[INTERNAL] OpenSwath diaPASEF Speedup

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

@@ -10,61 +10,74 @@
 
 #include <OpenMS/CHEMISTRY/AASequence.h>
 #include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>
-
+#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
 #include <vector>
-
 namespace OpenMS
 {
+  struct RangeMZ;
+  struct RangeMobility;
   class TheoreticalSpectrumGenerator;
   namespace DIAHelpers
   {
-
     /**
       @brief Helper functions for the DIA scoring of OpenSWATH
     */
     ///@{
 
     /**
-      @brief Integrate intensity in a spectrum from start to end
-
-      This function will integrate the intensity in a spectrum between mz_start
-      and mz_end, returning the total intensity and an intensity-weighted m/z
-      value.
+      @brief Integrate intensity in a spectrum from in @p mz_range (and @p im_range if defined)
+      returning the intensity-weighted m/z and im values as well as the total intensity.
 
-      @note If there is no signal, mz will be set to -1 and intensity to 0
+      @note If there is no signal, @p mz and @p im will be set to -1 and intensity to 0
       @return Returns true if a signal was found (and false if no signal was found)
 
     */
-    OPENMS_DLLAPI bool integrateWindow(const OpenSwath::SpectrumPtr& spectrum, double mz_start,
-                                       double mz_end, double& mz, double& intensity, bool centroided = false);
+    OPENMS_DLLAPI bool integrateWindow(const OpenSwath::SpectrumPtr& spectrum,
+                                       double& mz, double& im, double& intensity, const RangeMZ& mz_range, const RangeMobility& im_range, bool centroided = false);
 
     /**
-      @brief Integrate intensities in a spectrum from start to end
+      @brief Integrate intensity in SpectrumSequence in range @p mz_range (and @p im_range if defined)
+      returning the intensity-weighted m/z and im values as well as the total intensity.
+
+      @note If there is no signal, @p mz and @p im will be set to -1 and intensity to 0
+      @return Returns true if a signal was found (and false if no signal was found)
+    */
+    OPENMS_DLLAPI bool integrateWindow(const SpectrumSequence& spectrum,
+                                       double& mz, double& im, double& intensity, const RangeMZ& mz_range, const RangeMobility& im_range, bool centroided = false);
+
+    /**
+      @brief Integrate intensities in a spectrum in range @p im_range (if defined) for multiple windows.
+      @param windows_center is a vector of the center location of the windows.
+      @param width is the width of the windows across mz
+      @param im_range is the range of the IM dimension (if defined)
+      @param remove_zero is a flag indicating whether to remove zero intensity windows
+
+      Returns:
+      @param[out] integrated_windows_intensity is a vector of the integrated intensity for each window
+      @param[out] integrated_windows_mz is a vector of the integrated intensity-weighted m/z for each window
+      @param[out] integrated_windows_im is a vector of the integrated intensity-weighted im for each window
     */
     OPENMS_DLLAPI void integrateWindows(const OpenSwath::SpectrumPtr& spectrum, //!< [in] Spectrum
                                         const std::vector<double>& windows_center, //!< [in] center location
                                         double width,
                                         std::vector<double>& integrated_windows_intensity,
                                         std::vector<double>& integrated_windows_mz,
+					std::vector<double>& integrated_windows_im,
+                                        const RangeMobility& im_range,
                                         bool remove_zero = false);
 
-    /**
-      @brief Integrate intensity in an ion mobility spectrum from start to end
-
-      This function will integrate the intensity in a spectrum between mz_start
-      and mz_end, returning the total intensity and an intensity-weighted drift
-      time value.
 
-      @note If there is no signal, mz will be set to -1 and intensity to 0
+    /**
+      @brief Integrate intensities of a SpectrumSequence in range @p im_range for multiple windows.
     */
-    OPENMS_DLLAPI void integrateDriftSpectrum(const OpenSwath::SpectrumPtr& spectrum,
-                                              double mz_start,
-                                              double mz_end,
-                                              double & im,
-                                              double & intensity,
-                                              double drift_start,
-                                              double drift_end);
-
+    OPENMS_DLLAPI void integrateWindows(const SpectrumSequence& spectrum, //!< [in] Spectrum
+                                        const std::vector<double>& windows_center, //!< [in] center location
+                                        double width,
+                                        std::vector<double>& integrated_windows_intensity,
+                                        std::vector<double>& integrated_windows_mz,
+                                        std::vector<double>& integrated_windows_im,
+                                        const RangeMobility& im_range,
+                                        bool remove_zero = false);
     /**
       @brief Adjust left/right window based on window and whether its ppm or not
     */
@@ -136,8 +149,27 @@ namespace OpenMS
     OPENMS_DLLAPI void extractFirst(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
     /// extract second from vector of pairs
     OPENMS_DLLAPI void extractSecond(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
-
+
+    /** @brief optionally convert a DIA extraction window from ppm to m/z
+      @param dia_extraction_window - how wide the extraction window is total (can be in m/z or ppm)
+      @param ppm  - whether the extraction window is in ppm or not
+      @return the extraction window in m/z
+    */
+    OPENMS_DLLAPI RangeMZ createMZRangePPM(double mz_ref, double dia_extraction_window, const bool ppm);
+
+
+    /**
+      @brief Helper function for integrating a spectrum.
+    */
+    OPENMS_DLLAPI void integrateWindow_(const OpenSwath::SpectrumPtr& spectrum,
+                                double & mz,
+                                double & im,
+                                double & intensity,
+                                const RangeMZ & mz_range,
+                                const RangeMobility & im_range,
+                                bool centroided);
+    }
+
     ///}@
-  }
-}
+} //namespace OpenMS
 

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

@@ -13,6 +13,7 @@
 #include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
+#include <OpenMS/ANALYSIS/OPENSWATH/DIAHelper.h>
 
 namespace OpenMS
 {
@@ -53,8 +54,9 @@ namespace OpenMS
       and compute manhattan distance and dotprod score between spectrum intensities
       and simulated spectrum.
     */
-    void score(OpenSwath::SpectrumPtr spec,
+    void score(const SpectrumSequence& spec,
                const std::vector<OpenSwath::LightTransition>& lt,
+               const RangeMobility& im_range,
                double& dotprod,
                double& manhattan) const;
 
@@ -63,7 +65,7 @@ namespace OpenMS
       the SpectrumAccessPtr for all transitions groups in the LightTargetedExperiment.
     */
     void operator()(const OpenSwath::SpectrumAccessPtr& swath_ptr,
-                    OpenSwath::LightTargetedExperiment& transition_exp_used,
+                    OpenSwath::LightTargetedExperiment& transition_exp_used, const RangeMobility& range_im,
                     OpenSwath::IDataFrameWriter* ivw) const;
   };
 

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

@@ -16,6 +16,8 @@
 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h>
 #include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
+#include <OpenMS/KERNEL/RangeManager.h>
+
 namespace OpenMS
 {
   class TheoreticalSpectrumGenerator;
@@ -82,15 +84,17 @@ namespace OpenMS
     //@{
     /// Isotope scores, see class description
     void dia_isotope_scores(const std::vector<TransitionType>& transitions,
-                            SpectrumPtrType spectrum,
+                            SpectrumSequence& spectrum,
                             OpenSwath::IMRMFeature* mrmfeature,
+                            const RangeMobility& im_range,
                             double& isotope_corr,
                             double& isotope_overlap) const;
 
     /// Massdiff scores, see class description
     void dia_massdiff_score(const std::vector<TransitionType>& transitions,
-                            const SpectrumPtrType& spectrum,
+                            const SpectrumSequence& spectrum,
                             const std::vector<double>& normalized_library_intensity,
+                            const RangeMobility& im_range,
                             double& ppm_score,
                             double& ppm_score_weighted,
                             std::vector<double>& diff_ppm) const;
@@ -103,23 +107,23 @@ namespace OpenMS
       @param ppm_score Resulting score
       @return False if no signal was found (and no sensible score calculated), true otherwise
     */
-    bool dia_ms1_massdiff_score(double precursor_mz, SpectrumPtrType spectrum,
+    bool dia_ms1_massdiff_score(double precursor_mz, const SpectrumSequence& spectrum, const RangeMobility& im_range,
                                 double& ppm_score) const;
 
