Feature/auto add up new

src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.h

@@ -63,6 +63,8 @@ namespace OpenMS
 
     std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;
 
+    std::vector<std::size_t> getSpectraRTRange(double rt_start, double rt_end) const override;
+
     size_t getNrSpectra() const override;
 
     SpectrumSettings getSpectraMetaInfo(int id) const;

src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSCached.h

@@ -72,6 +72,8 @@ namespace OpenMS
 
     std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;
 
+    std::vector<std::size_t> getSpectraRTRange(double rt_start, double rt_end) const override;
+
     size_t getNrSpectra() const override;
 
     SpectrumSettings getSpectraMetaInfo(int id) const;

src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.h

@@ -21,16 +21,16 @@ namespace OpenMS
 {
   /**
    * @brief An implementation of the OpenSWATH Spectrum Access interface completely in memory
-   * 
+   *
    * This implementation of the spectrum access interface ensures that all data
    * is held completely in memory and is quickly accessible. This class can be
    * generated by passing any object implementing the Spectrum Access interface
    * and guarantees to provide the same access to the raw data as the original
    * object with the added benefits (and downside) of keeping all data in system
    * memory.
-   * 
+   *
    * A possible example
-   * 
+   *
    * @code
    * OpenSwath::ISpectrumAccess * data_access;
    * fillData(data_access); // assume that data_access points to some data
@@ -70,6 +70,8 @@ namespace OpenMS
 
     std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;
 
+    std::vector<std::size_t> getSpectraRTRange(double rt_start, double rt_end) const override;
+
     size_t getNrSpectra() const override;
 
     OpenSwath::ChromatogramPtr getChromatogramById(int id) override;

src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessSqMass.h

@@ -89,6 +89,8 @@ namespace OpenMS
 
     std::vector<std::size_t> getSpectraByRT(double /* RT */, double /* deltaRT */) const override;
 
+    std::vector<std::size_t> getSpectraRTRange(double /* rt_start */, double /* rt_end */) const override;
+
     size_t getNrSpectra() const override;
 
     OpenSwath::ChromatogramPtr getChromatogramById(int /* id */) override;

src/openms/include/OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.h

@@ -24,7 +24,7 @@ namespace OpenMS
 public:
 
     explicit SpectrumAccessTransforming(OpenSwath::SpectrumAccessPtr sptr);
-        
+
     ~SpectrumAccessTransforming() override = 0;
 
     boost::shared_ptr<ISpectrumAccess> lightClone() const override = 0;
@@ -35,6 +35,8 @@ namespace OpenMS
 
     std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;
 
+    std::vector<std::size_t> getSpectraRTRange(double rt_start, double rt_end) const override;
+
     size_t getNrSpectra() const override;
 
     OpenSwath::ChromatogramPtr getChromatogramById(int id) override;

src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h

@@ -126,6 +126,8 @@ namespace OpenMS
     double dotprod_score_dia = 0;
     double manhatt_score_dia = 0;
 
+    int numSpectraAdd = 1; // num spectra that are summed up when computing DIA scores
+
     OpenSwath_Scores() = default;
 
     double get_quick_lda_score(double library_corr_,

src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h

@@ -28,6 +28,7 @@
 
 class RangeMZ;
 class RangeMobility;
+class RangeRT;
 
 namespace OpenMS
 {
@@ -169,6 +170,7 @@ namespace OpenMS
      * @param mzerror_ppm m/z and mass error (in ppm) for all transitions
      * @param[in] drift_target target drift value
      * @param[in] range_im drift time lower and upper bounds
+     * @param[in] range_rt retention time lower and upper bounds
      *
     */
     void calculateDIAScores(OpenSwath::IMRMFeature* imrmfeature,
@@ -180,7 +182,8 @@ namespace OpenMS
                             OpenSwath_Scores& scores,
                             std::vector<double>& mzerror_ppm,
                             const double drift_target,
-                            const RangeMobility& range_im);
+                            const RangeMobility& range_im,
+                            const RangeRT& range_rt);
 
     /** @brief Score a single chromatographic feature using the precursor map.
      *
@@ -286,17 +289,14 @@ namespace OpenMS
     */
     SpectrumSequence fetchSpectrumSwath(OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add, const RangeMobility& im_range);
 
