libpappsomspp
Library for mass spectrometry
pappso::MsRunXicExtractor Class Reference

#include <msrunxicextractor.h>

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

Classes

struct  MsRunXicExtractorPoints
 
class  MsRunXicExtractorReadPoints
 class to read retention time points of MsRun More...
 

Public Member Functions

 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

 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)
 
virtual void protectedExtractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end) override
 
- 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::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 Member Functions

void extractOneXicCoord (XicCoord &xic_coord)
 

Private Attributes

friend MsRunXicExtractorFactory
 

Detailed Description

Definition at line 41 of file msrunxicextractor.h.

Constructor & Destructor Documentation

◆ MsRunXicExtractor() [1/2]

pappso::MsRunXicExtractor::MsRunXicExtractor ( const MsRunXicExtractor other)

Definition at line 65 of file msrunxicextractor.cpp.

67 {
68  m_msrun_points = other.m_msrun_points;
69 }
MsRunXicExtractorInterface(MsRunReaderSPtr &msrun_reader)
constructor is private, use the MsRunXicExtractorFactory
std::vector< MsRunXicExtractorPoints > m_msrun_points

References m_msrun_points.

◆ ~MsRunXicExtractor()

pappso::MsRunXicExtractor::~MsRunXicExtractor ( )
virtual

Definition at line 60 of file msrunxicextractor.cpp.

61 {
62 }

◆ MsRunXicExtractor() [2/2]

pappso::MsRunXicExtractor::MsRunXicExtractor ( MsRunReaderSPtr msrun_reader)
protected

Definition at line 41 of file msrunxicextractor.cpp.

43 {
44 
45  MsRunXicExtractorReadPoints get_msrun_points(m_msrun_points);
46  msp_msrun_reader.get()->readSpectrumCollection(get_msrun_points);
47 
48  std::sort(m_msrun_points.begin(),
49  m_msrun_points.end(),
50  [](const MsRunXicExtractorPoints &a,
51  const MsRunXicExtractorPoints &b) { return a.rt < b.rt; });
52 
53 
54  if(m_msrun_points.size() == 0)
55  {
57  QObject::tr("error extracting XIC: no MS level 1 in data file"));
58  }
59 }

References pappso::a, pappso::b, m_msrun_points, and pappso::MsRunXicExtractorInterface::msp_msrun_reader.

Member Function Documentation

◆ extractOneXicCoord()

void pappso::MsRunXicExtractor::extractOneXicCoord ( XicCoord xic_coord)
private

Definition at line 101 of file msrunxicextractor.cpp.

102 {
103  FilterResampleKeepXRange keep_range(xic_coord.mzRange.lower(),
104  xic_coord.mzRange.upper());
105  std::shared_ptr<Xic> msrunxic_sp = xic_coord.xicSptr;
106 
107  double rt_begin = xic_coord.rtTarget - m_retentionTimeAroundTarget;
108  double rt_end = xic_coord.rtTarget + m_retentionTimeAroundTarget;
109 
110 
111  auto itpoints = m_msrun_points.begin();
112 
113  // find startint retention time :
114  while((itpoints != m_msrun_points.end()) && (itpoints->rt < rt_begin))
115  {
116  itpoints++;
117  }
118  MassSpectrumSPtr spectrum;
119  DataPoint peak;
120  while((itpoints != m_msrun_points.end()) && (itpoints->rt <= rt_end))
121  {
122  spectrum =
123  msp_msrun_reader.get()->massSpectrumSPtr(itpoints->spectrum_index);
124  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
125  // << spectrum->size(); spectrum->debugPrintValues();
126 
127  qDebug() << " spectrum->size()=" << spectrum->size();
128  keep_range.filter(*(spectrum.get()));
129  qDebug() << " spectrum->size()=" << spectrum->size();
130 
131  peak.x = itpoints->rt;
132 
134  {
135  peak.y = 0;
136  if(spectrum->size() > 0)
137  {
138  peak.y = maxYDataPoint(spectrum->begin(), spectrum->end())->y;
139 
140  qDebug() << " peak.y=" << peak.y
141  << " spectrum->size()=" << spectrum->size();
142  }
143  }
144  else
145  {
146  peak.y = sumYTrace(spectrum->begin(), spectrum->end(), 0);
147  }
148  msrunxic_sp->push_back(peak);
149 
150  itpoints++;
151  }
152 }
std::vector< DataPoint >::const_iterator maxYDataPoint(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
Definition: trace.cpp:141
double sumYTrace(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double init)
calculate the sum of y value of a trace
Definition: trace.cpp:205
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
@ max
maximum of intensities

References pappso::FilterResampleKeepXRange::filter(), pappso::MzRange::lower(), m_msrun_points, pappso::MsRunXicExtractorInterface::m_retentionTimeAroundTarget, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::max, pappso::maxYDataPoint(), pappso::MsRunXicExtractorInterface::msp_msrun_reader, pappso::XicCoord::mzRange, pappso::XicCoord::rtTarget, pappso::sumYTrace(), pappso::MzRange::upper(), pappso::DataPoint::x, pappso::XicCoord::xicSptr, and pappso::DataPoint::y.

