updateIsotopeCosineAndQScore(const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg, double min_cos);
 
     /// recruit peaks and then return as a spectrum.
@@ -161,6 +166,7 @@ namespace OpenMS
     /// get charge range - the actual charge values
     std::tuple<int, int> getAbsChargeRange() const;
 
+    /// get per isotope intensities
     std::vector<float> getIsotopeIntensities() const;
 
     /// get isotopic cosine score
@@ -249,6 +255,7 @@ namespace OpenMS
 
     /// set per abs_charge signal power
     void setChargePowers_(const int abs_charge, const float signal_pwr, const float noise_pwr, const float intensity);
+    /// update chargefit score and also update per charge intensities here.
     void updateChargeFitScoreAndChargeIntensities_();
     ///update avg ppm error
     void updateAvgPPMError_();

src/openms/include/OpenMS/ANALYSIS/TOPDOWN/QScore.h

@@ -34,10 +34,11 @@
 
 #pragma once
 
+#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
+#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
 #include <OpenMS/KERNEL/Peak1D.h>
 #include <OpenMS/METADATA/Precursor.h>
-#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
-#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
+
 
 namespace OpenMS
 {

src/openms/include/OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h

@@ -34,11 +34,11 @@
 
 #pragma once
 
-#include <OpenMS/KERNEL/StandardTypes.h>
+#include <OpenMS/CONCEPT/ProgressLogger.h>
+#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 #include <OpenMS/KERNEL/MassTrace.h>
 #include <OpenMS/KERNEL/MSExperiment.h>
-#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
-#include <OpenMS/CONCEPT/ProgressLogger.h>
+#include <OpenMS/KERNEL/StandardTypes.h>
 
 namespace OpenMS
 {

src/openms/include/OpenMS/FILTERING/TRANSFORMERS/SpectraMerger.h

@@ -34,18 +34,19 @@
 //
 #pragma once
 
-#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
-#include <OpenMS/COMPARISON/CLUSTERING/CompleteLinkage.h>
-#include <OpenMS/COMPARISON/CLUSTERING/SingleLinkage.h>
 #include <OpenMS/COMPARISON/CLUSTERING/ClusterAnalyzer.h>
 #include <OpenMS/COMPARISON/CLUSTERING/ClusterHierarchical.h>
+#include <OpenMS/COMPARISON/CLUSTERING/CompleteLinkage.h>
+#include <OpenMS/COMPARISON/CLUSTERING/SingleLinkage.h>
 #include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h>
-#include <OpenMS/FILTERING/DATAREDUCTION/SplineInterpolatedPeaks.h>
-#include <OpenMS/KERNEL/StandardTypes.h>
-#include <OpenMS/KERNEL/RangeUtils.h>
-#include <OpenMS/KERNEL/BaseFeature.h>
 #include <OpenMS/CONCEPT/LogStream.h>
 #include <OpenMS/CONCEPT/ProgressLogger.h>
+#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
+#include <OpenMS/FILTERING/DATAREDUCTION/SplineInterpolatedPeaks.h>
+#include <OpenMS/KERNEL/BaseFeature.h>
+#include <OpenMS/KERNEL/RangeUtils.h>
+#include <OpenMS/KERNEL/StandardTypes.h>
+
 #include <vector>
 
 namespace OpenMS
@@ -252,7 +253,6 @@ namespace OpenMS
         DistanceMatrix<float> dist; // will be filled
         ClusterHierarchical ch;
 
-        //ch.setThreshold(0.99);
         // clustering ; threshold is implicitly at 1.0, i.e. distances of 1.0 (== similarity 0) will not be clustered
         ch.cluster<BaseFeature, SpectraDistance_>(data, llc, sl, tree, dist);
       }
@@ -275,9 +275,6 @@ namespace OpenMS
       }
       ca.cut(data_size - node_count, tree, clusters);
 
-      //std::cerr << "Treesize: " << (tree.size()+1) << "   #clusters: " << clusters.size() << std::endl;
-      //std::cerr << "tree:\n" << ca.newickTree(tree, true) << "\n";
-
       // convert to blocks
       MergeBlocks spectra_to_merge;
 
@@ -629,10 +626,8 @@ namespace OpenMS
         typename MapType::SpectrumType consensus_spec = exp[it->first];
         consensus_spec.setMSLevel(ms_level);
 
-        //consensus_spec.unify(exp[it->first]); // append meta info
         merged_indices.insert(it->first);
 
-        //typename MapType::SpectrumType all_peaks = exp[it->first];
         double rt_average = consensus_spec.getRT();
         double precursor_mz_average = 0.0;
         Size precursor_count(0);
@@ -665,7 +660,6 @@ namespace OpenMS
 