-
-  protected:
-
-    /** @breif converts a ion mobility enhanced spectrum to a non ion mobility spectrum by filtering by drift time
+    /** @breif similar to fetchSpectrumSwath() however select spectra across entire rt range of the feature
      */
-    OpenSwath::SpectrumPtr filterByDrift_(const OpenSwath::SpectrumPtr& input, const RangeMobility& range_im);
+    SpectrumSequence fetchSpectrumSwathAuto(OpenSwath::SpectrumAccessPtr swathmap, const RangeMobility& im_range, const RangeRT& rt_range);
 
 
-    /** @breif Adds up an array of spectrum into one spectrum. If the spectra are ion mobility enhanced, first filter by drift time and then add up spectra
+    /** @breif similar to fetchSpectrumSwath() however select spectra across entire rt range of the feature
      */
-    OpenSwath::SpectrumPtr getAddedSpectra_(std::vector<OpenSwath::SpectrumPtr>&, const RangeMobility& range_im);
+    SpectrumSequence fetchSpectrumSwathAuto(std::vector<OpenSwath::SwathMap> swath_maps, const RangeMobility& im_range, const RangeRT& rt_range); 
 
   };
 }

src/openms/include/OpenMS/INTERFACES/ISpectrumAccess.h

@@ -32,6 +32,8 @@ namespace Interfaces
     virtual SpectrumPtr getSpectrumById(const std::string& id) const = 0;
     /// Return a vector of ids of spectra that are within RT +/- deltaRT
     virtual std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const = 0;
+    /// Return a vector of ids of spectra between rt_start and rt_end
+    virtual std::vector<std::size_t> getSpectraRTRange(double rt_start, double rt_end) const = 0;
     /// Returns the number of spectra available
     virtual size_t getNrSpectra() const = 0;
     /// Returns the meta information for a spectrum

src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.cpp

@@ -23,7 +23,7 @@ namespace OpenMS
   SpectrumAccessOpenMS::SpectrumAccessOpenMS(const SpectrumAccessOpenMS & rhs) :
     ms_experiment_(rhs.ms_experiment_)
   {
-    // this only copies the pointers and not the actual data ... 
+    // this only copies the pointers and not the actual data ...
   }
 
 
@@ -159,6 +159,25 @@ namespace OpenMS
     return result;
   }
 
+  std::vector<std::size_t> SpectrumAccessOpenMS::getSpectraRTRange(double rt_start, double rt_end) const
+  {
+
+    // Start at the rt_start
+    std::vector<std::size_t> result;
+    auto spectrum = ms_experiment_->RTBegin(rt_start);
+    if (spectrum == ms_experiment_->end()) return result;
+
+    result.push_back(std::distance(ms_experiment_->begin(), spectrum));
+    spectrum++;
+
+    while (spectrum != ms_experiment_->end() && spectrum->getRT() <= rt_end)
+    {
+      result.push_back(spectrum - ms_experiment_->begin());
+      spectrum++;
+    }
+    return result;
+  }
+
   size_t SpectrumAccessOpenMS::getNrChromatograms() const
   {
     return ms_experiment_->getChromatograms().size();

src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSCached.cpp

@@ -104,6 +104,23 @@ namespace OpenMS
     return result;
   }
 
+  std::vector<std::size_t> SpectrumAccessOpenMSCached::getSpectraRTRange(double rt_start, double rt_end) const
+  {
+    std::vector<std::size_t> result;
+    auto spectrum = meta_ms_experiment_.RTBegin(rt_start);
+    if (spectrum == meta_ms_experiment_.end()) return result;
+
+    result.push_back(std::distance(meta_ms_experiment_.begin(), spectrum));
+    spectrum++;
+
+    while (spectrum != meta_ms_experiment_.end() && spectrum->getRT() < rt_end)
+    {
+      result.push_back(spectrum - meta_ms_experiment_.begin());
+      spectrum++;
+    }
+    return result;
+  }
+
   size_t SpectrumAccessOpenMSCached::getNrSpectra() const
   {
     return meta_ms_experiment_.size();

src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.cpp

@@ -48,7 +48,7 @@ namespace OpenMS
     chromatograms_(rhs.chromatograms_),
     chromatogram_ids_(rhs.chromatogram_ids_)
   {
-    // this only copies the pointers and not the actual data ... 
+    // this only copies the pointers and not the actual data ...
   }
 
   boost::shared_ptr<OpenSwath::ISpectrumAccess> SpectrumAccessOpenMSInMemory::lightClone() const
@@ -93,6 +93,25 @@ namespace OpenMS
     return result;
   }
 
