OpenMS  3.0.0
GoodDiffFilter.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 2002-2022.
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: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 //
35 
36 #pragma once
37 
39 
40 #include <map>
41 #include <string>
42 #include <cmath>
43 
44 namespace OpenMS
45 {
53  class OPENMS_DLLAPI GoodDiffFilter :
54  public FilterFunctor
55  {
56 public:
57 
58  // @name Constructors and Destructors
59  // @{
62 
64  GoodDiffFilter(const GoodDiffFilter & source);
65 
67  ~GoodDiffFilter() override;
68  // @}
69 
70  // @name Operators
71  // @{
73  GoodDiffFilter & operator=(const GoodDiffFilter & source);
74  // @}
75 
76  // @name Accessors
77  // @{
79  static FilterFunctor * create() { return new GoodDiffFilter(); }
80 
82  template <typename SpectrumType>
83  double apply(SpectrumType & spectrum)
84  {
85  double tolerance = (double)param_.getValue("tolerance");
86  double gooddiff = 0;
87  //iterate over all peaks
88  double totaldiff = 0;
89  for (Size i = 0; i < spectrum.size(); ++i)
90  {
91  //look for each peakdifference that is in range of aa residuemasses (56/187), if it could be a aa (aamass)
92  for (Size j = i; i + j < spectrum.size(); ++j)
93  {
94  double diff = spectrum[i + j].getPosition()[0] - spectrum[i].getPosition()[0];
95  if (diff < 56)
96  {
97  continue;
98  }
99 
100  if (diff > 187)
101  {
102  j = spectrum.size();
103  }
104  else
105  {
106  totaldiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
107  std::map<double, char>::const_iterator aait = aamass_.lower_bound(diff);
108  if (aait == aamass_.end())
109  {
110  continue;
111  }
112  //look for aamasses that fit diff
113  if (fabs(aait->first - diff) <= tolerance)
114  {
115  gooddiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
116  }
117  else
118  {
119  ++aait;
120  if ((aait) != aamass_.end() && fabs((aait)->first - diff) <= tolerance)
121  {
122  gooddiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
123  }
124  }
125  }
126  }
127  }
128 
129  return gooddiff / totaldiff;
130  }
131 
133  static const String getProductName()
134  {
135  return "GoodDiffFilter";
136  }
137 
138  // @}
139 
140 
141 private:
142 
144  std::map<double, char> aamass_;
145  };
146 }
147 
OpenMS::GoodDiffFilter
GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid ...
Definition: GoodDiffFilter.h:53
double
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
FilterFunctor.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::FilterFunctor
A FilterFunctor extracts some spectrum characteristics for quality assessment.
Definition: FilterFunctor.h:44
OpenMS::GoodDiffFilter::getProductName
static const String getProductName()
Definition: GoodDiffFilter.h:133
OpenMS::GoodDiffFilter::create
static FilterFunctor * create()
Definition: GoodDiffFilter.h:79
OpenMS::GoodDiffFilter::aamass_
std::map< double, char > aamass_
list of unique amino acid masses
Definition: GoodDiffFilter.h:144
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::GoodDiffFilter::apply
double apply(SpectrumType &spectrum)
Definition: GoodDiffFilter.h:83