libpappsomspp
Library for mass spectrometry
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Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
pappso::MsRunXicExtractorInterface Class Referenceabstract

#include <msrunxicextractorinterface.h>

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

Public Member Functions

void setXicExtractMethod (Enums::XicExtractMethod method)
 set the XIC extraction method
 
void setRetentionTimeAroundTarget (double range_in_seconds)
 set the retention time range in seconds around the target rt
 
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
 
virtual void extractXicCoordSPtrListParallelized (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) final
 multithreaded XIC extraction
 
const MsRunIdCstSPtr & getMsRunId () const
 
const MsRunReaderSPtr & getMsRunReaderSPtr () const
 get the msrunreader currently used for XIC extraction
 
void setPostExtractionTraceFilterCstSPtr (pappso::FilterInterfaceCstSPtr &filter)
 filter interface to apply just after XIC extration on each trace
 

Protected Member Functions

 MsRunXicExtractorInterface (MsRunReaderSPtr &msrun_reader)
 constructor is private, use the MsRunXicExtractorFactory
 
 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
 
virtual void protectedExtractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end)=0
 

Protected Attributes

MsRunReaderSPtr msp_msrun_reader
 
Enums::XicExtractMethod m_xicExtractMethod = Enums::XicExtractMethod::max
 
double m_retentionTimeAroundTarget = std::numeric_limits<double>::max()
 
pappso::FilterInterfaceCstSPtr mcsp_postExtractionTraceFilter = nullptr
 

Detailed Description

Definition at line 48 of file msrunxicextractorinterface.h.

Constructor & Destructor Documentation

◆ MsRunXicExtractorInterface() [1/2]

pappso::MsRunXicExtractorInterface::MsRunXicExtractorInterface ( MsRunReaderSPtr & msrun_reader)
protected

constructor is private, use the MsRunXicExtractorFactory

Definition at line 40 of file msrunxicextractorinterface.cpp.

42 : msp_msrun_reader(msrun_reader)
43{
44}

References msp_msrun_reader.

Referenced by pappso::MsRunXicExtractor::MsRunXicExtractor(), pappso::MsRunXicExtractor::MsRunXicExtractor(), MsRunXicExtractorInterface(), and pappso::TimsXicExtractorInterface::TimsXicExtractorInterface().

◆ MsRunXicExtractorInterface() [2/2]

pappso::MsRunXicExtractorInterface::MsRunXicExtractorInterface ( const MsRunXicExtractorInterface & other)
protected

Definition at line 47 of file msrunxicextractorinterface.cpp.

49 : msp_msrun_reader(other.msp_msrun_reader)
50{
51 m_xicExtractMethod = other.m_xicExtractMethod;
52}

References MsRunXicExtractorInterface(), m_xicExtractMethod, and msp_msrun_reader.

◆ ~MsRunXicExtractorInterface()

pappso::MsRunXicExtractorInterface::~MsRunXicExtractorInterface ( )
protectedvirtual

Definition at line 54 of file msrunxicextractorinterface.cpp.

55{
56}

Member Function Documentation

◆ extractXicCoordSPtrList()

void pappso::MsRunXicExtractorInterface::extractXicCoordSPtrList ( UiMonitorInterface & monitor,
std::vector< XicCoordSPtr > & xic_coord_list )
finalvirtual

extract a list of XIC given a list of xic coordinates to extract

XicCoord is a vessel containing the xic to fill and coordinates of this XIC in the MS run

Parameters
monitorprocess monitoring
xic_coord_listlist of xic coordinates to extract. The order of xic coordinates may change.

Definition at line 181 of file msrunxicextractorinterface.cpp.

183{
184
185 monitor.setStatus(
186 QObject::tr("extracting %1 XICs").arg(xic_coord_list.size()));
187 monitor.setTotalSteps(xic_coord_list.size());
188 protectedExtractXicCoordSPtrList(
189 monitor, xic_coord_list.begin(), xic_coord_list.end());
190 monitor.setTotalSteps(0);
191 postExtractionProcess(monitor, xic_coord_list.begin(), xic_coord_list.end());
192}
pappso::MsRunXicExtractorInterface::postExtractionProcess
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
Definition msrunxicextractorinterface.cpp:195
pappso::MsRunXicExtractorInterface::protectedExtractXicCoordSPtrList
virtual void protectedExtractXicCoordSPtrList(UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end)=0

References postExtractionProcess(), protectedExtractXicCoordSPtrList(), pappso::UiMonitorInterface::setStatus(), and pappso::UiMonitorInterface::setTotalSteps().

Referenced by extractXicCoordSPtrListParallelized().

◆ extractXicCoordSPtrListParallelized()

void pappso::MsRunXicExtractorInterface::extractXicCoordSPtrListParallelized ( UiMonitorInterface & monitor,
std::vector< XicCoordSPtr > & xic_coord_list )
finalvirtual

multithreaded XIC extraction

divide xic_coord_list and run extractXicCoordSPtrList separated threads

Parameters
monitorprocess monitoring
xic_coord_listlist of xic coordinates to extract. The order of xic coordinates may change.

Definition at line 92 of file msrunxicextractorinterface.cpp.

94{
95 qDebug();
96 // get the number of available threads :
97 int number_of_threads = QThreadPool::globalInstance()->maxThreadCount();
98
99 if(number_of_threads == 1)
100 {
101 extractXicCoordSPtrList(monitor, xic_coord_list);
102 }
103 else
104 {
105 monitor.setStatus(QObject::tr("parallelized extraction of %1 XICs")
106 .arg(xic_coord_list.size()));
107
108 std::size_t chunck_size = xic_coord_list.size() / number_of_threads;
109 chunck_size += 1;
110 if(chunck_size < 1000)
111 chunck_size = 1000;
112
113 struct parallelExtractChunck
114 {
115 std::vector<XicCoordSPtr>::iterator it_xic_coord_begin;
116 std::vector<XicCoordSPtr>::iterator it_xic_coord_end;
117 };
118
119 std::vector<parallelExtractChunck> chunck_list;
120 qDebug();
121 for(auto it = xic_coord_list.begin(); it != xic_coord_list.end();)
122 {
123 qDebug() << "chunck_size=" << chunck_size;
124 parallelExtractChunck chunck;
125 chunck.it_xic_coord_begin = it;
126 for(std::size_t i = 0; i < chunck_size && it != xic_coord_list.end();
127 i++)
128 {
129 it++;
130 }
131 chunck.it_xic_coord_end = it;
132 chunck_list.push_back(chunck);
133 }
134 qDebug();
135 auto self = this;
136
137 qDebug();
138 std::function<std::size_t(const parallelExtractChunck &)> extractChunck =
139 [self](const parallelExtractChunck &extract_chunck) {
140 qDebug();
141 UiMonitorVoid monitor;
142 self->protectedExtractXicCoordSPtrList(
143 monitor,
144 extract_chunck.it_xic_coord_begin,
145 extract_chunck.it_xic_coord_end);
146 self->postExtractionProcess(monitor,
147 extract_chunck.it_xic_coord_begin,
148 extract_chunck.it_xic_coord_end);
149 qDebug();
150 return 1;
151 };
152 qDebug();
153 monitor.setTotalSteps(chunck_list.size());
154 UiMonitorInterface *monitorRef = &monitor;
155 std::function<void(std::size_t & result, const std::size_t &value)>
156 monitorExtract2 =
157 [monitorRef](std::size_t &result [[maybe_unused]],
158 const std::size_t &value
159 [[maybe_unused]]) { monitorRef->count(); };
160 qDebug();
161
162 QFuture<std::size_t> res =
163 QtConcurrent::mappedReduced<std::size_t>(chunck_list.begin(),
164 chunck_list.end(),
165 extractChunck,
166 monitorExtract2,
167 QtConcurrent::UnorderedReduce);
168 qDebug();
169
170 /*
171 QFuture<std::size_t> res =
172 QtConcurrent::mapped(chunck_list.begin(), chunck_list.end(),
173 extractChunck);
174 */
175 res.waitForFinished();
176 monitor.setTotalSteps(0);
177 }
178}
pappso::MsRunXicExtractorInterface::extractXicCoordSPtrList
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
Definition msrunxicextractorinterface.cpp:181

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

◆ getMsRunId()

const MsRunIdCstSPtr & pappso::MsRunXicExtractorInterface::getMsRunId ( ) const

Definition at line 72 of file msrunxicextractorinterface.cpp.

73{
74 return msp_msrun_reader.get()->getMsRunId();
75}

References msp_msrun_reader.

◆ getMsRunReaderSPtr()

const MsRunReaderSPtr & pappso::MsRunXicExtractorInterface::getMsRunReaderSPtr ( ) const

get the msrunreader currently used for XIC extraction

Definition at line 78 of file msrunxicextractorinterface.cpp.

79{
80 return msp_msrun_reader;
81}

References msp_msrun_reader.

◆ postExtractionProcess()

void pappso::MsRunXicExtractorInterface::postExtractionProcess ( UiMonitorInterface & monitor,
std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin,
std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end )
protectedvirtual

possible post extraction process, eventually trace filters

Definition at line 195 of file msrunxicextractorinterface.cpp.

