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CentroidPeak.h
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Markus Mueller $
33 // --------------------------------------------------------------------------
34 //
35 /*
36 * CentroidPeak.h
37 * PeakDetection
38 *
39 * Created by Markus Mueller on 10/19/06.
40 *
41 * Ported to OpenMS by Florian Zeller, florian.zeller@bsse.ethz.ch
42 * December 2010
43 *
44 */
45
46 #pragma once
47
48 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.h>
49
50 #include <OpenMS/CONCEPT/Types.h>
51
52 #include <ostream>
53 #include <cmath>
54 #include <vector>
55
56 namespace OpenMS
57 {
58
59 class SUPERHIRN_DLLAPI CentroidPeak
60 {
61 public:
62
63 //static int sfCentroidWindowWidth;
64
65 CentroidPeak();
66 CentroidPeak(double, double);
67 CentroidPeak(double, double, double);
68 CentroidPeak(const CentroidPeak &);
69 // Copy constructor
70 CentroidPeak(const CentroidPeak *);
71
72 CentroidPeak & operator=(const CentroidPeak &);
73
74 bool operator<(const CentroidPeak &);
75
76 virtual ~CentroidPeak();
77
78 // getters and setters
79 double getMass();
80 double getIntensity();
81 int getIsotopIdx();
82 double getSignalToNoise();
83 double getFittedIntensity();
84 double getOrgIntensity();
85 std::string getExtraPeakInfo();
86 double getRetentionTime();
87
88 void setMass(double pMass);
89 void setIntensity(double pIntensity);
90 void setIsotopIdx(double pIsotopIdx);
91 void setSignalToNoise(double in);
92 void setFittedIntensity(double pFittedIntensity);
93 void setOrgIntensity(double pOrgIntensity);
94 void setExtraPeakInfo(std::string in);
95 void setRetentionTime(double in);
96
97 void show_info();
98 void subtractIntensity(double);
99
100 protected:
101
102 int isotopIdx_;
103 double mass_;
104 double intensity_;
105 double fittedIntensity_;
106 double orgIntensity_;
107 double tr_;
108 double signalToNoise_;
109 std::string extraPeakInfo_;
110 };
111
112 // Class for deconvoluted isotopic patterns
113 class DeconvPeak :
114 public CentroidPeak
115 {
116 public:
117
118 DeconvPeak();
119 DeconvPeak(double, double, int, int, double, double);
120 DeconvPeak(const DeconvPeak &);
121 DeconvPeak(const DeconvPeak *);
122
123 DeconvPeak & operator=(const DeconvPeak &);
124
125 ~DeconvPeak() override;
126
127 // shows the info of the peak:
128 void show_info();
129
130 // getters and setters
131 int getCharge();
132 int getNrIsotopes();
133 double getC13MassError();
134 double getScore();
135 std::vector<CentroidPeak> getIsotopicPeaks();
136
137 void setCharge(int pCharge);
138 void setNrIsotopes(int pNrIsotopes);
139 void setC13MassError(double pC13MassError);
140 void setScore(double pScore);
141 void setIsotopicPeaks(std::vector<CentroidPeak> pIsotopicPeaks);
142
143 protected:
144
145 int charge_;
146 int nrIsotopes_;
147 double c13MassError_;
148 double score_;
149 std::vector<CentroidPeak> isotopicPeaks_;
150 };
151
152 // stream operators
153 std::ostream & operator<<(std::ostream &, CentroidPeak &);
154 std::ostream & operator<<(std::ostream &, DeconvPeak &);
155
156 // inline implementation of getters and setters
157
158 inline double CentroidPeak::getMass()
159 {
160 return mass_;
161 }
162
163 inline double CentroidPeak::getIntensity()