+  std::vector<std::size_t> SpectrumAccessOpenMSInMemory::getSpectraRTRange(double rt_start, double rt_end) const
+  {
+
+    std::vector<std::size_t> result;
+    OpenSwath::SpectrumMeta s;
+    s.RT = rt_start;
+    auto spectrum = std::lower_bound(spectra_meta_.begin(), spectra_meta_.end(), s, OpenSwath::SpectrumMeta::RTLess());
+    if (spectrum == spectra_meta_.end()) return result;
+
+    result.push_back(std::distance(spectra_meta_.begin(), spectrum));
+    ++spectrum;
+    while ( spectrum != spectra_meta_.end() && spectrum->RT < rt_end)
+    {
+      result.push_back(std::distance(spectra_meta_.begin(), spectrum));
+      ++spectrum;
+    }
+    return result;
+  }
+
   size_t SpectrumAccessOpenMSInMemory::getNrSpectra() const
   {
     OPENMS_PRECONDITION(spectra_.size() == spectra_meta_.size(), "Spectra and meta data needs to match")

src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessSqMass.cpp

@@ -138,7 +138,7 @@ namespace OpenMS
       }
       spectra.reserve(tmp_spectra.size());
       spectra_meta.reserve(tmp_spectra.size());
-    
+
       for (Size k = 0; k < tmp_spectra.size(); k++)
       {
         const MSSpectrumType& spectrum = tmp_spectra[k];
@@ -187,6 +187,11 @@ namespace OpenMS
       }
     }
 
+    std::vector<std::size_t> SpectrumAccessSqMass::getSpectraRTRange(double rt_start, double rt_end) const
+    {
+      throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
+    }
+
     size_t SpectrumAccessSqMass::getNrSpectra() const
     {
       size_t res;

src/openms/source/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.cpp

@@ -40,6 +40,11 @@ namespace OpenMS
     return sptr_->getSpectraByRT(RT, deltaRT);
   }
 
+  std::vector<std::size_t> SpectrumAccessTransforming::getSpectraRTRange(double rt_start, double rt_end) const
+  {
+    return sptr_->getSpectraRTRange(rt_start, rt_end);
+  }
+
   size_t SpectrumAccessTransforming::getNrSpectra() const
   {
     return sptr_->getNrSpectra();

src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp

@@ -72,8 +72,8 @@ namespace OpenMS
     defaults_.setValidStrings("write_convex_hull", {"true","false"});
     defaults_.setValue("spectrum_addition_method", "simple", "For spectrum addition, either use simple concatenation or use peak resampling", {"advanced"});
     defaults_.setValidStrings("spectrum_addition_method", {"simple", "resample"});
-    defaults_.setValue("add_up_spectra", 1, "Add up spectra around the peak apex (needs to be a non-even integer)", {"advanced"});
-    defaults_.setMinInt("add_up_spectra", 1);
+    defaults_.setValue("add_up_spectra", 1, "Add up spectra around the peak apex (needs to be a non-even integer), if set to -1 all spectra across peak width are summed", {"advanced"});
+    //defaults_.setMinInt("add_up_spectra", 1);
     defaults_.setValue("spacing_for_spectra_resampling", 0.005, "If spectra are to be added, use this spacing to add them up", {"advanced"});
     defaults_.setMinFloat("spacing_for_spectra_resampling", 0.0);
     defaults_.setValue("uis_threshold_sn", -1, "S/N threshold to consider identification transition (set to -1 to consider all)");
@@ -169,7 +169,7 @@ namespace OpenMS
   void MRMFeatureFinderScoring::pickExperiment(const OpenSwath::SpectrumAccessPtr& input,
                                                FeatureMap& output,
                                                const OpenSwath::LightTargetedExperiment& transition_exp,
-                                               const TransformationDescription& trafo,
+                                               const TransformationDescription& trafo, 
                                                const std::vector<OpenSwath::SwathMap>& swath_maps,
                                                TransitionGroupMapType& transition_group_map)
   {
@@ -306,7 +306,7 @@ namespace OpenMS
   {
     MRMFeature idmrmfeature = trgr_ident.getFeaturesMuteable()[feature_idx];
     OpenSwath::IMRMFeature* idimrmfeature;
-    idimrmfeature = new MRMFeatureOpenMS(idmrmfeature);
+    idimrmfeature = new MRMFeatureOpenMS(idmrmfeature);  
 
