Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
EmgFitter1D.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2013.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Clemens Groepl $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 
35 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_EMGFITTER1D_H
36 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_EMGFITTER1D_H
37 
39 
40 namespace OpenMS
41 {
47  class OPENMS_DLLAPI EmgFitter1D :
48  public LevMarqFitter1D
49  {
50 public:
51 
53  EmgFitter1D();
54 
56  EmgFitter1D(const EmgFitter1D & source);
57 
59  virtual ~EmgFitter1D();
60 
62  virtual EmgFitter1D & operator=(const EmgFitter1D & source);
63 
65  static Fitter1D * create()
66  {
67  return new EmgFitter1D();
68  }
69 
71  static const String getProductName()
72  {
73  return "EmgFitter1D";
74  }
75 
77  QualityType fit1d(const RawDataArrayType & range, InterpolationModel * & model);
78 
79 protected:
80 
82  struct Data
83  {
84  typedef Peak1D PeakType;
85  typedef std::vector<PeakType> RawDataArrayType;
86 
89  };
90 
92  virtual void setInitialParameters_(const RawDataArrayType & set);
93 
95  static Int residual_(const gsl_vector * x, void * params, gsl_vector * f);
96 
98  static Int jacobian_(const gsl_vector * x, void * params, gsl_matrix * J);
99 
101  static Int evaluate_(const gsl_vector * x, void * params, gsl_vector * f, gsl_matrix * J);
102 
106  void printState_(Int iter, gsl_multifit_fdfsolver * s);
107 
116 
117  void updateMembers_();
118  };
119 
120 }
121 
122 #endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_EMGFITTER1D_H
Peak1D PeakType
Definition: EmgFitter1D.h:84
Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization...
Definition: LevMarqFitter1D.h:52
A more convenient string class.
Definition: String.h:56
CoordinateType width_
Parameter of emg - peak width.
Definition: EmgFitter1D.h:111
CoordinateType retention_
Parameter of emg - peak retention time.
Definition: EmgFitter1D.h:115
Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL...
Definition: EmgFitter1D.h:47
static Fitter1D * create()
create new EmgFitter1D object (function needed by Factory)
Definition: EmgFitter1D.h:65
RawDataArrayType set
Definition: EmgFitter1D.h:88
Helper struct (contains the size of an area and a raw data container)
Definition: EmgFitter1D.h:82
Abstract class for 1D-models that are approximated using linear interpolation.
Definition: InterpolationModel.h:55
CoordinateType symmetry_
Parameter of emg - peak symmetry.
Definition: EmgFitter1D.h:113
static const String getProductName()
name of the model (needed by Factory)
Definition: EmgFitter1D.h:71
CoordinateType height_
Parameter of emg - peak height.
Definition: EmgFitter1D.h:109
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:55
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
Abstract base class for all 1D-dimensional model fitter.
Definition: Fitter1D.h:59
Size n
Definition: EmgFitter1D.h:87
std::vector< PeakType > RawDataArrayType
Definition: EmgFitter1D.h:85
int Int
Signed integer type.
Definition: Types.h:100
std::vector< PeakType > RawDataArrayType
Raw data container type using for the temporary storage of the input data.
Definition: Fitter1D.h:76

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:13 using doxygen 1.8.5