libpappsomspp
Library for mass spectrometry
pappso::MsRunXicExtractorDiskBuffer Class Reference

#include <msrunxicextractordiskbuffer.h>

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

Public Member Functions

 MsRunXicExtractorDiskBuffer (const MsRunXicExtractorDiskBuffer &other)
 
virtual ~MsRunXicExtractorDiskBuffer ()
 
- Public Member Functions inherited from pappso::MsRunXicExtractorDisk
 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

 MsRunXicExtractorDiskBuffer (MsRunReaderSPtr &msrun_reader, const QDir &temporary_dir)
 
virtual void storeSlices (std::map< unsigned int, MassSpectrum > &slice_vector, std::size_t ipos) override
 store MassSpectrum slices (by daltons) for a given retention time More...
 
void appendSliceInBuffer (unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos)
 
void flushBufferOnDisk ()
 
virtual void endPwizRead () override
 
- Protected Member Functions inherited from pappso::MsRunXicExtractorDisk
 MsRunXicExtractorDisk (MsRunReaderSPtr &msrun_reader, const QDir &temporary_dir)
 
void prepareExtractor ()
 
void serializeMsRun ()
 
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...
 
- 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

std::map< unsigned int, QByteArray > m_sliceBufferMap
 
std::size_t m_bufferSize = 0
 
std::size_t m_bufferMaxSize = 150
 
- Protected Attributes inherited from pappso::MsRunXicExtractorDisk
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 43 of file msrunxicextractordiskbuffer.h.

Constructor & Destructor Documentation

◆ MsRunXicExtractorDiskBuffer() [1/2]

pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorDiskBuffer ( const MsRunXicExtractorDiskBuffer other)

Definition at line 69 of file msrunxicextractordiskbuffer.cpp.

72  {
74  }
75 }

◆ ~MsRunXicExtractorDiskBuffer()

pappso::MsRunXicExtractorDiskBuffer::~MsRunXicExtractorDiskBuffer ( )
virtual

Definition at line 77 of file msrunxicextractordiskbuffer.cpp.

◆ MsRunXicExtractorDiskBuffer() [2/2]

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

Definition at line 61 of file msrunxicextractordiskbuffer.cpp.

63 {
64 
65  m_bufferSize++;
66  for(auto &&msrun_slice : slice_vector)
67  {

References appendSliceInBuffer(), and m_bufferSize.

Member Function Documentation

◆ appendSliceInBuffer()

void pappso::MsRunXicExtractorDiskBuffer::appendSliceInBuffer ( unsigned int  slice_number,
MassSpectrum spectrum,
std::size_t  ipos 
)
protected

Definition at line 99 of file msrunxicextractordiskbuffer.cpp.

103  {
104  QDataStream outstream(&ret.first->second,
105  QIODevice::WriteOnly | QIODevice::Append);
106  outstream << (quint32)ipos;
107  outstream << spectrum;
108  }
109  }
110  catch(PappsoException &error_pappso)
111  {
113  QObject::tr("appendSliceInBuffer : error ipos=%1 :\n%2")
114  .arg(ipos)
115  .arg(error_pappso.qwhat()));
116  }
117  catch(std::exception &error)
118  {
120  QObject::tr("appendSliceInBuffer slice_number=%1 ipos=%2 error :\n%3")
121  .arg(slice_number)
122  .arg(ipos)
123  .arg(error.what()));
124  }
125  qDebug();
126 }
127 
128 
129 void
131 {
132  qDebug();
133 
134  try
135  {
136  for(auto &buffer_pair : m_sliceBufferMap)
137  {
138 
139  if(buffer_pair.second.size() > 0)
140  {
141  QFile slice_file(QString("%1/%2")
142  .arg(mpa_temporaryDirectory->path())
143  .arg(buffer_pair.first));
144  bool new_file = false;
145  if(!slice_file.exists())
146  {
147  new_file = true;

Referenced by MsRunXicExtractorDiskBuffer().

◆ endPwizRead()

void pappso::MsRunXicExtractorDiskBuffer::endPwizRead ( )
overrideprotectedvirtual

Reimplemented from pappso::MsRunXicExtractorDisk.

Definition at line 227 of file msrunxicextractordiskbuffer.cpp.

