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BelaPfeffer wants to merge 38 commits into cbielow:develop from BelaPfeffer:abgabe

AUTHORS

-Original file line number
+Diff line change
@@ Expand Up / @@ -15,6 +15,7 @@ the authors tag in the respective file header. @@
      - Anton Kriese
      - Anton Pervukhin
      - Bastian Blank
+     - Bela Pfeffer
      - Chenghao Zhu
      - Chris Bauer
      - Chris Bielow
@@ Expand Down Expand Up / @@ -120,4 +121,4 @@ the authors tag in the respective file header. @@
      - Witold Wolski
      - Xiao Liang
      - Yasset Perez-Riverol
-     - Peter Jones
+     - Peter Jones

contrib

Submodule contrib updated 1 files

+12 −11		CMakeLists.txt

src/openms/include/OpenMS/FORMAT/HANDLERS/XMLHandler.h

-Original file line number
+Diff line change
@@ Expand Up / @@ -11,7 +11,7 @@ @@
     #include <OpenMS/CONCEPT/Types.h>
     #include <OpenMS/CONCEPT/Macros.h>
-    #include <OpenMS/DATASTRUCTURES/ListUtils.h> // StringList
     #include <OpenMS/DATASTRUCTURES/DateTime.h>
     #include <OpenMS/DATASTRUCTURES/DataValue.h>
     #include <OpenMS/DATASTRUCTURES/ListUtils.h>
@@ Expand All / @@ -21,6 +21,7 @@ @@
     #include <xercesc/util/XMLString.hpp>
     #include <iosfwd>
+    #include <iostream>
     #include <string>
     #include <memory>
@@ Expand Down Expand Up / @@ -224,8 +225,18 @@ namespace OpenMS @@
           // Converts from a wide-character string to a narrow-character string.
           inline static String toNative_(const XMLCh* str)
-          {
-            return String(unique_xerces_ptr<char>(xercesc::XMLString::transcode(str)).get());
+          {
+            String r;
+            XMLSize_t l = xercesc::XMLString::stringLen(str);
+            if(isASCII(str, l))
+            {
+              appendASCII(str,l,r);
+            }
+            else
+            {
+              r = (unique_xerces_ptr<char>(xercesc::XMLString::transcode(str)).get());
+            }
+            return r;
           }
           // Converts from a wide-character string to a narrow-character string.
@@ Expand All / @@ -242,6 +253,9 @@ namespace OpenMS @@
           /// Destructor
           ~StringManager();
+          /// Calculates the length of a XMLCh* string using SIMDe
+          static int strLength(const XMLCh* input_ptr);
           /// Transcode the supplied C string to a xerces string
           inline static XercesString convert(const char * str)
           {
@@ Expand Down Expand Up / @@ -283,7 +297,12 @@ namespace OpenMS @@
           {
             return toNative_(str);
           }
+          /// Checks if supplied if chars in XMLCh* can be encoded with ASCII
+          static bool isASCII(const XMLCh * chars, const XMLSize_t length);
+          /// Compresses eight 8x16bit Chars in XMLCh* to 8x8bit Chars by cutting upper byte
+          static void compress64 (const XMLCh * input_it, char* output_it);
           /**
            * @brief Transcodes the supplied XMLCh* and appends it to the OpenMS String
            *
@@ Expand Down @@

src/openms/include/OpenMS/IONMOBILITY/IMTypes.h

-Original file line number
+Diff line change
@@ Expand Up / @@ -40,12 +40,18 @@ namespace OpenMS @@
       OPENMS_DLLAPI const std::string& toString(const DriftTimeUnit value);
       /// Different ways to represent ion mobility data in a spectrum
+      /// Note:
+      /// 1. MIXED is only used for MSExperiment, not for MSSpectrum
+      /// 2. UNKNOWN should be used if the format is not yet determined.
+      /// FileHandler or e.g. IM peak picker should ideally set the format a known value.
       enum class IMFormat
       {
         NONE,            ///< no ion mobility
         CONCATENATED,    ///< ion mobility frame is stacked in a single spectrum (i.e. has an IM float data array)
         MULTIPLE_SPECTRA,///< ion mobility is recorded as multiple spectra per frame (i.e. has one IM annotation per spectrum)
         MIXED,           ///< an MSExperiment contains both CONCATENATED and MULTIPLE_SPECTRA
+        CENTROIDED,      ///< ion mobility of peaks after centroiding in IM dimension. Ion mobility is annotated in a single float data array (i.e., each peak might have a different IM value in the data array); identical to CONCATENATED in terms of data layout.
+        UNKNOWN,         ///< ion mobility format not yet determined.
         SIZE_OF_IMFORMAT
       };
       /// Names of IMFormat
@@ Expand Down @@

src/openms/include/OpenMS/METADATA/MetaInfoInterface.h

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -36,7 +36,7 @@ namespace OpenMS
  
    public:

        /// Constructor

        MetaInfoInterface();

        MetaInfoInterface() = default;

        /// Copy constructor

        MetaInfoInterface(const MetaInfoInterface& rhs);

        /// Move constructor

    @@ -107,8 +107,8 @@ namespace OpenMS
  
        /// Creates the MetaInfo object if it does not exist

        inline void createIfNotExists_();

        /// Pointer to the MetaInfo object (0 by default)

        MetaInfo* meta_;

        /// Pointer to the MetaInfo object

        MetaInfo* meta_ = nullptr;

      };

    } // namespace OpenMS

src/openms/include/OpenMS/METADATA/SpectrumSettings.h

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -3,7 +3,7 @@
  
    //

    // --------------------------------------------------------------------------

    // $Maintainer: Timo Sachsenberg $

    // $Authors: Marc Sturm $

    // $Authors: Marc Sturm, Timo Sachsenberg $

    // --------------------------------------------------------------------------

    #pragma once

    @@ -16,6 +16,7 @@
  
    #include <OpenMS/METADATA/Product.h>

    #include <OpenMS/METADATA/PeptideIdentification.h>

    #include <OpenMS/METADATA/DataProcessing.h>

    #include <OpenMS/IONMOBILITY/IMTypes.h>

    #include <map>

    #include <vector>

    @@ -52,13 +53,13 @@ namespace OpenMS
  
        static const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE];

        /// Constructor

        SpectrumSettings();

        SpectrumSettings() = default;

        /// Copy constructor

        SpectrumSettings(const SpectrumSettings &) = default;

        /// Move constructor

        SpectrumSettings(SpectrumSettings&&) = default;

        SpectrumSettings(SpectrumSettings&&) noexcept = default;

        /// Destructor

        ~SpectrumSettings();

        ~SpectrumSettings() noexcept = default;

        // Assignment operator

        SpectrumSettings & operator=(const SpectrumSettings &) = default;

    @@ -78,6 +79,16 @@ namespace OpenMS
  
        ///sets the spectrum type

        void setType(SpectrumType type);

        /// @brief sets the IMFormat of the spectrum

        /// @param im_type

        void setIMFormat(const IMFormat& im_type);

        /// @brief returns the IMFormat of the spectrum if set. Otherwise UNKNOWN (default). 

        /// 

        /// Note: If UNKNOWN, use IMFormat::determineIMFormat to determine the IMFormat based on the data.

        /// @return IMFormat of the spectrum

        IMFormat getIMFormat() const;

        /// returns the native identifier for the spectrum, used by the acquisition software.

        const String & getNativeID() const;

        /// sets the native identifier for the spectrum, used by the acquisition software.

    @@ -141,7 +152,8 @@ namespace OpenMS
  
    protected:

        SpectrumType type_;

        SpectrumType type_ = UNKNOWN;

        IMFormat im_type_ = IMFormat::UNKNOWN;

        String native_id_;

        String comment_;

        InstrumentSettings instrument_settings_;

src/openms/include/OpenMS/PROCESSING/CENTROIDING/PeakPickerIM.h

-Original file line number
+Diff line change
@@ -0,0 +1,71 @@
+    // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+    // SPDX-License-Identifier: BSD-3-Clause
+    //
+    // --------------------------------------------------------------------------
+    // $Author: Timo Sachsenberg, Mohammed Alhigaylan $
+    // $Maintainer: Timo Sachsenberg $
+    // -------------------------------------------------------------------------------------------------------------------------------------------
+    #pragma once
+    #include <OpenMS/KERNEL/MSSpectrum.h>
+    #include <OpenMS/DATASTRUCTURES/Param.h>
+    namespace OpenMS
+    {
+      /**
+        @brief Peak picking algorithm for ion mobility data
+      @ingroup PeakPicking
+          */
+      class OPENMS_DLLAPI PeakPickerIM
+      {
+      public:
+        /// Default constructor initializing parameters with default values.
+        PeakPickerIM();
+        /// Destructor.
+        virtual ~PeakPickerIM();
+        /// Picks ion mobility traces from the given spectrum.
+        void pickIMTraces(MSSpectrum& spectrum);
+        /// Sets the parameters for peak picking.
+        void setParameters(const Param& param);
+        /// Gets the current parameters.
+        Param getParameters() const;
+      protected:
+        /// Updates internal member variables when parameters are changed.
+        void updateMembers_();
+        /// Returns the default parameters.
+        Param getDefaultParameters() const;
+        /// Stores the parameters for peak picking.
+        Param parameters_;
+      private:
+        /// determine sampling rate for linear resampler
+        double computeOptimalSamplingRate(const std::vector<MSSpectrum>& spectra);
+        /// Sum up the intensity of data points with nearly identical float values
+        MSSpectrum SumFrame(const MSSpectrum& spectrum, double ppm_tolerance = 0.01);
+        /// Compute lower and upper m/z bounds based on ppm
+        std::pair<double, double> ppmBounds(double mz, double ppm);
+        /// Extract ion mobility traces as MSSpectra from the raw TimsTOF frame
+        /// Ion mobility is temporarily written in place of m/z inside Peak1D object.
+        /// raw m/z values are allocated to float data arrays with the label 'raw_mz'
+        std::vector<MSSpectrum> extractIonMobilityTraces(
+          const MSSpectrum& picked_spectrum,
+          const MSSpectrum& raw_spectrum);
+        /// compute m/z and ion mobility centers for picked traces. Returns centroided spectrum.
+        MSSpectrum ComputeCenters(const std::vector<MSSpectrum>& mobilogram_traces,
+                                  const std::vector<MSSpectrum>& picked_traces);
+      };
+    } // namespace OpenMS

src/openms/include/OpenMS/PROCESSING/CENTROIDING/sources.cmake

-Original file line number
+Diff line change
@@ Expand Up / @@ -5,6 +5,7 @@ set(directory include/OpenMS/PROCESSING/CENTROIDING) @@
     set(sources_list_h
     PeakPickerHiRes.h
     PeakPickerIterative.h
+    PeakPickerIM.h
     )
     ### add path to the filenames
@@ Expand Down @@

src/openms/source/FEATUREFINDER/FeatureFinderAlgorithmPicked.cpp

-Original file line number
+Diff line change
@@ Expand Up / @@ -1007,7 +1007,7 @@ namespace OpenMS @@
         {
           //store map of abort reasons for failed seeds
           FeatureMap abort_map;
-          abort_map.reserve(abort_reasons_.size());
+          abort_map.reserve( abort_reasons_.size());
           Size counter = 0;
           for (std::map<Seed, String>::iterator it2 = abort_reasons_.begin(); it2 != abort_reasons_.end(); ++it2, ++counter)
           {
@@ Expand Down @@

src/openms/source/FEATUREFINDER/GaussTraceFitter.cpp

-Original file line number
+Diff line change
@@ Expand Up / @@ -7,7 +7,7 @@ @@
     // --------------------------------------------------------------------------
     #include <OpenMS/FEATUREFINDER/GaussTraceFitter.h>
+    #include <iostream>
     #include <OpenMS/CONCEPT/LogStream.h>
     #include <Eigen/Core>
@@ Expand Down Expand Up / @@ -171,19 +171,23 @@ namespace OpenMS @@
         double sig_sq = pow(sig, 2);
         double sig_3 = pow(sig, 3);
         double c_fac = -0.5 / sig_sq;
+        // std::cout << sig_3 << std::endl;
         Size count = 0;
         for (Size t = 0; t < m_data->traces_ptr->size(); ++t)
         {
           const FeatureFinderAlgorithmPickedHelperStructs::MassTrace& trace = (*m_data->traces_ptr)[t];
           double weight = m_data->weighted ? trace.theoretical_int : 1.0;
+          double constant = trace.theoretical_int * weight;
           for (Size i = 0; i < trace.peaks.size(); ++i)
           {
             double rt = trace.peaks[i].first;
             double e = exp(c_fac * pow(rt - x0, 2));
-            J(count, 0) = trace.theoretical_int * e * weight;
-            J(count, 1) = trace.theoretical_int * height * e * (rt - x0) / sig_sq * weight;
-            J(count, 2) = 0.125* trace.theoretical_int* height* e* pow(rt - x0, 2) / sig_3 * weight;
+            double eConstant = constant * e;
+            J(count, 0) = eConstant;
+            J(count, 1) = eConstant* height * (rt - x0) / sig_sq;
+            J(count, 2) = 0.125* eConstant * height * pow(rt - x0, 2) / sig_3;
             ++count;
           }
         }
@@ Expand Down @@

src/openms/source/FORMAT/HANDLERS/MzMLHandler.cpp

-Original file line number
+Diff line change
@@ Expand Up / @@ -18,8 +18,11 @@ @@
     #include <OpenMS/INTERFACES/IMSDataConsumer.h>
     #include <OpenMS/SYSTEM/File.h>
     #include <map>
     namespace OpenMS::Internal
     {
@@ Expand Down @@

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