     // get drift time upper/lower offset (this assumes that all chromatograms
     // are derived from the same precursor with the same drift time)
@@ -549,6 +549,9 @@ namespace OpenMS
     for (SignedSize feature_idx = 0; feature_idx < (SignedSize) mrmfeatures.size(); ++feature_idx)
     {
       auto& mrmfeature = mrmfeatures[feature_idx];
+
+      RangeRT rt_range(mrmfeature.getMetaValue("leftWidth"), mrmfeature.getMetaValue("rightWidth"));
+
       OpenSwath::IMRMFeature* imrmfeature;
       imrmfeature = new MRMFeatureOpenMS(mrmfeature);
 
@@ -686,7 +689,7 @@ namespace OpenMS
           scorer.calculateDIAScores(imrmfeature,
                                     transition_group_detection.getTransitions(),
                                     swath_maps, ms1_map_, diascoring_, *pep, scores, masserror_ppm,
-                                    drift_target, im_range);
+                                    drift_target, im_range, rt_range);
           mrmfeature.setMetaValue("masserror_ppm", masserror_ppm);
         }
         if (sonar_present && su_.use_sonar_scores)
@@ -826,6 +829,8 @@ namespace OpenMS
         // Add the DIA / SWATH scores, ion mobility scores and SONAR scores
         if (swath_present && su_.use_dia_scores_)
         {
+          mrmfeature.addScore("num_spectra_add", scores.numSpectraAdd);
+
           if (su_.use_ms2_isotope_scores)
           {
             mrmfeature.addScore("var_isotope_correlation_score", scores.isotope_correlation);

src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.cpp

@@ -81,6 +81,7 @@ namespace OpenMS
       "EXP_IM REAL," \
       "DELTA_IM REAL," \
       "TOTAL_MI REAL NULL," \
+      "NUM_SPEC_ADD INT NULL," \
       "VAR_BSERIES_SCORE REAL NULL," \
       "VAR_DOTPROD_SCORE REAL NULL," \
       "VAR_INTENSITY_SCORE REAL NULL," \
@@ -258,7 +259,7 @@ namespace OpenMS
                   << feature_it.getMetaValue("rightWidth") << "); ";
 
       sql_feature_ms2 << "INSERT INTO FEATURE_MS2 " \
-        "(FEATURE_ID, AREA_INTENSITY, TOTAL_AREA_INTENSITY, APEX_INTENSITY, EXP_IM, DELTA_IM, TOTAL_MI, "\
+        "(FEATURE_ID, AREA_INTENSITY, TOTAL_AREA_INTENSITY, APEX_INTENSITY, EXP_IM, DELTA_IM, TOTAL_MI, NUM_SPEC_ADD," \
         "VAR_BSERIES_SCORE, VAR_DOTPROD_SCORE, VAR_INTENSITY_SCORE, " \
         "VAR_ISOTOPE_CORRELATION_SCORE, VAR_ISOTOPE_OVERLAP_SCORE, VAR_LIBRARY_CORR,  "\
         "VAR_LIBRARY_DOTPROD, VAR_LIBRARY_MANHATTAN, VAR_LIBRARY_RMSD, VAR_LIBRARY_ROOTMEANSQUARE, "\
@@ -276,6 +277,7 @@ namespace OpenMS
                       << getScore(feature_it, "im_drift") << ", "
                       << getScore(feature_it, "im_delta") << ", "
                       << getScore(feature_it, "total_mi") << ", "
+                      << getScore(feature_it, "num_spectra_add") << ", "
                       << getScore(feature_it, "var_bseries_score") << ", "
                       << getScore(feature_it, "var_dotprod_score") << ", "
                       << getScore(feature_it, "var_intensity_score") << ", "