| OpenMS 2.5.0

ParentPeakMower.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Mathias Walzer $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 //
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
39 #include <OpenMS/KERNEL/MSSpectrum.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41
42 #include <vector>
43
44 namespace OpenMS
45 {
46
54 class OPENMS_DLLAPI ParentPeakMower :
55 public DefaultParamHandler
56 {
57 public:
58
59 // @name Constructors and Destructors
60 // @{
62 ParentPeakMower();
63
65 ParentPeakMower(const ParentPeakMower& source);
66
68 ~ParentPeakMower() override;
69 // @}
70
71 // @name Operators
72 // @{
74 ParentPeakMower& operator=(const ParentPeakMower& source);
75 // @}
76
77 // @name Accessors
78 // @{
80
82 template <typename SpectrumType>
83 void filterSpectrum(SpectrumType& spectrum)
84 {
85 typedef typename SpectrumType::Iterator Iterator;
86
87 clean_all_charge_states_ = (Int)param_.getValue("clean_all_charge_states");
88 consider_NH3_loss_ = (Int)param_.getValue("consider_NH3_loss");
89 consider_H2O_loss_ = (Int)param_.getValue("consider_H2O_loss");
90 window_size_ = (double)param_.getValue("window_size");
91 reduce_by_factor_ = (Int)param_.getValue("reduce_by_factor");
92 factor_ = (double)param_.getValue("factor");
93 set_to_zero_ = (Int)param_.getValue("set_to_zero");
94
95 if (spectrum.getMSLevel() == 1)
96 {
97 std::cerr << "Error: ParentPeakMower cannot be applied to MS level 1" << std::endl;
98 return;
99 }
100
101 //get precursor peak position precursor peak
102 double pre_pos = 0.0;
103 if (!spectrum.getPrecursors().empty()) pre_pos = spectrum.getPrecursors()[0].getMZ();
104
105 if (pre_pos == 0)
106 {
107 std::cerr << "ParentPeakMower: Warning, Precursor Position not set" << std::endl;
108 return;
109 }
110
111 Size pre_charge = spectrum.getPrecursors()[0].getCharge();
112 if (pre_charge == 0)
113 {
114 default_charge_ = (Size)param_.getValue("default_charge");
115 std::cerr << "ParentPeakMower: Warning, Precursor charge not set, assuming default charge (" << default_charge_ << ")" << std::endl;
116 pre_charge = default_charge_;
117 }
118
119 pre_pos *= pre_charge;
120
121 // identify the ranges which are to be considered
122 std::vector<DRange<1> > ranges;
123 for (Size z = 1; z <= pre_charge; ++z)
124 {
125 if (clean_all_charge_states_ || z == pre_charge)
126 {
127 // no adjusting needed for this charge
128 DPosition<1> pre_z_pos, pos;
129 DRange<1> range;
130
131 // adjust the m/z by weight of precursor and charge
132 pre_z_pos = DPosition<1>(pre_pos / double(z));
133 range = DRange<1>(pre_z_pos - window_size_, pre_z_pos + window_size_);
134 ranges.push_back(range);
135
136 if (consider_NH3_loss_)
137 {
138 pos = DPosition<1>(pre_z_pos - 17.0 / double(z));
139 range = DRange<1>(pos - window_size_, pos + window_size_);
140 ranges.push_back(range);
141 }
142 if (consider_H2O_loss_)
143 {
144 pos = DPosition<1>(pre_z_pos - 18.0 / double(z));
145 range = DRange<1>(pos - window_size_, pos + window_size_);
146 ranges.push_back(range);
147 }
148 }
149 }
150
151 //for (std::vector<DRange<1> >::const_iterator rit = ranges.begin(); rit != ranges.end(); ++rit)
152 //{
153 //std::cerr << *rit << std::endl;
154 //}
155
156 // apply the intensity reduction to the collected ranges
157 for (Iterator it = spectrum.begin(); it != spectrum.end(); ++it)
158 {
159 for (std::vector<DRange<1> >::const_iterator rit = ranges.begin(); rit != ranges.end(); ++rit)
160 {
161 if (rit->encloses(it->getPosition()))
162 {
163 if (reduce_by_factor_)
164 {
165 it->setIntensity(it->getIntensity() / factor_);
166 break;
167 }
168
169 if (set_to_zero_)
170 {
171 it->setIntensity(0.0);
172 break;
173 }
174 }
175 }
176 }
177
178 return;
179 }
180
181 void filterPeakSpectrum(PeakSpectrum& spectrum);
182
183 void filterPeakMap(PeakMap& exp);
184
185 //TODO reimplement DefaultParamHandler::updateMembers_()
186
188
189 private:
190 Size default_charge_;
191 bool clean_all_charge_states_;
192 bool consider_NH3_loss_;
193 bool consider_H2O_loss_;
194 double window_size_;
195 bool reduce_by_factor_;
196 double factor_;
197 bool set_to_zero_;
198
199 };
200
201 }
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::ParentPeakMower::window_size_
double window_size_
Definition: ParentPeakMower.h:194
OpenMS::ParentPeakMower::consider_NH3_loss_
bool consider_NH3_loss_
Definition: ParentPeakMower.h:192
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::ParentPeakMower::factor_
double factor_
Definition: ParentPeakMower.h:196
OpenMS::ParentPeakMower::reduce_by_factor_
bool reduce_by_factor_
Definition: ParentPeakMower.h:195
OpenMS::MSSpectrum::Iterator
ContainerType::iterator Iterator
Mutable iterator.
Definition: MSSpectrum.h:102
StandardTypes.h
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
Iterator
OpenMS::ParentPeakMower::clean_all_charge_states_
bool clean_all_charge_states_
Definition: ParentPeakMower.h:191
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::ParentPeakMower
ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions...
Definition: ParentPeakMower.h:54
OpenMS::ParentPeakMower::filterSpectrum
void filterSpectrum(SpectrumType &spectrum)
Definition: ParentPeakMower.h:83
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::DRange< 1 >
MSExperiment.h
OpenMS::ParentPeakMower::set_to_zero_
bool set_to_zero_
Definition: ParentPeakMower.h:197
DefaultParamHandler.h
MSSpectrum.h
OpenMS::ParentPeakMower::default_charge_
Size default_charge_
Definition: ParentPeakMower.h:190
OpenMS::DPosition< 1 >
OpenMS::ParentPeakMower::consider_H2O_loss_
bool consider_H2O_loss_
Definition: ParentPeakMower.h:193
double
OpenMS::MSSpectrum::getMSLevel
UInt getMSLevel() const
Returns the MS level.
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127