libpappsomspp
Library for mass spectrometry
filtertandemremovec13.cpp
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1 /**
2  * \file pappsomspp/filers/filtertandemremovec13.h
3  * \date 26/04/2019
4  * \author Olivier Langella
5  * \brief new implementation of the X!Tandem filter to remove isotopes in an MS2
6  * signal
7  */
8 
9 /*******************************************************************************
10  * Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.fr>.
11  *
12  * This file is part of the PAPPSOms++ library.
13  *
14  * PAPPSOms++ is free software: you can redistribute it and/or modify
15  * it under the terms of the GNU General Public License as published by
16  * the Free Software Foundation, either version 3 of the License, or
17  * (at your option) any later version.
18  *
19  * PAPPSOms++ is distributed in the hope that it will be useful,
20  * but WITHOUT ANY WARRANTY; without even the implied warranty of
21  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22  * GNU General Public License for more details.
23  *
24  * You should have received a copy of the GNU General Public License
25  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
26  *
27  ******************************************************************************/
28 
29 #include "filtertandemremovec13.h"
30 
31 #include "../../massspectrum/massspectrum.h"
32 #include <algorithm>
33 
34 using namespace pappso;
35 
37  double minimum_mz)
38 {
39  m_arbitrary_minimum_mz = minimum_mz;
41 }
42 
43 
45 {
48 }
49 
52 {
53 
54  MassSpectrum massSpectrum;
55 
56  if(data_points.size() > 0)
57  {
58  // auto it_write = data_points.begin();
59  auto it_read = data_points.begin() + 1;
60  auto it_end = data_points.end();
61 
62 
63  DataPoint value_write = *data_points.begin();
64  double last_mz = value_write.x;
65  while(it_read != it_end)
66  {
67  if((it_read->x - last_mz) >= m_arbitrary_range_between_isotopes ||
68  it_read->x < m_arbitrary_minimum_mz)
69  {
70  massSpectrum.push_back(value_write);
71  value_write = *it_read;
72  last_mz = value_write.x;
73  }
74  else if(it_read->y > value_write.y)
75  {
76  value_write = *it_read;
77  }
78  it_read++;
79  }
80  massSpectrum.push_back(value_write);
81  }
82 
83  data_points = std::move(massSpectrum);
84  return data_points;
85 }
Deisotope the mass spectrum this mass spectrum is iterated over and according to a data point-based m...
MassSpectrum & filter(MassSpectrum &data_points) const override
FilterTandemDeisotope(double mz_range_max=0.95, double minimum_mz=200.0)
Class to represent a mass spectrum.
Definition: massspectrum.h:71
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
pappso_double x
Definition: datapoint.h:23
pappso_double y
Definition: datapoint.h:24