           // merge data points
           sas.getSpectrumAlignment(alignment, consensus_spec, exp[*sit]);
-          //std::cerr << "alignment of " << it->first << " with " << *sit << " yielded " << alignment.size() << " common peaks!\n";
           count_peaks_aligned += alignment.size();
           count_peaks_overall += exp[*sit].size();
 
@@ -730,7 +724,6 @@ namespace OpenMS
             precursor_mz_average /= precursor_count;
           }
           auto& pcs = consensus_spec.getPrecursors();
-          //if (pcs.size()>1) OPENMS_LOG_WARN << "Removing excessive precursors - leaving only one per MS2 spectrum.\n";
           pcs.resize(1);
           pcs[0].setMZ(precursor_mz_average);
           consensus_spec.setPrecursors(pcs);
@@ -769,15 +762,11 @@ namespace OpenMS
         }
       }
 
-      //typedef std::vector<typename MapType::SpectrumType> Base;
-      //exp.Base::operator=(exp_tmp);
       //Meta_Data will not be cleared
       exp.clear(false);
       exp.getSpectra().insert(exp.end(), std::make_move_iterator(exp_tmp.begin()),
                                          std::make_move_iterator(exp_tmp.end()));
 
-      // exp.erase(remove_if(exp.begin(), exp.end(), InMSLevelRange<typename MapType::SpectrumType>(ListUtils::create<int>(String(ms_level)), false)), exp.end());
-
       // ... and add consensus spectra
       exp.getSpectra().insert(exp.end(), std::make_move_iterator(merged_spectra.begin()),
                                          std::make_move_iterator(merged_spectra.end()));
@@ -873,7 +862,6 @@ namespace OpenMS
         // update spectrum
         typename MapType::SpectrumType average_spec = exp[it->first];
         average_spec.clear(false); // Precursors are part of the meta data, which are not deleted.
-        //average_spec.setMSLevel(ms_level);
 
         // refill spectrum
         for (Size i = 0; i < mz_positions.size(); ++i)
@@ -892,11 +880,9 @@ namespace OpenMS
 
       // loop over blocks
       int n(0);
-      //typename MapType::SpectrumType empty_spec;
       for (AverageBlocks::const_iterator it = spectra_to_average_over.begin(); it != spectra_to_average_over.end(); ++it)
       {
         exp[it->first] = exp_tmp[n];
-        //exp_tmp[n] = empty_spec;
         ++n;
       }
     }
@@ -990,7 +976,6 @@ namespace OpenMS
         // update spectrum
         typename MapType::SpectrumType average_spec = exp[it->first];
         average_spec.clear(false); // Precursors are part of the meta data, which are not deleted.
-        //average_spec.setMSLevel(ms_level);
 
         // refill spectrum
         for (Size i = 0; i < mz_new.size(); ++i)

src/openms/include/OpenMS/FORMAT/FLASHDeconvFeatureFile.h

@@ -35,9 +35,10 @@
 
 #pragma once
 
-#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
-#include <OpenMS/ANALYSIS//TOPDOWN/PeakGroup.h>
 #include <OpenMS/config.h>
+#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
+#include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>
+
 #include <iostream>
 #include <iomanip>
 

src/openms/include/OpenMS/FORMAT/FLASHDeconvSpectrumFile.h

@@ -33,9 +33,10 @@
 // --------------------------------------------------------------------------
 #pragma once
 
+#include <OpenMS/config.h>
 #include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
 #include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
-#include <OpenMS/config.h>
+
 #include <iomanip>
 
 namespace OpenMS
@@ -99,7 +100,6 @@ namespace OpenMS
     */
     //      @param avg averagine information to calculate monoisotopic and average mass difference
     static void writeTopFD(const DeconvolvedSpectrum& dspec, std::fstream& fs,
-//                           const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg,
                            const double snr_threshold = 1.0,
                            const double decoy_harmonic_factor = 1.0,
                            const double decoy_precursor_offset = .0);

src/openms/source/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.cpp

@@ -90,9 +90,6 @@ namespace OpenMS
     if (!precursor_peak_group_.empty() && !precursor_peak_.empty())
     {
       Precursor precursor(spec_.getPrecursors()[0]);
-      // precursor.setCharge((precursor_peak_group_.isPositive() ?
-      //                      precursor_peak_group_.getRepAbsCharge() :
-      //                      -precursor_peak_group_.getRepAbsCharge()));//getChargeMass
       precursor.setCharge(to_charge);
       precursor.setMZ(precursor_peak_group_.getMonoMass() + charge_mass_offset);
       precursor.setIntensity(precursor_peak_group_.getIntensity());