Referenced by protectedExtractXicCoordSPtrList().

◆ getXicFromPwizMSDataFile()

void pappso::MsRunXicExtractor::getXicFromPwizMSDataFile ( std::vector< Xic * > &  xic_list,
const std::vector< MzRange > &  mass_range_list,
pappso::pappso_double  rt_begin,
pappso::pappso_double  rt_end 
)
protectedvirtual

Definition at line 155 of file msrunxicextractor.cpp.

160 {
161  qDebug();
162 
163  std::vector<DataPoint> peak_for_mass;
164  for(const MzRange &mass_range : mass_range_list)
165  {
166  peak_for_mass.push_back(DataPoint());
167  qDebug() << " mass_range=" << mass_range.getMz();
168  }
169 
170 
171  qDebug();
172 
173  auto itpoints = m_msrun_points.begin();
174 
175  while((itpoints != m_msrun_points.end()) && (itpoints->rt < rt_begin))
176  {
177  itpoints++;
178  }
179 
180  MassSpectrumCstSPtr spectrum;
181  while((itpoints != m_msrun_points.end()) && (itpoints->rt <= rt_end))
182  {
183  spectrum =
184  msp_msrun_reader.get()->massSpectrumCstSPtr(itpoints->spectrum_index);
185 
186  for(DataPoint &peak : peak_for_mass)
187  {
188  peak.x = itpoints->rt;
189  peak.y = 0;
190  }
191 
192 
193  // iterate through the m/z-intensity pairs
194  for(auto &&spectrum_point : *(spectrum.get()))
195  {
196  // qDebug() << "getXicFromPwizMSDataFile it->mz " << it->mz <<
197  // " it->intensity" << it->intensity;
198  for(std::size_t i = 0; i < mass_range_list.size(); i++)
199  {
200  if(mass_range_list[i].contains(spectrum_point.x))
201  {
203  {
204  if(peak_for_mass[i].y < spectrum_point.y)
205  {
206  peak_for_mass[i].y = spectrum_point.y;
207  }
208  }
209  else
210  {
211  peak_for_mass[i].y += spectrum_point.y;
212  }
213  }
214  }
215  }
216 
217  for(std::size_t i = 0; i < mass_range_list.size(); i++)
218  {
219  // qDebug() << "getXicFromPwizMSDataFile push_back " <<
220  // peak_for_mass[i].rt;
221  xic_list[i]->push_back(peak_for_mass[i]);
222  }
223 
224  itpoints++;
225  }
226 
227 
228  qDebug();
229 } // namespace pappso
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55

References m_msrun_points, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::max, pappso::MsRunXicExtractorInterface::msp_msrun_reader, and pappso::y.

◆ protectedExtractXicCoordSPtrList()

void pappso::MsRunXicExtractor::protectedExtractXicCoordSPtrList ( UiMonitorInterface monitor,
std::vector< XicCoordSPtr >::iterator  it_xic_coord_list_begin,
std::vector< XicCoordSPtr >::iterator  it_xic_coord_list_end 
)
overrideprotectedvirtual

Implements pappso::MsRunXicExtractorInterface.

Reimplemented in pappso::MsRunXicExtractorDisk.

Definition at line 73 of file msrunxicextractor.cpp.

77 {
78 
79  // sort xic by mz:
80  std::sort(it_xic_coord_list_begin,
81  it_xic_coord_list_end,
82  [](XicCoordSPtr &a, XicCoordSPtr &b) {
83  return a.get()->rtTarget < b.get()->rtTarget;
84  });
85 
86  for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++)
87  {
88  // XicCoord *p_xic_coord = sp_xic_coord.get();
89  extractOneXicCoord(*(it->get()));
90  monitor.count();
91  if(monitor.shouldIstop())
92  {
94  QObject::tr("Xic extraction process interrupted"));
95  }
96  }
97 }
void extractOneXicCoord(XicCoord &xic_coord)
std::shared_ptr< XicCoord > XicCoordSPtr
Definition: xiccoord.h:41

References pappso::a, pappso::b, pappso::UiMonitorInterface::count(), extractOneXicCoord(), and pappso::UiMonitorInterface::shouldIstop().

Member Data Documentation

◆ m_msrun_points

std::vector<MsRunXicExtractorPoints> pappso::MsRunXicExtractor::m_msrun_points
protected

◆ MsRunXicExtractorFactory

friend pappso::MsRunXicExtractor::MsRunXicExtractorFactory
private

Definition at line 43 of file msrunxicextractor.h.


The documentation for this class was generated from the following files: