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 ()
 
- 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...
 
void setRetentionTimeAroundTarget (double range_in_seconds)
 set the retention time range in seconds around the target rt More...
 
virtual void extractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) final
 extract a list of XIC given a list of xic coordinates to extract More...
 
virtual void extractXicCoordSPtrListParallelized (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) final
 multithreaded XIC extraction More...
 
const MsRunIdCstSPtrgetMsRunId () const
 
const MsRunReaderSPtrgetMsRunReaderSPtr () const
 get the msrunreader currently used for XIC extraction More...
 
void setPostExtractionTraceFilterCstSPtr (pappso::FilterInterfaceCstSPtr &filter)
 filter interface to apply just after XIC extration on each trace More...
 

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)
 
virtual void protectedExtractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end) override
 
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 ()
 
virtual void postExtractionProcess (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end)
 possible post extraction process, eventually trace filters More...
 

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< MsRunXicExtractorPointsm_msrun_points
 
- Protected Attributes inherited from pappso::MsRunXicExtractorInterface
MsRunReaderSPtr msp_msrun_reader
 
XicExtractMethod m_xicExtractMethod = XicExtractMethod::max
 
double m_retentionTimeAroundTarget = std::numeric_limits<double>::max()
 
pappso::FilterInterfaceCstSPtr mcsp_postExtractionTraceFilter = nullptr
 

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 48 of file msrunxicextractordiskbuffer.cpp.

50  : MsRunXicExtractorDisk(other)
51 {
52 
53  m_sliceBufferMap.clear();
54 }
std::map< unsigned int, QByteArray > m_sliceBufferMap
MsRunXicExtractorDisk(MsRunReaderSPtr &msrun_reader)

References m_sliceBufferMap.

◆ ~MsRunXicExtractorDiskBuffer()

pappso::MsRunXicExtractorDiskBuffer::~MsRunXicExtractorDiskBuffer ( )
virtual

Definition at line 56 of file msrunxicextractordiskbuffer.cpp.

57 {
58 }

◆ MsRunXicExtractorDiskBuffer() [2/2]

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

Definition at line 40 of file msrunxicextractordiskbuffer.cpp.

42  : MsRunXicExtractorDisk(msrun_reader, temporary_dir)
43 {
44 
45  m_sliceBufferMap.clear();
46 }

References m_sliceBufferMap.

Member Function Documentation

◆ appendSliceInBuffer()

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

Definition at line 78 of file msrunxicextractordiskbuffer.cpp.

81 {
82  qDebug();
83 
84  std::size_t spectrum_size = spectrum.size();
85 
86  if(spectrum_size == 0)
87  return;
88  try
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
97  ret.first->second.resize(0);
98  QDataStream outstream(&ret.first->second, QIODevice::WriteOnly);
99  outstream << (quint32)ipos;
100  outstream << spectrum;
101  }
102  else
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 }

References m_sliceBufferMap, and pappso::PappsoException::qwhat().

Referenced by storeSlices().

◆ endPwizRead()

void pappso::MsRunXicExtractorDiskBuffer::endPwizRead ( )
overrideprotectedvirtual

◆ flushBufferOnDisk()

void pappso::MsRunXicExtractorDiskBuffer::flushBufferOnDisk ( )
protected

Definition at line 130 of file msrunxicextractordiskbuffer.cpp.

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;
148 
149  if(!slice_file.open(QIODevice::WriteOnly))
150  {
152  QObject::tr("unable to open file %1")
153  .arg(slice_file.fileName()));
154  }
155  }
156  else
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 }

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

Referenced by endPwizRead(), and storeSlices().

◆ 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 61 of file msrunxicextractordiskbuffer.cpp.

63 {
64 
65  m_bufferSize++;
66  for(auto &&msrun_slice : slice_vector)
67  {
68  appendSliceInBuffer(msrun_slice.first, msrun_slice.second, ipos);
69  }
70 
72  {
74  }
75 }
void appendSliceInBuffer(unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos)

References appendSliceInBuffer(), flushBufferOnDisk(), m_bufferMaxSize, and m_bufferSize.

Member Data Documentation

◆ m_bufferMaxSize

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

Definition at line 69 of file msrunxicextractordiskbuffer.h.

Referenced by storeSlices().

◆ m_bufferSize

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

Definition at line 68 of file msrunxicextractordiskbuffer.h.

Referenced by flushBufferOnDisk(), and storeSlices().

◆ m_sliceBufferMap

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

◆ 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: