Swath3

src/openswathalgo/include/OpenMS/OPENSWATHALGO/ALGO/MRMScoring.h

@@ -36,6 +36,7 @@
 
 #include <string>
 
+#include <OpenMS/OPENSWATHALGO/DATASTRUCTURES/Matrix.h>
 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
 
 #include "OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h"
@@ -78,7 +79,7 @@ namespace OpenSwath
     /// Cross Correlation array
     typedef OpenSwath::Scoring::XCorrArrayType XCorrArrayType;
     /// Cross Correlation matrix
-    typedef std::vector<std::vector<XCorrArrayType> > XCorrMatrixType;
+    typedef OpenMS::Matrix<XCorrArrayType> XCorrMatrixType;
 
     typedef std::string String;
 
@@ -218,29 +219,29 @@ namespace OpenSwath
         std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators);
 
     /// non-mutable access to the MI matrix
-    const std::vector< std::vector<double> > & getMIMatrix() const;
+    const OpenMS::Matrix<double> & getMIMatrix() const;
     //@}
 
     /// non-mutable access to the MI contrast matrix
-    const std::vector< std::vector<double> > & getMIContrastMatrix() const;
+    const OpenMS::Matrix<double> & getMIContrastMatrix() const;
     //@}
 
     /// non-mutable access to the MI precursor contrast matrix
-    const std::vector< std::vector<double> > & getMIPrecursorContrastMatrix() const;
+    const OpenMS::Matrix<double> & getMIPrecursorContrastMatrix() const;
     //@}
 
     /// non-mutable access to the MI precursor combined matrix
-    const std::vector< std::vector<double> > & getMIPrecursorCombinedMatrix() const;
+    const OpenMS::Matrix<double> & getMIPrecursorCombinedMatrix() const;
     //@}
 
     /// Initialize the scoring object and building the MI matrix
-    void initializeMIMatrix(OpenSwath::IMRMFeature* mrmfeature, std::vector<String> native_ids);
+    void initializeMIMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<String>& native_ids);
 
     /// Initialize the scoring object and building the MI matrix of chromatograms of set1 (e.g. identification transitions) vs set2 (e.g. detection transitions)
-    void initializeMIContrastMatrix(OpenSwath::IMRMFeature* mrmfeature, std::vector<String> native_ids_set1, std::vector<String> native_ids_set2);
+    void initializeMIContrastMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<String>& native_ids_set1, const std::vector<String>& native_ids_set2);
 
     /// Initialize the scoring object and building the MI matrix
-    void initializeMIPrecursorMatrix(OpenSwath::IMRMFeature* mrmfeature, std::vector<String> precursor_ids);
+    void initializeMIPrecursorMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<String>& precursor_ids);
 
     /// Initialize the mutual information vector against the MS1 trace
     void initializeMIPrecursorContrastMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<String>& precursor_ids, const std::vector<String>& native_ids);
@@ -264,36 +265,50 @@ namespace OpenSwath
     /// the precomputed cross correlation matrix
     XCorrMatrixType xcorr_matrix_;
 
+    /// contains max Peaks from xcorr_matrix_
+    OpenMS::Matrix<int> xcorr_matrix_max_peak_;
+    OpenMS::Matrix<double> xcorr_matrix_max_peak_sec_;
     /// the precomputed contrast cross correlation
     XCorrMatrixType xcorr_contrast_matrix_;
     //@}
 
+    /// contains max Peaks from xcorr_contrast_matrix_
+    OpenMS::Matrix<int> xcorr_contrast_matrix_max_peak_;
+    OpenMS::Matrix<double > xcorr_contrast_matrix_max_peak_sec_;
     /// the precomputed cross correlation matrix of the MS1 trace
     XCorrMatrixType xcorr_precursor_matrix_;
 
+    /// contains max Peaks from xcorr_precursor_matrix_
+    OpenMS::Matrix<int> xcorr_precursor_matrix_max_peak_;
+    OpenMS::Matrix<double> xcorr_precursor_matrix_max_peak_sec_;
     /// the precomputed cross correlation against the MS1 trace
     XCorrMatrixType xcorr_precursor_contrast_matrix_;
     //@}
 
+    /// contains max Peaks from xcorr_precursor_contrast_matrix_
+    OpenMS::Matrix<int> xcorr_precursor_contrast_matrix_max_peak_;
+    OpenMS::Matrix<double > xcorr_precursor_contrast_matrix_max_peak_sec_;
     /// the precomputed cross correlation with the MS1 trace
     XCorrMatrixType xcorr_precursor_combined_matrix_;
     //@}
-
+    /// contains max Peaks from xcorr_precursor_combined_matrix_;
+    OpenMS::Matrix<int> xcorr_precursor_combined_matrix_max_peak_;
+    OpenMS::Matrix<double> xcorr_precursor_combined_matrix_max_peak_sec_;
     /// the precomputed mutual information matrix
-    std::vector< std::vector<double> > mi_matrix_;
 
+    OpenMS::Matrix<double> mi_matrix_;
     /// the precomputed contrast mutual information matrix
-    std::vector< std::vector<double> > mi_contrast_matrix_;
+    OpenMS::Matrix<double> mi_contrast_matrix_;
 
     /// the precomputed mutual information matrix of the MS1 trace
-    std::vector< std::vector<double> > mi_precursor_matrix_;
+    OpenMS::Matrix<double> mi_precursor_matrix_;
 
     /// the precomputed contrast mutual information matrix against the MS1 trace
-    std::vector< std::vector<double> > mi_precursor_contrast_matrix_;
+    OpenMS::Matrix<double> mi_precursor_contrast_matrix_;
     //@}
 
     /// the precomputed contrast mutual information matrix with the MS1 trace
-    std::vector< std::vector<double> > mi_precursor_combined_matrix_;
+    OpenMS::Matrix<double> mi_precursor_combined_matrix_;
     //@}
 
   };

src/openswathalgo/include/OpenMS/OPENSWATHALGO/ALGO/Scoring.h

@@ -115,11 +115,11 @@ namespace OpenSwath
     /// Calculate crosscorrelation on std::vector data (which is first normalized)
     /// NOTE: this replaces calcxcorr 
     OPENSWATHALGO_DLLAPI XCorrArrayType normalizedCrossCorrelation(std::vector<double>& data1,
-                                                                   std::vector<double>& data2, const int& maxdelay, const int& lag);
+                                                                   std::vector<double>& data2, const int maxdelay, const int lag);
 
     /// Calculate crosscorrelation on std::vector data without normalization
     OPENSWATHALGO_DLLAPI XCorrArrayType calculateCrossCorrelation(const std::vector<double>& data1,
-                                                                  const std::vector<double>& data2, const int& maxdelay, const int& lag);
+                                                                  const std::vector<double>& data2, const int maxdelay, const int lag);
 
     /// Find best peak in an cross-correlation (highest apex)
     OPENSWATHALGO_DLLAPI XCorrArrayType::const_iterator xcorrArrayGetMaxPeak(const XCorrArrayType & array);
@@ -131,11 +131,14 @@ namespace OpenSwath
     OPENSWATHALGO_DLLAPI void normalize_sum(double x[], unsigned int n);
 
     // Compute rank of vector elements
-    OPENSWATHALGO_DLLAPI std::vector<unsigned int> computeRank(const std::vector<double>& w);
+    OPENSWATHALGO_DLLAPI void computeRank(const std::vector<double>& v_temp, std::vector<unsigned int>& result);
 
     // Estimate rank-transformed mutual information between two vectors of data points
     OPENSWATHALGO_DLLAPI double rankedMutualInformation(std::vector<double>& data1, std::vector<double>& data2);
 
+    // Estimate rank-transformed mutual information between two vectors of rank
+    OPENSWATHALGO_DLLAPI double preCalcRankedMutualInformation(std::vector<unsigned int>& rank_vector1, std::vector<unsigned int>& rank_vector2);
+
     //@}
 
   }

src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATASTRUCTURES/Matrix.cpp

@@ -0,0 +1,41 @@
+// --------------------------------------------------------------------------
+//                   OpenMS -- Open-Source Mass Spectrometry
+// --------------------------------------------------------------------------
+// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
+// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
+//
+// This software is released under a three-clause BSD license:
+//  * Redistributions of source code must retain the above copyright
+//    notice, this list of conditions and the following disclaimer.
+//  * Redistributions in binary form must reproduce the above copyright
+//    notice, this list of conditions and the following disclaimer in the
+//    documentation and/or other materials provided with the distribution.
+//  * Neither the name of any author or any participating institution
+//    may be used to endorse or promote products derived from this software
+//    without specific prior written permission.
+// For a full list of authors, refer to the file AUTHORS.
+// --------------------------------------------------------------------------
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
+// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// --------------------------------------------------------------------------
+// $Maintainer: Timo Sachsenberg $
+// $Authors: $
+// --------------------------------------------------------------------------
+
+#include <OPENSWATHALGO/DATASTRUCTURES/Matrix.h>
+
+namespace OpenMS
+{
+    Matrix<int>    default_matrix_int;
+    Matrix<double> default_matrix_double;
+}