libpappsomspp
Library for mass spectrometry
pappso::MsRunXicExtractorDisk Class Reference

#include <msrunxicextractordisk.h>

Inheritance diagram for pappso::MsRunXicExtractorDisk:
pappso::MsRunXicExtractor pappso::MsRunXicExtractorInterface pappso::MsRunXicExtractorDiskBuffer

Public Member Functions

 MsRunXicExtractorDisk (MsRunReaderSPtr &msrun_reader)
 
 MsRunXicExtractorDisk (const MsRunXicExtractorDisk &other)
 
virtual ~MsRunXicExtractorDisk ()
 
virtual XicCstSPtr getXicCstSPtr (const MzRange &mz_range, pappso::pappso_double rt_begin, pappso::pappso_double rt_end) override
 get a XIC on this MsRun at the given mass range More...
 
virtual std::vector< XicCstSPtrgetXicCstSPtrList (const std::vector< MzRange > &mz_range_list) override
 extract a list of XIC given a list of mass to extract More...
 
- Public Member Functions inherited from pappso::MsRunXicExtractor
 MsRunXicExtractor (const MsRunXicExtractor &other)
 
virtual ~MsRunXicExtractor ()
 
- Public Member Functions inherited from pappso::MsRunXicExtractorInterface
void setXicExtractMethod (XicExtractMethod method)
 set the XIC extraction method More...
 
virtual XicCstSPtr getXicCstSPtr (const MzRange &mz_range) final
 get a XIC on this MsRun at the given mass range More...
 
const MsRunIdCstSPtrgetMsRunId () const
 

Protected Member Functions

 MsRunXicExtractorDisk (MsRunReaderSPtr &msrun_reader, const QDir &temporary_dir)
 
void prepareExtractor ()
 
void serializeMsRun ()
 
virtual void storeSlices (std::map< unsigned int, MassSpectrum > &slice_vector, std::size_t ipos)
 store MassSpectrum slices (by daltons) for a given retention time More...
 
void appendSliceOnDisk (unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos)
 append a slice on disk (in a file) More...
 
std::vector< MsRunSliceSPtracquireSlices (const MzRange &mz_range)
 retrieve all the slices corresponding to a given mz_range More...
 
MsRunSliceSPtr unserializeSlice (unsigned int slice_number)
 get one slice from disk by her slice number (dalton) More...
 
virtual void endPwizRead ()
 
- Protected Member Functions inherited from pappso::MsRunXicExtractor
 MsRunXicExtractor (MsRunReaderSPtr &msrun_reader)
 
virtual void getXicFromPwizMSDataFile (std::vector< Xic * > &xic_list, const std::vector< MzRange > &mass_range_list, pappso::pappso_double rt_begin, pappso::pappso_double rt_end)
 
- Protected Member Functions inherited from pappso::MsRunXicExtractorInterface
 MsRunXicExtractorInterface (MsRunReaderSPtr &msrun_reader)
 constructor is private, use the MsRunXicExtractorFactory More...
 
 MsRunXicExtractorInterface (const MsRunXicExtractorInterface &other)
 
virtual ~MsRunXicExtractorInterface ()
 

Protected Attributes

QString m_temporaryDirectory
 
QTemporaryDir * mpa_temporaryDirectory = nullptr
 
std::vector< pappso::pappso_doublem_retentionTimeList
 
pappso::pappso_double m_maxMz = 0
 
pappso::pappso_double m_minMz = 5000
 
std::size_t m_rtSize = 0
 
std::deque< MsRunSliceSPtrm_msRunSliceListCache
 
QMutex m_mutex
 
- Protected Attributes inherited from pappso::MsRunXicExtractor
std::vector< MsRunXicExtractorPoints > m_msrun_points
 
- Protected Attributes inherited from pappso::MsRunXicExtractorInterface
MsRunReaderSPtr msp_msrun_reader
 
XicExtractMethod m_xicExtractMethod = XicExtractMethod::max
 

Private Attributes

friend MsRunXicExtractorFactory
 

Detailed Description

Definition at line 44 of file msrunxicextractordisk.h.