◆ flushBufferOnDisk()

void pappso::MsRunXicExtractorDiskBuffer::flushBufferOnDisk ( )
protected

Definition at line 151 of file msrunxicextractordiskbuffer.cpp.

157  {
158  if(!slice_file.open(QIODevice::WriteOnly | QIODevice::Append))
159  {
161  QObject::tr("unable to open file %1")
162  .arg(slice_file.fileName()));
163  }
164  }
165 
166  QDataStream stream(&slice_file);
167 
168  if(new_file)
169  {
170  stream << (quint32)buffer_pair.first;
171  stream << (quint32)m_rtSize;
172  stream.writeRawData(buffer_pair.second.constData(),
173  buffer_pair.second.size());
174  }
175  else
176  {
177  stream.writeRawData(buffer_pair.second.constData(),
178  buffer_pair.second.size());
179  }
180 
181 
182  slice_file.flush();
183  slice_file.close();
184  }
185  // buffer_pair.second = std::vector<MassSpectrum>();
186  }
187 
188  m_bufferSize = 0;
189  m_sliceBufferMap.clear();
190  }
191  catch(PappsoException &error_pappso)
192  {
194  QObject::tr("flushBufferOnDisk error :\n%1").arg(error_pappso.qwhat()));
195  }
196  catch(std::exception &error)
197  {
199  QObject::tr("flushBufferOnDisk error :\n%1").arg(error.what()));
200  }
201  qDebug();
202 }
203 
204 
205 void
207 {
209 
210  m_sliceBufferMap.clear();
211 
212  msp_msrun_reader.get()->releaseDevice();
213 }
214 } // namespace pappso

◆ storeSlices()

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

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 from pappso::MsRunXicExtractorDisk.

Definition at line 82 of file msrunxicextractordiskbuffer.cpp.

89  {
90  std::pair<std::map<unsigned int, QByteArray>::iterator, bool> ret =
91  m_sliceBufferMap.insert(
92  std::pair<unsigned int, QByteArray>(slice_number, QByteArray()));
93 
94 
95  if(ret.second)
96  { // new buffer

Member Data Documentation

◆ m_bufferMaxSize

std::size_t pappso::MsRunXicExtractorDiskBuffer::m_bufferMaxSize = 150
protected

Definition at line 69 of file msrunxicextractordiskbuffer.h.

◆ m_bufferSize

std::size_t pappso::MsRunXicExtractorDiskBuffer::m_bufferSize = 0
protected

Definition at line 68 of file msrunxicextractordiskbuffer.h.

Referenced by MsRunXicExtractorDiskBuffer().

◆ m_sliceBufferMap

std::map<unsigned int, QByteArray> pappso::MsRunXicExtractorDiskBuffer::m_sliceBufferMap
protected

Definition at line 66 of file msrunxicextractordiskbuffer.h.

◆ MsRunXicExtractorFactory

friend pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorFactory
private

Definition at line 45 of file msrunxicextractordiskbuffer.h.


The documentation for this class was generated from the following files:
pappso::MsRunXicExtractorDiskBuffer::flushBufferOnDisk
void flushBufferOnDisk()
Definition: msrunxicextractordiskbuffer.cpp:151
pappso::MsRunXicExtractorDisk::mpa_temporaryDirectory
QTemporaryDir * mpa_temporaryDirectory
Definition: msrunxicextractordisk.h:99
pappso::MsRunXicExtractorDisk::m_rtSize
std::size_t m_rtSize
Definition: msrunxicextractordisk.h:105
pappso::MsRunXicExtractorInterface::msp_msrun_reader
MsRunReaderSPtr msp_msrun_reader
Definition: msrunxicextractorinterface.h:141
pappso::MsRunXicExtractorDiskBuffer::m_bufferSize
std::size_t m_bufferSize
Definition: msrunxicextractordiskbuffer.h:68
pappso::MsRunXicExtractorDiskBuffer::m_sliceBufferMap
std::map< unsigned int, QByteArray > m_sliceBufferMap
Definition: msrunxicextractordiskbuffer.h:66
pappso::PappsoException
Definition: pappsoexception.h:63
pappso::MsRunXicExtractorDiskBuffer::endPwizRead
virtual void endPwizRead() override
Definition: msrunxicextractordiskbuffer.cpp:227