libpappsomspp
Library for mass spectrometry
timsframebase.h
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1/**
2 * \file pappsomspp/vendors/tims/timsframebase.h
3 * \date 16/12/2019
4 * \author Olivier Langella
5 * \brief handle a single Bruker's TimsTof frame without binary data
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.fr>.
10 *
11 * This file is part of the PAPPSOms++ library.
12 *
13 * PAPPSOms++ is free software: you can redistribute it and/or modify
14 * it under the terms of the GNU General Public License as published by
15 * the Free Software Foundation, either version 3 of the License, or
16 * (at your option) any later version.
17 *
18 * PAPPSOms++ is distributed in the hope that it will be useful,
19 * but WITHOUT ANY WARRANTY; without even the implied warranty of
20 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 * GNU General Public License for more details.
22 *
23 * You should have received a copy of the GNU General Public License
24 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25 *
26 ******************************************************************************/
27
28#pragma once
29
30#include <memory>
31#include <vector>
32#include <QtGlobal>
33#include "../../massspectrum/massspectrum.h"
35
36namespace pappso
37{
38
39class TimsFrameBase;
40typedef std::shared_ptr<TimsFrameBase> TimsFrameBaseSPtr;
41typedef std::shared_ptr<const TimsFrameBase> TimsFrameBaseCstSPtr;
42
43
44/**
45 * @todo write docs
46 */
48{
49 public:
50 /** @brief constructor for binary independant tims frame
51 * @param timsId tims frame identifier in the database
52 * @param scanNum the total number of scans contained in this frame
53 */
54 TimsFrameBase(std::size_t timsId, quint32 scanNum);
55 /**
56 * Copy constructor
57 *
58 * @param other TODO
59 */
60 TimsFrameBase(const TimsFrameBase &other);
61
62 /**
63 * Destructor
64 */
65 virtual ~TimsFrameBase();
66
67 /** @brief tells if 2 tims frame has the same calibration data
68 * Usefull to know if raw data can be handled between frames
69 */
70 virtual bool hasSameCalibrationData(const TimsFrameBase &other) const;
71
72 /** @brief get the number of peaks in this spectrum
73 * need the binary file
74 * @param scanNum scan number in the frame in the order it lies in binary
75 * file, from 0 to N-1
76 */
77 virtual std::size_t getNbrPeaks(std::size_t scanNum) const;
78
79 /** @brief get the number of scans contained in this frame
80 * each scan represents an ion mobility slice
81 */
82
83 virtual std::size_t getTotalNumberOfScans() const;
84
85
86 /** @brief get the maximum raw mass index contained in this frame
87 */
88 virtual quint32 getMaximumRawMassIndex() const;
89
90 /** @brief get Mass spectrum with peaks for this scan number
91 * need the binary file
92 * @param scanNum scan number in the frame in the order it lies in binary
93 * file, from 0 to N-1
94 */
95 virtual MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const;
96
97 /** @brief cumulate spectrum given a scan number range
98 * need the binary file
99 * The intensities are normalized with respect to the frame accumulation time
100 *
101 * @param scanNumBegin scan number in the frame in the order it lies in binary
102 * file, from 0 to N-1
103 * @param scanNumEnd scan number in the frame in the order it lies in binary
104 * file, from 0 to N-1
105 */
106 virtual Trace cumulateScanToTrace(std::size_t scanNumBegin,
107 std::size_t scanNumEnd) const;
108
109
110 /** @brief cumulate scan list into a trace into a raw spectrum map
111 * The intensities are NOT normalized with respect to the frame accumulation
112 * time
113 *
114 * @param rawSpectrum simple map of integers to cumulate raw counts
115 * @param scanNumBegin scan number in the frame in the order it lies in binary
116 * file, from 0 to N-1
117 * @param scanNumEnd scan number in the frame in the order it lies in binary
118 * file, from 0 to N-1
119 */
120 virtual void cumulateScansInRawMap(std::map<quint32, quint32> &rawSpectrum,
121 std::size_t scanNumBegin,
122 std::size_t scanNumEnd) const;
123
124 virtual quint64 cumulateSingleScanIntensities(std::size_t scanNum) const;
125
126 virtual quint64 cumulateScansIntensities(std::size_t scanNumBegin,
127 std::size_t scanNumEnd) const;
128
129 /** @brief check that this scan number exists
130 * @param scanNum scan number in the frame in the order it lies in binary
131 * file, from 0 to N-1
132 */
133 bool checkScanNum(std::size_t scanNum) const;
134
135
136 void setAccumulationTime(double accumulation_time_ms);
137 void setMzCalibration(double T1_frame,
138 double T2_frame,
139 double digitizerTimebase,
140 double digitizerDelay,
141 double C0,
142 double C1,
143 double C2,
144 double C3,
145 double C4,
146 double T1_ref,
147 double T2_ref,
148 double dC1,
149 double dC2);
150 void setTimsCalibration(int tims_model_type,
151 double C0,
152 double C1,
153 double C2,
154 double C3,
155 double C4,
156 double C5,
157 double C6,
158 double C7,
159 double C8,
160 double C9);
161 void setTime(double time);
162 void setMsMsType(quint8 type);
163 unsigned int getMsLevel() const;
164 double getTime() const;
165
166 std::size_t getId() const;
167
168 /** @brief get drift time of a scan number in milliseconds
169 * @param scanNum scan number in the frame in the order it lies in binary
170 * file, from 0 to N-1
171 * @return time in milliseconds of mobility delay (drift time)
172 * */
173 double getDriftTime(std::size_t scanNum) const;
174
175 /** @brief get 1/K0 value of a given scan (mobility value)
176 * @param scanNum scan number in the frame in the order it lies in binary
177 * file, from 0 to N-1
178 * */
179 double getOneOverK0Transformation(std::size_t scanNum) const;
180
181
182 /** @brief get the scan number from a given 1/Ko mobility value
183 * @param one_over_k0 the mobility value to tranform
184 * @return integer the scan number in the frame in the order it lies in binary
185 * file, from 0 to N-1
186 */
187 std::size_t getScanNumFromOneOverK0(double one_over_k0) const;
188
189 /** @brief get voltage for a given scan number
190 * @param scanNum scan number in the frame in the order it lies in binary
191 * file, from 0 to N-1
192 * @return double volt measure
193 * */
194 double getVoltageTransformation(std::size_t scanNum) const;
195
196
197 /** @brief transform accumulation of raw scans into a real mass spectrum
198 */
200 std::map<quint32, quint32> &accumulated_scans) const;
201
202 /** @brief transform accumulation of raw scans into a real mass spectrum with
203 * a simple centroid on raw integers
204 */
206 std::map<quint32, quint32> &accumulated_scans) const;
207
208 /** @brief get the MzCalibration model to compute mz and TOF for this frame
209 */
210 virtual const MzCalibrationInterfaceSPtr &
211 getMzCalibrationInterfaceSPtr() const final;
212
214
215
216 /** @brief get raw index list for one given scan
217 * index are not TOF nor m/z, just index on digitizer
218 */
219 virtual std::vector<quint32> getScanIndexList(std::size_t scanNum) const;
220
221 /** @brief get raw intensities without transformation from one scan
222 * it needs intensity normalization
223 */
224 virtual std::vector<quint32> getScanIntensities(std::size_t scanNum) const;
225
226 /** @brief get a mobility trace cumulating intensities inside the given mass
227 * index range
228 * @param mz_index_lower_bound raw mass index lower bound
229 * @param mz_index_upper_bound raw mass index upper bound
230 * @param method max or sum intensities
231 */
232 virtual Trace
233 getIonMobilityTraceByMzIndexRange(std::size_t mz_index_lower_bound,
234 std::size_t mz_index_upper_bound,
235 XicExtractMethod method) const;
236
237
238 protected:
239 /** @brief total number of scans contained in this frame
240 */
242
243 /** @brief Tims frame database id (the SQL identifier of this frame)
244 * @warning in sqlite, there is another field called TimsId : this is not
245 * that, because it is in fact an offset in bytes in the binary file.
246 * */
247 std::size_t m_timsId;
248
249 /** @brief accumulation time in milliseconds
250 */
252
253 quint8 m_msMsType = 0;
254
255 /** @brief retention time
256 */
257 double m_time = 0;
258
259 double m_timsDvStart = 0; // C2 from TimsCalibration
260 double m_timsSlope =
261 0; // (dv_end - dv_start) / ncycles //C3 from TimsCalibration // C2 from
262 // TimsCalibration // C1 from TimsCalibration
263 double m_timsTtrans = 0; // C4 from TimsCalibration
264 double m_timsNdelay = 0; // C0 from TimsCalibration
265 double m_timsVmin = 0; // C8 from TimsCalibration
266 double m_timsVmax = 0; // C9 from TimsCalibration
267 double m_timsC6 = 0;
268 double m_timsC7 = 0;
269
271};
272} // namespace pappso
double m_accumulationTime
accumulation time in milliseconds
double getTime() const
virtual quint64 cumulateSingleScanIntensities(std::size_t scanNum) const
double getVoltageTransformation(std::size_t scanNum) const
get voltage for a given scan number
virtual Trace cumulateScanToTrace(std::size_t scanNumBegin, std::size_t scanNumEnd) const
cumulate spectrum given a scan number range need the binary file The intensities are normalized with ...