Constructor & Destructor Documentation

◆ MsRunXicExtractorDisk() [1/3]

pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk ( MsRunReaderSPtr msrun_reader)

◆ MsRunXicExtractorDisk() [2/3]

pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk ( const MsRunXicExtractorDisk other)

Definition at line 47 of file msrunxicextractordisk.cpp.

49 {
50 
51  m_temporaryDirectory = other.m_temporaryDirectory;
52  mpa_temporaryDirectory = new QTemporaryDir(
53  QString("%1/msrun_%2_")
55  .arg(msp_msrun_reader.get()->getMsRunId().get()->getXmlId()));
56 }

References m_temporaryDirectory, mpa_temporaryDirectory, and pappso::MsRunXicExtractorInterface::msp_msrun_reader.

◆ ~MsRunXicExtractorDisk()

pappso::MsRunXicExtractorDisk::~MsRunXicExtractorDisk ( )
virtual

Definition at line 58 of file msrunxicextractordisk.cpp.

59 {
60  if(mpa_temporaryDirectory != nullptr)
61  {
63  }
64 }

References mpa_temporaryDirectory.

◆ MsRunXicExtractorDisk() [3/3]

pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk ( MsRunReaderSPtr msrun_reader,
const QDir &  temporary_dir 
)
protected

Definition at line 39 of file msrunxicextractordisk.cpp.

41  : pappso::MsRunXicExtractor(msrun_reader)
42 {
43  mpa_temporaryDirectory = nullptr;
44  m_temporaryDirectory = temporary_dir.absolutePath();
45 }

References m_temporaryDirectory, and mpa_temporaryDirectory.

Member Function Documentation

◆ acquireSlices()

std::vector< MsRunSliceSPtr > pappso::MsRunXicExtractorDisk::acquireSlices ( const MzRange mz_range)
protected

retrieve all the slices corresponding to a given mz_range

Parameters
mz_rangedesired mz range

Definition at line 319 of file msrunxicextractordisk.cpp.

320 {
321  QMutexLocker lock(&m_mutex);
322  std::vector<MsRunSliceSPtr> slice_list;
323  for(unsigned int i = mz_range.lower(); i <= mz_range.upper(); i++)
324  {
325  auto it = std::find_if(m_msRunSliceListCache.begin(),
326  m_msRunSliceListCache.end(),
327  [i](const MsRunSliceSPtr &slice_sp) {
328  return slice_sp.get()->getSliceNumber() == i;
329  });
330  if(it != m_msRunSliceListCache.end())
331  {
332  slice_list.push_back(*it);
333  m_msRunSliceListCache.push_back(*it);
334  }
335  else
336  {
337  MsRunSliceSPtr slice_sp = unserializeSlice(i);
338  slice_list.push_back(slice_sp);
339  m_msRunSliceListCache.push_back(slice_sp);
340  }
341  }
342 
343  if(m_msRunSliceListCache.size() > 20)
344  {
345  m_msRunSliceListCache.pop_front();
346  }
347  return slice_list;
348 }

References pappso::MzRange::lower(), m_msRunSliceListCache, m_mutex, unserializeSlice(), and pappso::MzRange::upper().

Referenced by getXicCstSPtr().

◆ appendSliceOnDisk()

void pappso::MsRunXicExtractorDisk::appendSliceOnDisk ( unsigned int  slice_number,
MassSpectrum spectrum,
std::size_t  ipos 
)
protected

append a slice on disk (in a file)

Parameters
slice_numberthe slice number == dalton integer
spectrumthe part of the mass spectrum (mz/intensity) in the range of the slice number
iposthe position in the retention time vector

Definition at line 244 of file msrunxicextractordisk.cpp.

