libpappsomspp
Library for mass spectrometry
timsframe.h
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1 /**
2  * \file pappsomspp/vendors/tims/timsframe.h
3  * \date 23/08/2019
4  * \author Olivier Langella
5  * \brief handle a single Bruker's TimsTof frame
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 <QByteArray>
32 #include <vector>
33 #include "timsframebase.h"
34 #include "../../xic/xic.h"
35 #include "../../msrun/xiccoord/xiccoordtims.h"
36 
37 namespace pappso
38 {
39 
40 class TimsFrame;
41 typedef std::shared_ptr<TimsFrame> TimsFrameSPtr;
42 typedef std::shared_ptr<const TimsFrame> TimsFrameCstSPtr;
43 
44 class TimsBinDec;
45 
47 
48 /**
49  * @todo write docs
50  */
51 class TimsFrame : public TimsFrameBase
52 {
54 
55  public:
56  /**
57  * @param timsId tims frame id
58  * @param scanNum total number of scans in this frame
59  * @param p_bytes pointer on the decompressed binary buffer
60  * @param len size of the decompressed binary buffer
61  */
62  TimsFrame(std::size_t timsId,
63  quint32 scanNum,
64  char *p_bytes,
65  std::size_t len);
66  /**
67  * Copy constructor
68  *
69  * @param other TODO
70  */
71  TimsFrame(const TimsFrame &other);
72 
73  /**
74  * Destructor
75  */
76  virtual ~TimsFrame();
77 
78 
79  virtual std::size_t getNbrPeaks(std::size_t scanNum) const override;
80 
81  /** @brief cumulate scan list into a trace
82  * @param scanNumBegin first scan to cumulate
83  * @param scanNumEnd last scan to cumulate
84  * @return Trace mz and intensity values
85  */
86  virtual Trace cumulateScanToTrace(std::size_t scanNumBegin,
87  std::size_t scanNumEnd) const override;
88 
89  /** @brief cumulate scan list into a trace into a raw spectrum map
90  * @param rawSpectrum simple map of integers to cumulate raw counts
91  * @param scanNumBegin first scan to cumulate
92  * @param scanNumEnd last scan to cumulate
93  */
94  virtual void cumulateScansInRawMap(std::map<quint32, quint32> &rawSpectrum,
95  std::size_t scanNumBegin,
96  std::size_t scanNumEnd) const override;
97 
98  virtual quint64 cumulateSingleScanIntensities(std::size_t scanNum) const override;
99 
100  virtual quint64
101  cumulateScansIntensities(std::size_t scanNumBegin,
102  std::size_t scanNumEnd) const override;
103 
104  /** @brief get raw index list for one given scan
105  * index are not TOF nor m/z, just index on digitizer
106  */
107  virtual std::vector<quint32>
108  getScanIndexList(std::size_t scanNum) const override;
109 
110  /** @brief get raw intensities without transformation from one scan
111  * it needs intensity normalization
112  */
113  virtual std::vector<quint32>
114  getScanIntensities(std::size_t scanNum) const override;
115 
116  /** @brief get the mass spectrum corresponding to a scan number
117  * @param scanNum the scan number to retrieve
118  * */
120  getMassSpectrumCstSPtr(std::size_t scanNum) const;
121 
123  getMassSpectrumSPtr(std::size_t scanNum) const override;
124 
125 
126  protected:
127  /** @brief constructor for binary independant tims frame
128  * @param timsId tims frame identifier in the database
129  * @param scanNum the total number of scans contained in this frame
130  */
131  TimsFrame(std::size_t timsId, quint32 scanNum);
132 
134  std::vector<XicCoordTims *>::iterator &itXicListbegin,
135  std::vector<XicCoordTims *>::iterator &itXicListend,
136  XicExtractMethod method) const;
137 
138 
139  /** @brief cumulate a scan into a map
140  *
141  * @param scanNum scan number 0 to (m_scanNumber-1)
142  */
143  virtual void cumulateScan(std::size_t scanNum,
144  std::map<quint32, quint32> &accumulate_into) const;
145 
146 
147  /** @brief get the raw index tof_index and intensities (normalized)
148  *
149  * @param scanNum the scan number to extract
150  * @return trace vector
151  *
152  */
153  virtual pappso::TraceSPtr getRawTraceSPtr(std::size_t scanNum) const;
154 
155 
156  private:
157  /** @brief unshuffle data packet of tims compression type 2
158  * @param src is a zstd decompressed buffer pointer