     /// Precursor isotope scores for precursors (peptides and metabolites)
-    void dia_ms1_isotope_scores_averagine(double precursor_mz, const SpectrumPtrType& spectrum,
-                                          double& isotope_corr, double& isotope_overlap, int charge_state) const;
-    void dia_ms1_isotope_scores(double precursor_mz, const SpectrumPtrType& spectrum,
+    void dia_ms1_isotope_scores_averagine(double precursor_mz, const SpectrumSequence& spectrum, int charge_state, RangeMobility& im_range,
+                                          double& isotope_corr, double& isotope_overlap) const;
+    void dia_ms1_isotope_scores(double precursor_mz, const std::vector<SpectrumPtrType>& spectrum, RangeMobility& im_range,
                                 double& isotope_corr, double& isotope_overlap, const EmpiricalFormula& sum_formula) const;
 
-
     /// b/y ion scores
-    void dia_by_ion_score(const SpectrumPtrType& spectrum, AASequence& sequence,
-                          int charge, double& bseries_score, double& yseries_score) const;
+    void dia_by_ion_score(const SpectrumSequence& spectrum, AASequence& sequence,
+                          int charge, const RangeMobility& im_range, double& bseries_score, double& yseries_score) const;
 
     /// Dotproduct / Manhattan score with theoretical spectrum
-    void score_with_isotopes(SpectrumPtrType spectrum,
+    void score_with_isotopes(SpectrumSequence& spectrum,
                              const std::vector<TransitionType>& transitions,
+                             const RangeMobility& im_range,
                              double& dotprod,
                              double& manhattan) const;
     //@}
@@ -137,8 +141,9 @@ namespace OpenMS
 
     /// Subfunction of dia_isotope_scores
     void diaIsotopeScoresSub_(const std::vector<TransitionType>& transitions,
-                              const SpectrumPtrType& spectrum,
+                              const SpectrumSequence& spectrum,
                               std::map<std::string, double>& intensities,
+                              const RangeMobility& im_range,
                               double& isotope_corr,
                               double& isotope_overlap) const;
 
@@ -152,8 +157,8 @@ namespace OpenMS
 private:
 
     /**
-      @brief Determine whether the current m/z value is a monoisotopic peak 
-      
+      @brief Determine whether the current m/z value is a monoisotopic peak
+
       This function will try to determine whether the current peak is a
       monoisotopic peak or not. It will do so by searching for an intense peak
       at a lower m/z that could explain the current peak as part of a isotope
@@ -166,7 +171,7 @@ namespace OpenMS
       @param nr_occurrences Will contain the maximum ratio of a peaks intensity compared to the monoisotopic peak intensity how often a peak is found at lower m/z than mono_mz with an intensity higher than mono_int. Multiple charge states are tested, see class parameter dia_nr_charges_
 
     */
-    void largePeaksBeforeFirstIsotope_(const SpectrumPtrType& spectrum, double mono_mz, double mono_int, int& nr_occurrences, double& max_ratio) const;
+    void largePeaksBeforeFirstIsotope_(const SpectrumSequence& spectrum, double mono_mz, double mono_int, int& nr_occurrences, double& max_ratio, const RangeMobility& im_range) const;
 
     /**
       @brief Compare an experimental isotope pattern to a theoretical one
@@ -202,9 +207,8 @@ namespace OpenMS
 
     /// Get the intensities of isotopes around @p precursor_mz in experimental @p spectrum
     /// and fill @p isotopes_int.
-    void getIsotopeIntysFromExpSpec_(double precursor_mz, const SpectrumPtrType& spectrum,
-                                     std::vector<double>& isotopes_int,
-                                     int charge_state) const;
+    void getIsotopeIntysFromExpSpec_(double precursor_mz, const SpectrumSequence& spectrum, int charge_state, const RangeMobility& im_range,
+                                     std::vector<double>& isotopes_int) const;
 
     // Parameters
     double dia_extract_window_;
@@ -219,4 +223,3 @@ namespace OpenMS
     TheoreticalSpectrumGenerator * generator;
   };
 }
-