199{
200
201 if(mcsp_postExtractionTraceFilter != nullptr)
202 {
203 monitor.setStatus(
204 QObject::tr("filtering %1 XICs")
205 .arg(std::distance(it_xic_coord_list_begin, it_xic_coord_list_end)));
206 for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++)
207 {
208 mcsp_postExtractionTraceFilter.get()->filter(
209 *(it->get()->xicSptr.get()));
210 }
211 }
212}
pappso::MsRunXicExtractorInterface::mcsp_postExtractionTraceFilter
pappso::FilterInterfaceCstSPtr mcsp_postExtractionTraceFilter
Definition msrunxicextractorinterface.h:129

References mcsp_postExtractionTraceFilter, and pappso::UiMonitorInterface::setStatus().

Referenced by extractXicCoordSPtrList().

◆ protectedExtractXicCoordSPtrList()

virtual void pappso::MsRunXicExtractorInterface::protectedExtractXicCoordSPtrList ( UiMonitorInterface & monitor,
std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin,
std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end )
protectedpure virtual

Implemented in pappso::MsRunXicExtractor, pappso::MsRunXicExtractorDisk, and pappso::TimsDirectXicExtractor.

Referenced by extractXicCoordSPtrList().

◆ setPostExtractionTraceFilterCstSPtr()

void pappso::MsRunXicExtractorInterface::setPostExtractionTraceFilterCstSPtr ( pappso::FilterInterfaceCstSPtr & filter)

filter interface to apply just after XIC extration on each trace

Definition at line 84 of file msrunxicextractorinterface.cpp.

86{
87 mcsp_postExtractionTraceFilter = filter;
88}
pappso::ProjectParamCategory::filter
@ filter
concerning filters (psm, peptide, protein validation)
Definition projectparameters.h:48

References pappso::filter, and mcsp_postExtractionTraceFilter.

◆ setRetentionTimeAroundTarget()

void pappso::MsRunXicExtractorInterface::setRetentionTimeAroundTarget ( double range_in_seconds)

set the retention time range in seconds around the target rt

only the interesting part of the xic will be extracted, form the rt target

  • range_in_seconds to rt target + range in seconds by default, all the LC run time is extracted
Parameters
range_in_secondsrange in seconds

Definition at line 65 of file msrunxicextractorinterface.cpp.

67{
68 m_retentionTimeAroundTarget = range_in_seconds;
69}

References m_retentionTimeAroundTarget.

◆ setXicExtractMethod()

void pappso::MsRunXicExtractorInterface::setXicExtractMethod ( Enums::XicExtractMethod method)

set the XIC extraction method

Definition at line 59 of file msrunxicextractorinterface.cpp.

60{
61 m_xicExtractMethod = method;
62}

References m_xicExtractMethod.

Member Data Documentation

◆ m_retentionTimeAroundTarget

double pappso::MsRunXicExtractorInterface::m_retentionTimeAroundTarget = std::numeric_limits<double>::max()
protected

Definition at line 128 of file msrunxicextractorinterface.h.

Referenced by pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::MsRunXicExtractorDisk::extractOneXicCoord(), pappso::TimsDirectXicExtractor::protectedExtractXicCoordSPtrList(), and setRetentionTimeAroundTarget().

◆ m_xicExtractMethod

Enums::XicExtractMethod pappso::MsRunXicExtractorInterface::m_xicExtractMethod = Enums::XicExtractMethod::max
protected

Definition at line 127 of file msrunxicextractorinterface.h.

Referenced by MsRunXicExtractorInterface(), pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::MsRunXicExtractorDisk::extractOneXicCoord(), pappso::MsRunXicExtractor::getXicFromPwizMSDataFile(), pappso::TimsDirectXicExtractor::protectedExtractXicCoordSPtrList(), and setXicExtractMethod().

◆ mcsp_postExtractionTraceFilter

pappso::FilterInterfaceCstSPtr pappso::MsRunXicExtractorInterface::mcsp_postExtractionTraceFilter = nullptr
protected

Definition at line 129 of file msrunxicextractorinterface.h.

Referenced by postExtractionProcess(), and setPostExtractionTraceFilterCstSPtr().

◆ msp_msrun_reader

MsRunReaderSPtr pappso::MsRunXicExtractorInterface::msp_msrun_reader
protected

Definition at line 126 of file msrunxicextractorinterface.h.

Referenced by pappso::MsRunXicExtractor::MsRunXicExtractor(), pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk(), MsRunXicExtractorInterface(), MsRunXicExtractorInterface(), pappso::MsRunXicExtractorDisk::endPwizRead(), pappso::MsRunXicExtractorDiskBuffer::endPwizRead(), pappso::MsRunXicExtractor::extractOneXicCoord(), getMsRunId(), getMsRunReaderSPtr(), pappso::MsRunXicExtractor::getXicFromPwizMSDataFile(), pappso::MsRunXicExtractorDisk::prepareExtractor(), and pappso::MsRunXicExtractorDisk::serializeMsRun().

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