159  */
160  void unshufflePacket(const char *src);
161 
162 
163  /** @brief get offset for this spectrum in the binary file
164  *
165  * @param scanNum scan number in the frame in the order it lies in binary
166  * file, from 0 to N-1
167  */
168 
169  std::size_t getScanOffset(std::size_t scanNum) const;
170 
171  private:
173  {
174  XicComputeStructure(const TimsFrame *fram_p,
175  const XicCoordTims &xic_struct);
176 
177 
178  Xic *xic_ptr = nullptr;
179  std::size_t mobilityIndexBegin;
180  std::size_t mobilityIndexEnd;
181  std::size_t mzIndexLowerBound;
182  std::size_t mzIndexUpperBound;
183  double tmpIntensity = 0;
184  };
185 
186  protected:
187  QByteArray m_timsDataFrame;
188 };
189 } // namespace pappso
QByteArray m_timsDataFrame
Definition: timsframe.h:187
virtual std::vector< quint32 > getScanIndexList(std::size_t scanNum) const override
get raw index list for one given scan index are not TOF nor m/z, just index on digitizer
Definition: timsframe.cpp:172
virtual std::size_t getNbrPeaks(std::size_t scanNum) const override
get the number of peaks in this spectrum need the binary file
Definition: timsframe.cpp:130
virtual ~TimsFrame()
Definition: timsframe.cpp:97
virtual quint64 cumulateScansIntensities(std::size_t scanNumBegin, std::size_t scanNumEnd) const override
...
Definition: timsframe.cpp:268
virtual void cumulateScan(std::size_t scanNum, std::map< quint32, quint32 > &accumulate_into) const
cumulate a scan into a map
Definition: timsframe.cpp:306
TimsFrame(std::size_t timsId, quint32 scanNum, char *p_bytes, std::size_t len)
Definition: timsframe.cpp:62
friend TimsDirectXicExtractor
Definition: timsframe.h:53
virtual pappso::MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const override
get Mass spectrum with peaks for this scan number need the binary file
Definition: timsframe.cpp:449
virtual quint64 cumulateSingleScanIntensities(std::size_t scanNum) const override
Definition: timsframe.cpp:221
virtual std::vector< quint32 > getScanIntensities(std::size_t scanNum) const override
get raw intensities without transformation from one scan it needs intensity normalization
Definition: timsframe.cpp:197
void unshufflePacket(const char *src)
unshuffle data packet of tims compression type 2
Definition: timsframe.cpp:103
std::size_t getScanOffset(std::size_t scanNum) const
get offset for this spectrum in the binary file
Definition: timsframe.cpp:160
virtual void cumulateScansInRawMap(std::map< quint32, quint32 > &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const override
cumulate scan list into a trace into a raw spectrum map
Definition: timsframe.cpp:404
virtual Trace cumulateScanToTrace(std::size_t scanNumBegin, std::size_t scanNumEnd) const override
cumulate scan list into a trace
Definition: timsframe.cpp:344
void extractTimsXicListInRtRange(std::vector< XicCoordTims * >::iterator &itXicListbegin, std::vector< XicCoordTims * >::iterator &itXicListend, XicExtractMethod method) const
Definition: timsframe.cpp:505
virtual pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr(std::size_t scanNum) const
get the mass spectrum corresponding to a scan number
Definition: timsframe.cpp:441
virtual pappso::TraceSPtr getRawTraceSPtr(std::size_t scanNum) const
get the raw index tof_index and intensities (normalized)
Definition: timsframe.cpp:598
A simple container of DataPoint instances.
Definition: trace.h:148
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< TimsFrame > TimsFrameSPtr
Definition: timsframe.h:40
std::shared_ptr< Trace > TraceSPtr
Definition: trace.h:135
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
XicExtractMethod
Definition: types.h:201
std::shared_ptr< const TimsFrame > TimsFrameCstSPtr
Definition: timsframe.h:42
XicComputeStructure(const TimsFrame *fram_p, const XicCoordTims &xic_struct)
Definition: timsframe.cpp:40
coordinates of the XIC to extract and the resulting XIC after extraction
Definition: xiccoordtims.h:51
handle a single Bruker's TimsTof frame without binary data