247 {
248  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
249  QFile slice_file(
250  QString("%1/%2").arg(mpa_temporaryDirectory->path()).arg(slice_number));
251  bool new_file = false;
252  if(!slice_file.exists())
253  {
254  new_file = true;
255  }
256  if(!slice_file.open(QIODevice::WriteOnly | QIODevice::Append))
257  {
259  QObject::tr("unable to open file %1").arg(slice_file.fileName()));
260  }
261  QDataStream stream(&slice_file);
262 
263  if(new_file)
264  {
265  stream << (quint32)slice_number;
266  stream << (quint32)m_rtSize;
267  }
268 
269  stream << (quint32)ipos;
270  stream << spectrum;
271 
272  slice_file.flush();
273  slice_file.close();
274  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
275 }

References m_rtSize, and mpa_temporaryDirectory.

Referenced by storeSlices().

◆ endPwizRead()

void pappso::MsRunXicExtractorDisk::endPwizRead ( )
protectedvirtual

Reimplemented in pappso::MsRunXicExtractorDiskBuffer.

Definition at line 352 of file msrunxicextractordisk.cpp.

353 {
354  msp_msrun_reader.get()->releaseDevice();
355 }

References pappso::MsRunXicExtractorInterface::msp_msrun_reader.

Referenced by serializeMsRun().

◆ getXicCstSPtr()

XicCstSPtr pappso::MsRunXicExtractorDisk::getXicCstSPtr ( const MzRange mz_range,
pappso::pappso_double  rt_begin,
pappso::pappso_double  rt_end 
)
overridevirtual

get a XIC on this MsRun at the given mass range

Parameters
mz_rangemz range to extract
rt_beginbegining of the XIC in seconds
rt_endend of the XIC in seconds

Reimplemented from pappso::MsRunXicExtractor.

Definition at line 94 of file msrunxicextractordisk.cpp.

97 {
98  std::shared_ptr<Xic> msrunxic_sp = std::make_shared<Xic>(Xic());
99 
100  std::vector<MsRunSliceSPtr> slice_list;
101  slice_list = acquireSlices(mz_range);
102 
103  if(slice_list.size() == 0)
104  {
106  QObject::tr("Error getMsRunXicSp slice_list.size() == 0"));
107  }
108 
109  for(std::size_t i = 0; i < m_retentionTimeList.size(); i++)
110  {
111 
112  DataPoint xic_element;
113  xic_element.x = m_retentionTimeList[i];
114  xic_element.y = 0;
115  if((xic_element.x < rt_begin) || (xic_element.x > rt_end))
116  continue;
117 
118  for(auto &&msrun_slice : slice_list)
119  {
120  const MassSpectrum &spectrum = msrun_slice.get()->getSpectrum(i);
121  for(auto &&peak : spectrum)
122  {
123  if(mz_range.contains(peak.x))
124  {
125  if(m_xicExtractMethod == XicExtractMethod::sum)
126  {
127  xic_element.y += peak.y;
128  }
129  else
130  {
131  if(xic_element.y < peak.y)
132  {
133  xic_element.y = peak.y;
134  }
135  }
136  }
137  }
138  }
139  msrunxic_sp.get()->push_back(xic_element);
140  }
141 
142  return (msrunxic_sp);
143 }

References acquireSlices(), pappso::MzRange::contains(), m_retentionTimeList, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::DataPoint::x, and pappso::DataPoint::y.

Referenced by getXicCstSPtrList().

◆ getXicCstSPtrList()

std::vector< XicCstSPtr > pappso::MsRunXicExtractorDisk::getXicCstSPtrList ( const std::vector< MzRange > &  mz_range_list)
overridevirtual

extract a list of XIC given a list of mass to extract

Reimplemented from pappso::MsRunXicExtractor.

Definition at line 146 of file msrunxicextractordisk.cpp.

148 {
149 
150  std::vector<XicCstSPtr> xic_list_return;
151  for(auto &range : mz_range_list)
152  {
153  xic_list_return.push_back(getXicCstSPtr(range, 0, 40000000));
154  }
155  return xic_list_return;
156 }

References getXicCstSPtr().

◆ prepareExtractor()

void pappso::MsRunXicExtractorDisk::prepareExtractor ( )
protected

Definition at line 67 of file msrunxicextractordisk.cpp.

68 {
69  qDebug();
70  try
71  {
73  // msp_msrun_reader = nullptr;
74  }
75  catch(pappso::PappsoException &errora)
76  {
77  qDebug();
79  QObject::tr("Error reading file (%1) : %2")
80  .arg(msp_msrun_reader.get()->getMsRunId().get()->toString())
81  .arg(errora.qwhat()));
82  }
83  catch(std::exception &error)
84  {
85  qDebug();
87  QObject::tr("Error reading file (%1) using : %2")
88  .arg(msp_msrun_reader.get()->getMsRunId().get()->toString())
89  .arg(error.what()));
90  }
91 }

References pappso::MsRunXicExtractorInterface::msp_msrun_reader, pappso::PappsoException::qwhat(), and serializeMsRun().

◆ serializeMsRun()

void pappso::MsRunXicExtractorDisk::serializeMsRun ( )
protected

Definition at line 159 of file msrunxicextractordisk.cpp.

160 {
161  qDebug();
162  m_minMz = 5000;
163  m_maxMz = 0;
164 
165  unsigned int slice_number;
166  std::map<unsigned int, MassSpectrum> spectrum_map;
167 
168  /*
169  const pwiz::msdata::SpectrumList *p_spectrum_list =
170  p_msdatafile->run.spectrumListPtr.get();
171 
172  std::size_t spectrum_list_size = p_spectrum_list->size();
173  pwiz::msdata::SpectrumPtr pwiz_spectrum;
174  */
175 
176  m_rtSize = m_msrun_points.size();
177 
178 
179  MassSpectrumCstSPtr spectrum;
180  for(auto &&msrun_point : m_msrun_points)
181  {
182 
183  spectrum_map.clear();
184 
185  m_retentionTimeList.push_back(msrun_point.rt);
186 
187  spectrum =
188  msp_msrun_reader.get()->massSpectrumCstSPtr(msrun_point.spectrum_index);
189 
190  const MassSpectrum *p_spectrum = spectrum.get();
191  if(p_spectrum->size() > 0)
192  {
193  if(p_spectrum->begin()->x < m_minMz)
194  {
195  m_minMz = p_spectrum->begin()->x;
196  }
197  // iterate through the m/z-intensity pairs
198 
199  if(p_spectrum->back().x > m_maxMz)
200  {
201  m_maxMz = p_spectrum->back().x;
202  }
203 
204  for(auto &peak : *p_spectrum)
205  {
206 
207  slice_number = peak.x;
208 
209  std::pair<std::map<unsigned int, MassSpectrum>::iterator, bool>
210  ret = spectrum_map.insert(std::pair<unsigned int, MassSpectrum>(
211  slice_number, MassSpectrum()));
212 
213  ret.first->second.push_back(peak);
214  // auto ret = spectrum_map.insert(std::pair<unsigned int,
215  // MassSpectrum>(slice_number,MassSpectrum()));
216  // ret.first->second.push_back(peak);
217  }
218 
219  // slices are ready for this retention time
220  storeSlices(spectrum_map, m_retentionTimeList.size() - 1);
221  }
222  }
223 
224  endPwizRead();
225  qDebug();
226 }

References endPwizRead(), m_maxMz, m_minMz, pappso::MsRunXicExtractor::m_msrun_points, m_retentionTimeList, m_rtSize, pappso::MsRunXicExtractorInterface::msp_msrun_reader, and storeSlices().

Referenced by prepareExtractor().

◆ storeSlices()

void pappso::MsRunXicExtractorDisk::storeSlices ( std::map< unsigned int, MassSpectrum > &  slice_vector,
std::size_t  ipos 
)
protectedvirtual

store MassSpectrum slices (by daltons) for a given retention time

Parameters
slice_vectormass spectrum chunks (by daltons)
iposthe position in the retention time vector

Reimplemented in pappso::MsRunXicExtractorDiskBuffer.

Definition at line 230 of file msrunxicextractordisk.cpp.

232 {
233  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
234 
235  for(auto &&spectrum_pair : spectrum_map)
236  {
237  appendSliceOnDisk(spectrum_pair.first, spectrum_pair.second, ipos);
238  }
239 
240  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
241 }

References appendSliceOnDisk().

Referenced by serializeMsRun().

◆ unserializeSlice()

MsRunSliceSPtr pappso::MsRunXicExtractorDisk::unserializeSlice ( unsigned int  slice_number)
protected

get one slice from disk by her slice number (dalton)

Parameters
slice_numberthe slice number == dalton integer

Definition at line 278 of file msrunxicextractordisk.cpp.

279 {
280  qDebug();
281  try
282  {
283  std::shared_ptr<MsRunSlice> msrun_slice_sp =
284  std::make_shared<MsRunSlice>(MsRunSlice());
285 
286  QFile slice_file(
287  QString("%1/%2").arg(mpa_temporaryDirectory->path()).arg(slice_number));
288  if(!slice_file.exists())
289  {
290  msrun_slice_sp.get()->setSize(m_rtSize);
291  msrun_slice_sp.get()->setSliceNumber(slice_number);
292  return msrun_slice_sp;
293  }
294  if(!slice_file.open(QIODevice::ReadOnly))
295  {
297  QObject::tr("unable to open file %1 in readonly")
298  .arg(slice_file.fileName()));
299  }
300  QDataStream stream(&slice_file);
301 
302  stream >> *(msrun_slice_sp.get());
303 
304  slice_file.close();
305 
306  return msrun_slice_sp;
307  }
308  catch(pappso::PappsoException &error)
309  {
311  QObject::tr("error unserializing slice %1:\n%2")
312  .arg(slice_number)
313  .arg(error.qwhat()));
314  }
315  qDebug();
316 }

References m_rtSize, mpa_temporaryDirectory, and pappso::PappsoException::qwhat().

Referenced by acquireSlices().

Member Data Documentation

◆ m_maxMz

pappso::pappso_double pappso::MsRunXicExtractorDisk::m_maxMz = 0
protected

Definition at line 102 of file msrunxicextractordisk.h.

Referenced by serializeMsRun().

◆ m_minMz

pappso::pappso_double pappso::MsRunXicExtractorDisk::m_minMz = 5000
protected

Definition at line 103 of file msrunxicextractordisk.h.

Referenced by serializeMsRun().

◆ m_msRunSliceListCache

std::deque<MsRunSliceSPtr> pappso::MsRunXicExtractorDisk::m_msRunSliceListCache
protected

Definition at line 107 of file msrunxicextractordisk.h.

Referenced by acquireSlices().

◆ m_mutex

QMutex pappso::MsRunXicExtractorDisk::m_mutex
protected

Definition at line 109 of file msrunxicextractordisk.h.

Referenced by acquireSlices().

◆ m_retentionTimeList

std::vector<pappso::pappso_double> pappso::MsRunXicExtractorDisk::m_retentionTimeList
protected

Definition at line 100 of file msrunxicextractordisk.h.

Referenced by getXicCstSPtr(), and serializeMsRun().

◆ m_rtSize

std::size_t pappso::MsRunXicExtractorDisk::m_rtSize = 0
protected

◆ m_temporaryDirectory

QString pappso::MsRunXicExtractorDisk::m_temporaryDirectory
protected

Definition at line 98 of file msrunxicextractordisk.h.

Referenced by MsRunXicExtractorDisk().

◆ mpa_temporaryDirectory

QTemporaryDir* pappso::MsRunXicExtractorDisk::mpa_temporaryDirectory = nullptr
protected

◆ MsRunXicExtractorFactory

friend pappso::MsRunXicExtractorDisk::MsRunXicExtractorFactory
private

Definition at line 46 of file msrunxicextractordisk.h.


The documentation for this class was generated from the following files:
pappso::MassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
pappso::MsRunXicExtractorDisk::acquireSlices
std::vector< MsRunSliceSPtr > acquireSlices(const MzRange &mz_range)
retrieve all the slices corresponding to a given mz_range
Definition: msrunxicextractordisk.cpp:319
pappso::MsRunXicExtractorDisk::mpa_temporaryDirectory
QTemporaryDir * mpa_temporaryDirectory
Definition: msrunxicextractordisk.h:99
pappso::MsRunXicExtractorDisk::m_msRunSliceListCache
std::deque< MsRunSliceSPtr > m_msRunSliceListCache
Definition: msrunxicextractordisk.h:107
pappso::MsRunXicExtractorDisk::m_mutex
QMutex m_mutex
Definition: msrunxicextractordisk.h:109
pappso::MsRunXicExtractorDisk::m_rtSize
std::size_t m_rtSize
Definition: msrunxicextractordisk.h:105
pappso::MsRunXicExtractorDisk::m_retentionTimeList
std::vector< pappso::pappso_double > m_retentionTimeList
Definition: msrunxicextractordisk.h:100
pappso::MsRunXicExtractorDisk::m_minMz
pappso::pappso_double m_minMz
Definition: msrunxicextractordisk.h:103
pappso::MsRunXicExtractorInterface::m_xicExtractMethod
XicExtractMethod m_xicExtractMethod
Definition: msrunxicextractorinterface.h:124
pappso::MsRunXicExtractorDisk::m_maxMz
pappso::pappso_double m_maxMz
Definition: msrunxicextractordisk.h:102
pappso::MsRunXicExtractorDisk::storeSlices
virtual void storeSlices(std::map< unsigned int, MassSpectrum > &slice_vector, std::size_t ipos)
store MassSpectrum slices (by daltons) for a given retention time
Definition: msrunxicextractordisk.cpp:230
pappso::MsRunXicExtractorDisk::m_temporaryDirectory
QString m_temporaryDirectory
Definition: msrunxicextractordisk.h:98
pappso::MsRunXicExtractorInterface::msp_msrun_reader
MsRunReaderSPtr msp_msrun_reader
Definition: msrunxicextractorinterface.h:123
pappso::PappsoException::qwhat
virtual const QString & qwhat() const
Definition: pappsoexception.h:66
pappso::MsRunSliceSPtr
std::shared_ptr< const MsRunSlice > MsRunSliceSPtr
Definition: msrunslice.h:39
pappso::MsRunXicExtractorDisk::serializeMsRun
void serializeMsRun()
Definition: msrunxicextractordisk.cpp:159
pappso::MsRunXicExtractor
Definition: msrunxicextractor.h:42
pappso::MsRunXicExtractorDisk::getXicCstSPtr
virtual XicCstSPtr getXicCstSPtr(const MzRange &mz_range, pappso::pappso_double rt_begin, pappso::pappso_double rt_end) override
get a XIC on this MsRun at the given mass range
Definition: msrunxicextractordisk.cpp:94
pappso::MsRunXicExtractorDisk::unserializeSlice
MsRunSliceSPtr unserializeSlice(unsigned int slice_number)
get one slice from disk by her slice number (dalton)
Definition: msrunxicextractordisk.cpp:278
pappso::MsRunXicExtractor::m_msrun_points
std::vector< MsRunXicExtractorPoints > m_msrun_points
Definition: msrunxicextractor.h:65
pappso::MsRunXicExtractorDisk::appendSliceOnDisk
void appendSliceOnDisk(unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos)
append a slice on disk (in a file)
Definition: msrunxicextractordisk.cpp:244
pappso::MsRunXicExtractorDisk::endPwizRead
virtual void endPwizRead()
Definition: msrunxicextractordisk.cpp:352
pappso::PappsoException
Definition: pappsoexception.h:42