virtual std::size_t getTotalNumberOfScans() const
get the number of scans contained in this frame each scan represents an ion mobility slice
virtual Trace getIonMobilityTraceByMzIndexRange(std::size_t mz_index_lower_bound, std::size_t mz_index_upper_bound, XicExtractMethod method) const
get a mobility trace cumulating intensities inside the given mass index range
virtual std::size_t getNbrPeaks(std::size_t scanNum) const
get the number of peaks in this spectrum need the binary file
MzCalibrationInterfaceSPtr msp_mzCalibration
virtual MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const
get Mass spectrum with peaks for this scan number need the binary file
TimsFrameBase(std::size_t timsId, quint32 scanNum)
constructor for binary independant tims frame
virtual std::vector< quint32 > getScanIndexList(std::size_t scanNum) const
get raw index list for one given scan index are not TOF nor m/z, just index on digitizer
double getDriftTime(std::size_t scanNum) const
get drift time of a scan number in milliseconds
pappso::Trace getTraceFromCumulatedScansBuiltinCentroid(std::map< quint32, quint32 > &accumulated_scans) const
transform accumulation of raw scans into a real mass spectrum with a simple centroid on raw integers
double m_time
retention time
virtual quint64 cumulateScansIntensities(std::size_t scanNumBegin, std::size_t scanNumEnd) const
void setAccumulationTime(double accumulation_time_ms)
quint32 m_scanNumber
total number of scans contained in this frame
virtual void cumulateScansInRawMap(std::map< quint32, quint32 > &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const
cumulate scan list into a trace into a raw spectrum map The intensities are NOT normalized with respe...
void setTime(double time)
std::size_t m_timsId
Tims frame database id (the SQL identifier of this frame)
pappso::Trace getTraceFromCumulatedScans(std::map< quint32, quint32 > &accumulated_scans) const
transform accumulation of raw scans into a real mass spectrum
virtual bool hasSameCalibrationData(const TimsFrameBase &other) const
tells if 2 tims frame has the same calibration data Usefull to know if raw data can be handled betwee...
virtual quint32 getMaximumRawMassIndex() const
get the maximum raw mass index contained in this frame
unsigned int getMsLevel() const
void setTimsCalibration(int tims_model_type, double C0, double C1, double C2, double C3, double C4, double C5, double C6, double C7, double C8, double C9)
virtual const MzCalibrationInterfaceSPtr & getMzCalibrationInterfaceSPtr() const final
get the MzCalibration model to compute mz and TOF for this frame
std::size_t getScanNumFromOneOverK0(double one_over_k0) const
get the scan number from a given 1/Ko mobility value
void setMsMsType(quint8 type)
void setMzCalibration(double T1_frame, double T2_frame, double digitizerTimebase, double digitizerDelay, double C0, double C1, double C2, double C3, double C4, double T1_ref, double T2_ref, double dC1, double dC2)
double getOneOverK0Transformation(std::size_t scanNum) const
get 1/K0 value of a given scan (mobility value)
bool checkScanNum(std::size_t scanNum) const
check that this scan number exists
void setMzCalibrationInterfaceSPtr(MzCalibrationInterfaceSPtr mzCalibration)
std::size_t getId() const
virtual std::vector< quint32 > getScanIntensities(std::size_t scanNum) const
get raw intensities without transformation from one scan it needs intensity normalization
A simple container of DataPoint instances.
Definition: trace.h:148
handles different ways to compute m/z using calibration parameters
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< const TimsFrameBase > TimsFrameBaseCstSPtr
Definition: timsframebase.h:41
std::shared_ptr< TimsFrameBase > TimsFrameBaseSPtr
Definition: timsframebase.h:40
std::shared_ptr< MzCalibrationInterface > MzCalibrationInterfaceSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
XicExtractMethod
Definition: types.h:201