164 {
165 return intensity_;
166 }
167
168 inline int CentroidPeak::getIsotopIdx()
169 {
170 return isotopIdx_;
171 }
172
173 inline double CentroidPeak::getSignalToNoise()
174 {
175 return signalToNoise_;
176 }
177
178 inline double CentroidPeak::getFittedIntensity()
179 {
180 return fittedIntensity_;
181 }
182
183 inline double CentroidPeak::getOrgIntensity()
184 {
185 return orgIntensity_;
186 }
187
188 inline std::string CentroidPeak::getExtraPeakInfo()
189 {
190 return extraPeakInfo_;
191 }
192
193 inline double CentroidPeak::getRetentionTime()
194 {
195 return tr_;
196 }
197
198 inline void CentroidPeak::setMass(double pMass)
199 {
200 mass_ = pMass;
201 }
202
203 inline void CentroidPeak::setIntensity(double pIntensity)
204 {
205 intensity_ = pIntensity;
206 }
207
208 inline void CentroidPeak::setIsotopIdx(double pIsotopIdx)
209 {
210 isotopIdx_ = (int) pIsotopIdx;
211 }
212
213 inline void CentroidPeak::setSignalToNoise(double in)
214 {
215 signalToNoise_ = in;
216 }
217
218 inline void CentroidPeak::setFittedIntensity(double pFittedIntensity)
219 {
220 fittedIntensity_ = pFittedIntensity;
221 }
222
223 inline void CentroidPeak::setOrgIntensity(double pOrgIntensity)
224 {
225 orgIntensity_ = pOrgIntensity;
226 }
227
228 inline void CentroidPeak::setExtraPeakInfo(std::string in)
229 {
230 extraPeakInfo_ = in;
231 }
232
233 inline void CentroidPeak::setRetentionTime(double in)
234 {
235 tr_ = in;
236 }
237
238 //
239
240 inline int DeconvPeak::getCharge()
241 {
242 return charge_;
243 }
244
245 inline int DeconvPeak::getNrIsotopes()
246 {
247 return nrIsotopes_;
248 }
249
250 inline double DeconvPeak::getC13MassError()
251 {
252 return c13MassError_;
253 }
254
255 inline double DeconvPeak::getScore()
256 {
257 return score_;
258 }
259
260 inline std::vector<CentroidPeak> DeconvPeak::getIsotopicPeaks()
261 {
262 return isotopicPeaks_;
263 }
264
265 inline void DeconvPeak::setCharge(int pCharge)
266 {
267 charge_ = pCharge;
268 }
269
270 inline void DeconvPeak::setC13MassError(double pC13MassError)
271 {
272 c13MassError_ = pC13MassError;
273 }
274
275 inline void DeconvPeak::setNrIsotopes(int pNrIsotopes)
276 {
277 nrIsotopes_ = pNrIsotopes;
278 }
279
280 inline void DeconvPeak::setScore(double pScore)
281 {
282 score_ = pScore;
283 }
284
285 inline void DeconvPeak::setIsotopicPeaks(std::vector<CentroidPeak> pIsotopicPeaks)
286 {
287 isotopicPeaks_ = pIsotopicPeaks;
288 }
289
290 } // ns
291
OpenMS::CentroidPeak::getFittedIntensity
double getFittedIntensity()
Definition: CentroidPeak.h:178
OpenMS::CentroidPeak::intensity_
double intensity_
Definition: CentroidPeak.h:104
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::DeconvPeak::setC13MassError
void setC13MassError(double pC13MassError)
Definition: CentroidPeak.h:270
OpenMS::CentroidPeak::extraPeakInfo_
std::string extraPeakInfo_
Definition: CentroidPeak.h:109
OpenMS::CentroidPeak::getRetentionTime
double getRetentionTime()
Definition: CentroidPeak.h:193
OpenMS::CentroidPeak::setSignalToNoise
void setSignalToNoise(double in)
Definition: CentroidPeak.h:213
OpenMS::DeconvPeak::isotopicPeaks_
std::vector< CentroidPeak > isotopicPeaks_
Definition: CentroidPeak.h:149
OpenMS::CentroidPeak::orgIntensity_
double orgIntensity_
Definition: CentroidPeak.h:106
OpenMS::DeconvPeak::setNrIsotopes
void setNrIsotopes(int pNrIsotopes)
Definition: CentroidPeak.h:275
OpenMS::CentroidPeak::getExtraPeakInfo
std::string getExtraPeakInfo()
Definition: CentroidPeak.h:188
OpenMS::DeconvPeak::getScore
double getScore()
Definition: CentroidPeak.h:255
OpenMS::DeconvPeak::show_info
void show_info()
OpenMS::CentroidPeak::isotopIdx_
int isotopIdx_
Definition: CentroidPeak.h:102
OpenMS::DeconvPeak::c13MassError_
double c13MassError_
Definition: CentroidPeak.h:147
OpenMS::DeconvPeak::setIsotopicPeaks
void setIsotopicPeaks(std::vector< CentroidPeak > pIsotopicPeaks)
Definition: CentroidPeak.h:285
Types.h
OpenMS::DeconvPeak::charge_
int charge_
Definition: CentroidPeak.h:145
OpenMS::DeconvPeak::~DeconvPeak
~DeconvPeak() override
OpenMS::CentroidPeak::signalToNoise_
double signalToNoise_
Definition: CentroidPeak.h:108
OpenMS::CentroidPeak::getSignalToNoise
double getSignalToNoise()
Definition: CentroidPeak.h:173
OpenMS::DeconvPeak::getNrIsotopes
int getNrIsotopes()
Definition: CentroidPeak.h:245
OpenMS::CentroidPeak::setMass
void setMass(double pMass)
Definition: CentroidPeak.h:198
OpenMS::CentroidPeak::mass_
double mass_
Definition: CentroidPeak.h:103
OpenMS::DeconvPeak::getC13MassError
double getC13MassError()
Definition: CentroidPeak.h:250
OpenMS::CentroidPeak::setOrgIntensity
void setOrgIntensity(double pOrgIntensity)
Definition: CentroidPeak.h:223
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::DeconvPeak
Definition: CentroidPeak.h:113
OpenMS::DeconvPeak::DeconvPeak
DeconvPeak()
OpenMS::CentroidPeak::tr_
double tr_
Definition: CentroidPeak.h:107
OpenMS::CentroidPeak::setIntensity
void setIntensity(double pIntensity)
Definition: CentroidPeak.h:203
OpenMS::CentroidPeak::getOrgIntensity
double getOrgIntensity()
Definition: CentroidPeak.h:183
OpenMS::CentroidPeak::getIntensity
double getIntensity()
Definition: CentroidPeak.h:163
OpenMS::CentroidPeak
Definition: CentroidPeak.h:59
OpenMS::CentroidPeak::setRetentionTime
void setRetentionTime(double in)
Definition: CentroidPeak.h:233
OpenMS::CentroidPeak::setExtraPeakInfo
void setExtraPeakInfo(std::string in)
Definition: CentroidPeak.h:228
OpenMS::DeconvPeak::setScore
void setScore(double pScore)
Definition: CentroidPeak.h:280
OpenMS::CentroidPeak::fittedIntensity_
double fittedIntensity_
Definition: CentroidPeak.h:105
OpenMS::CentroidPeak::setFittedIntensity
void setFittedIntensity(double pFittedIntensity)
Definition: CentroidPeak.h:218
int
OpenMS::CentroidPeak::setIsotopIdx
void setIsotopIdx(double pIsotopIdx)
Definition: CentroidPeak.h:208
OpenMS::CentroidPeak::getIsotopIdx
int getIsotopIdx()
Definition: CentroidPeak.h:168
OpenMS::DeconvPeak::getIsotopicPeaks
std::vector< CentroidPeak > getIsotopicPeaks()
Definition: CentroidPeak.h:260
OpenMS::DeconvPeak::operator=
DeconvPeak & operator=(const DeconvPeak &)
OpenMS::DeconvPeak::getCharge
int getCharge()
Definition: CentroidPeak.h:240
OpenMS::CentroidPeak::getMass
double getMass()
Definition: CentroidPeak.h:158
OpenMS::DeconvPeak::score_
double score_
Definition: CentroidPeak.h:148
OpenMS::DeconvPeak::setCharge
void setCharge(int pCharge)
Definition: CentroidPeak.h:265
OpenMS::DeconvPeak::nrIsotopes_
int nrIsotopes_
Definition: CentroidPeak.h:146