libopenms-dev 1.11.1-3 / usr / include / OpenMS / TRANSFORMATIONS / FEATUREFINDER / LmaGaussFitter1D.h

This file is indexed.

/usr/include/OpenMS/TRANSFORMATIONS/FEATUREFINDER/LmaGaussFitter1D.h is in libopenms-dev 1.11.1-3.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below. 

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// 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: Clemens Groepl $
// $Authors: $
// --------------------------------------------------------------------------

#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_LMAGAUSSFITTER1D_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_LMAGAUSSFITTER1D_H

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/LevMarqFitter1D.h>

namespace OpenMS
{
  /**
    @brief Gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization.

    @htmlinclude OpenMS_LmaGaussFitter1D.parameters
  */
  class OPENMS_DLLAPI LmaGaussFitter1D :
    public LevMarqFitter1D
  {
public:

    /// Default constructor
    LmaGaussFitter1D();

    /// copy constructor
    LmaGaussFitter1D(const LmaGaussFitter1D & source);

    /// destructor
    virtual ~LmaGaussFitter1D();

    /// assignment operator
    virtual LmaGaussFitter1D & operator=(const LmaGaussFitter1D & source);

    /// create new LmaGaussFitter1D object (function needed by Factory)
    static Fitter1D * create()
    {
      return new LmaGaussFitter1D();
    }

    /// name of the model (needed by Factory)
    static const String getProductName()
    {
      return "LmaGaussFitter1D";
    }

    /// return interpolation model
    QualityType fit1d(const RawDataArrayType & range, InterpolationModel * & model);

protected:

    /// Helper struct (contains the size of an area and a raw data container)
    struct Data
    {
      typedef Peak1D PeakType;
      typedef std::vector<PeakType> RawDataArrayType;

      Size n;
      RawDataArrayType set;
    };

    /// Compute start parameter
    void setInitialParameters_(const RawDataArrayType & set);

    /// Evaluation of the target function for nonlinear optimization
    static Int residual_(const gsl_vector * x, void * params, gsl_vector * f);

    /// Compute the Jacobian matrix, where each row of the matrix corresponds to a point in the data
    static Int jacobian_(const gsl_vector * x, void * params, gsl_matrix * J);

    /// Driver function for the evaluation of function and jacobian
    static Int evaluate_(const gsl_vector * x, void * params, gsl_vector * f, gsl_matrix * J);

    /** Diplay the intermediate state of the solution. The solver state contains
        the vector s->x which is the current position, and the vector s->f with
        corresponding function values */
    void printState_(Int iter, gsl_multifit_fdfsolver * s);

    /// parameter of gauss function: standard deviation
    CoordinateType standard_deviation_;
    /// parameter of gauss function: scale factor
    CoordinateType scale_factor_;
    /// parameter of gauss function: expected value
    CoordinateType expected_value_;

    void updateMembers_();
  };

}

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_LMAGAUSSFITTER1D_H

APT Browse - Built by Thomas Orozco.