libpappsomspp
Library for mass spectrometry
pappso::TimsDirectXicExtractor Class Reference

#include <timsdirectxicextractor.h>

Inheritance diagram for pappso::TimsDirectXicExtractor:
pappso::TimsXicExtractorInterface pappso::MsRunXicExtractorInterface

Public Member Functions

 TimsDirectXicExtractor (MsRunReaderSPtr &msrun_reader)
 
virtual ~TimsDirectXicExtractor ()
 
- Public Member Functions inherited from pappso::TimsXicExtractorInterface
 TimsXicExtractorInterface (MsRunReaderSPtr &msrun_reader)
 
virtual ~TimsXicExtractorInterface ()
 
- 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

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...
 

Additional Inherited Members

- Protected Attributes inherited from pappso::TimsXicExtractorInterface
TimsDatamp_timsData
 
- 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
 

Detailed Description

Todo:
write docs

Definition at line 36 of file timsdirectxicextractor.h.

Constructor & Destructor Documentation

◆ TimsDirectXicExtractor()

TimsDirectXicExtractor::TimsDirectXicExtractor ( MsRunReaderSPtr msrun_reader)

Default constructor

Definition at line 35 of file timsdirectxicextractor.cpp.

◆ ~TimsDirectXicExtractor()

TimsDirectXicExtractor::~TimsDirectXicExtractor ( )
virtual

Destructor

Definition at line 40 of file timsdirectxicextractor.cpp.

41 {
42 }

Member Function Documentation

◆ protectedExtractXicCoordSPtrList()

void pappso::TimsDirectXicExtractor::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.

Definition at line 46 of file timsdirectxicextractor.cpp.

50 {
51  qDebug();
52  std::size_t xic_total_number =
53  std::distance(it_xic_coord_list_begin, it_xic_coord_list_end);
54  if(xic_total_number == 0)
55  return;
56 
57  std::vector<XicCoordTims *> xic_coord_tims_list;
58  xic_coord_tims_list.reserve(xic_total_number);
59 
60  for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++)
61  {
62  XicCoordTims *p_xic_coord_tims = dynamic_cast<XicCoordTims *>(it->get());
63  if(p_xic_coord_tims == nullptr)
64  {
65  }
66  else
67  {
68  xic_coord_tims_list.push_back(p_xic_coord_tims);
69  }
70  }
71 
72  std::sort(xic_coord_tims_list.begin(),
73  xic_coord_tims_list.end(),
74  [](const XicCoordTims *pa, const XicCoordTims *pb) {
75  return pa->rtTarget < pb->rtTarget;
76  });
77 
78 
79  std::vector<std::size_t> tims_frameid_list =
81  xic_coord_tims_list[0]->rtTarget - m_retentionTimeAroundTarget,
82  xic_coord_tims_list.back()->rtTarget + m_retentionTimeAroundTarget);
83 
84  monitor.setStatus(QObject::tr("extracting %1 XICs on %2 Tims frames")
85  .arg(xic_total_number)
86  .arg(tims_frameid_list.size()));
87  monitor.setTotalSteps(tims_frameid_list.size());
88 
89  qDebug() << " tims_frameid_list.size()=" << tims_frameid_list.size();
90  qDebug() << " rt begin=" << xic_coord_tims_list[0]->rtTarget;
91  qDebug() << " rt end=" << xic_coord_tims_list.back()->rtTarget;
92  for(std::size_t frame_id : tims_frameid_list)
93  {
94  std::vector<XicCoordTims *>::iterator itXicListbegin =
95  xic_coord_tims_list.begin();
96  std::vector<XicCoordTims *>::iterator itXicListend =
97  xic_coord_tims_list.end();
98  qDebug();
99  TimsFrameCstSPtr frame_sptr =
101  qDebug();
102  double rtframe = frame_sptr.get()->getTime();
103  qDebug();
104 
105  double rtbeginframe = rtframe - m_retentionTimeAroundTarget;
106  double rtendframe = rtframe + m_retentionTimeAroundTarget;
107 
108  if(rtbeginframe < 0)
109  rtbeginframe = 0;
110 
111  qDebug() << rtbeginframe;
112  while((itXicListbegin != itXicListend) &&
113  ((*itXicListbegin)->rtTarget < rtbeginframe))
114  {
115  itXicListbegin++;
116  }
117  qDebug();
118  itXicListend = itXicListbegin;
119  while((itXicListend != xic_coord_tims_list.end()) &&
120  ((*itXicListend)->rtTarget < rtendframe))
121  {
122  itXicListend++;
123  }
124  frame_sptr.get()->extractTimsXicListInRtRange(
125  itXicListbegin, itXicListend, m_xicExtractMethod);
126 
127  qDebug() << "" << frame_sptr.get()->getId();
128  monitor.count();
129  if(monitor.shouldIstop())
130  {
132  QObject::tr("Xic extraction process interrupted"));
133  }
134  }
135  qDebug();
136 }
TimsFrameCstSPtr getTimsFrameCstSPtrCached(std::size_t timsId)
get a Tims frame with his database ID but look in the cache first
Definition: timsdata.cpp:1094
std::vector< std::size_t > getTimsMS1FrameIdRange(double rt_begin, double rt_end) const
Definition: timsdata.cpp:492
virtual void setStatus(const QString &status)=0
current status of the process
virtual void setTotalSteps(std::size_t total_number_of_steps)
use it if the number of steps is known in an algorithm the total number of steps is usefull to report...
virtual bool shouldIstop()=0
should the procces be stopped ? If true, then cancel process Use this function at strategic point of ...
virtual void count()=0
count steps report when a step is computed in an algorithm
std::shared_ptr< const TimsFrame > TimsFrameCstSPtr
Definition: timsframe.h:42
coordinates of the XIC to extract and the resulting XIC after extraction
Definition: xiccoordtims.h:51

References pappso::UiMonitorInterface::count(), pappso::UiMonitorInterface::setStatus(), pappso::UiMonitorInterface::setTotalSteps(), and pappso::UiMonitorInterface::shouldIstop().


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