libpappsomspp
Library for mass spectrometry
pappso::GrpExperiment Class Reference

#include <grpexperiment.h>

Public Member Functions

GrpProteinSpgetGrpProteinSp (const QString &acc, const QString &description)
 
GrpPeptideSpsetGrpPeptide (const GrpProteinSp &proteinSp, const QString &sequence, pappso_double mass)
 
 GrpExperiment (GrpGroupingMonitorInterface *p_monitor)
 
virtual ~GrpExperiment ()
 
void startGrouping ()
 
std::vector< GrpProteinSpConstgetGrpProteinSpList () const
 
void setRemoveNonInformativeSubgroups (bool ok)
 
void addPostGroupingGrpProteinSpRemoval (GrpProteinSp sp_protein)
 protein to remove with its entire group after grouping is completed typically : to use with protein contaminants if you want to ignore any group containing one contaminant protein More...
 
void addPreGroupingGrpProteinSpRemoval (GrpProteinSp sp_protein)
 protein peptides to remove before grouping typically : remove protein contaminants in special metaproteomics cases More...
 
std::vector< GrpGroupSpConstgetGrpGroupSpList () const
 

Private Member Functions

void addSubGroupSp (GrpMapPeptideToGroup &grp_map_peptide_to_group, GrpSubGroupSp &grpSubGroupSp) const
 
void numbering ()
 
void removeNonInformativeSubGroups ()
 

Private Attributes

GrpGroupingMonitorInterfacemp_monitor = nullptr
 
bool m_isRemoveNonInformativeSubgroups = true
 
std::map< QString, GrpProteinSpm_mapProteins
 
std::map< QString, std::map< unsigned long, GrpPeptideSp > > m_mapPeptides
 
std::list< GrpPeptideSpm_grpPeptideList
 
std::list< GrpProteinSpm_grpProteinList
 
bool m_isGroupingStarted = false
 
std::list< GrpProtein * > m_remainingGrpProteinList
 
GrpPeptideSet m_grpPostGroupingProteinListRemoval
 
GrpPeptideSet m_grpPreGroupingProteinListRemoval
 
std::list< GrpGroupSpm_grpGroupSpList
 

Detailed Description

Definition at line 41 of file grpexperiment.h.

Constructor & Destructor Documentation

◆ GrpExperiment()

GrpExperiment::GrpExperiment ( GrpGroupingMonitorInterface p_monitor)

Definition at line 37 of file grpexperiment.cpp.

38 {
39  mp_monitor = p_monitor;
40 }
GrpGroupingMonitorInterface * mp_monitor
Definition: grpexperiment.h:44

References mp_monitor.

◆ ~GrpExperiment()

GrpExperiment::~GrpExperiment ( )
virtual

Definition at line 42 of file grpexperiment.cpp.

43 {
44 }

Member Function Documentation

◆ addPostGroupingGrpProteinSpRemoval()

void GrpExperiment::addPostGroupingGrpProteinSpRemoval ( GrpProteinSp  sp_protein)

protein to remove with its entire group after grouping is completed typically : to use with protein contaminants if you want to ignore any group containing one contaminant protein

Definition at line 52 of file grpexperiment.cpp.

53 {
54  GrpPeptideSet peptide_set(sp_protein.get());
56 }
GrpPeptideSet m_grpPostGroupingProteinListRemoval
Definition: grpexperiment.h:54
void addAll(const GrpPeptideSet &peptideSet)

References pappso::GrpPeptideSet::addAll(), and m_grpPostGroupingProteinListRemoval.

◆ addPreGroupingGrpProteinSpRemoval()

void GrpExperiment::addPreGroupingGrpProteinSpRemoval ( GrpProteinSp  sp_protein)

protein peptides to remove before grouping typically : remove protein contaminants in special metaproteomics cases

Definition at line 60 of file grpexperiment.cpp.

61 {
62  GrpPeptideSet peptide_set(sp_protein.get());
64 }
GrpPeptideSet m_grpPreGroupingProteinListRemoval
Definition: grpexperiment.h:56

References pappso::GrpPeptideSet::addAll(), and m_grpPreGroupingProteinListRemoval.

◆ addSubGroupSp()

void GrpExperiment::addSubGroupSp ( GrpMapPeptideToGroup grp_map_peptide_to_group,
GrpSubGroupSp grpSubGroupSp 
) const
private

Definition at line 203 of file grpexperiment.cpp.

205 {
206  qDebug() << "GrpExperiment::addSubGroupSp begin "
207  << grpSubGroupSp.get()->getFirstAccession();
208 
209  std::list<GrpGroupSp> new_group_list;
210  grp_map_peptide_to_group.getGroupList(grpSubGroupSp.get()->getPeptideSet(),
211  new_group_list);
212 
213  if(new_group_list.size() == 0)
214  {
215  qDebug() << "GrpExperiment::addSubGroupSp create a new group";
216  // create a new group
217  GrpGroupSp sp_group = GrpGroup(grpSubGroupSp).makeGrpGroupSp();
218  // m_grpGroupSpList.push_back(sp_group);
219 
220  grp_map_peptide_to_group.set(grpSubGroupSp.get()->getPeptideSet(),
221  sp_group);
222  }
223  else
224  {
225  qDebug() << "GrpExperiment::addSubGroupSp fusion groupList.size() "
226  << new_group_list.size();
227  // fusion group and add the subgroup
228  auto itGroup = new_group_list.begin();
229  GrpGroupSp p_keepGroup = *itGroup;
230  qDebug() << "GrpExperiment::addSubGroupSp "
231  "p_keepGroup->addSubGroupSp(grpSubGroupSp) "
232  << p_keepGroup.get();
233  p_keepGroup->addSubGroupSp(grpSubGroupSp);
234  grp_map_peptide_to_group.set(grpSubGroupSp.get()->getPeptideSet(),
235  p_keepGroup);
236 
237  itGroup++;
238  while(itGroup != new_group_list.end())
239  {
240  qDebug()
241  << "GrpExperiment::addSubGroupSp p_keepGroup->addGroup(*itGroup) "
242  << itGroup->get();
243  p_keepGroup->addGroup(itGroup->get());
244  grp_map_peptide_to_group.set((*itGroup)->getGrpPeptideSet(),
245  p_keepGroup);
246 
247  // m_grpGroupSpList.remove_if([itGroup](GrpGroupSp & groupSp) {
248  // return (itGroup->get() == groupSp.get()) ;
249  //});
250  itGroup++;
251  }
252  }
253 
254  qDebug() << "GrpExperiment::addSubGroupSp end";
255 }
GrpGroupSp makeGrpGroupSp()
Definition: grpgroup.cpp:98
void getGroupList(const GrpPeptideSet &peptide_set_in, std::list< GrpGroupSp > &impacted_group_list) const
get all groups concerned by a list of peptides
void set(const GrpPeptideSet &peptide_set_in, GrpGroupSp grp_group)
set peptide keys pointing on the group
std::shared_ptr< GrpGroup > GrpGroupSp
Definition: grpgroup.h:38

References pappso::GrpMapPeptideToGroup::getGroupList(), pappso::GrpGroup::makeGrpGroupSp(), and pappso::GrpMapPeptideToGroup::set().

Referenced by removeNonInformativeSubGroups(), and startGrouping().

◆ getGrpGroupSpList()

std::vector< GrpGroupSpConst > GrpExperiment::getGrpGroupSpList ( ) const

Definition at line 67 of file grpexperiment.cpp.

68 {
69  std::vector<GrpGroupSpConst> grp_list;
70  for(GrpGroupSp group : m_grpGroupSpList)
71  {
72  grp_list.push_back(group);
73  }
74  return grp_list;
75 }
std::list< GrpGroupSp > m_grpGroupSpList
Definition: grpexperiment.h:58

References m_grpGroupSpList.

◆ getGrpProteinSp()

GrpProteinSp & GrpExperiment::getGrpProteinSp ( const QString &  acc,
const QString &  description 
)

Definition at line 78 of file grpexperiment.cpp.

80 {
81  GrpProtein grpProtein(accession, description);
82  auto insertedPair = m_mapProteins.insert(std::pair<QString, GrpProteinSp>(
83  accession, std::make_shared<GrpProtein>(grpProtein)));
84  if(insertedPair.second)
85  {
86  m_grpProteinList.push_back(insertedPair.first->second);
87  m_remainingGrpProteinList.push_back(insertedPair.first->second.get());
88  }
89  return (insertedPair.first->second);
90 }
std::list< GrpProteinSp > m_grpProteinList
Definition: grpexperiment.h:50
std::list< GrpProtein * > m_remainingGrpProteinList
Definition: grpexperiment.h:52
std::map< QString, GrpProteinSp > m_mapProteins
Definition: grpexperiment.h:46

References m_grpProteinList, m_mapProteins, and m_remainingGrpProteinList.

◆ getGrpProteinSpList()

std::vector< GrpProteinSpConst > GrpExperiment::getGrpProteinSpList ( ) const

Definition at line 281 of file grpexperiment.cpp.

282 {
283  std::vector<GrpProteinSpConst> grouped_protein_list;
285  {
286  throw PappsoException(
287  QObject::tr("unable to get grouped protein list before grouping"));
288  }
289  for(auto &&protein_sp : m_grpProteinList)
290  {
291  if(protein_sp.get()->getGroupNumber() > 0)
292  {
293  grouped_protein_list.push_back(protein_sp);
294  }
295  }
296  return grouped_protein_list;
297 }

References m_grpProteinList, and m_isGroupingStarted.

◆ numbering()

void GrpExperiment::numbering ( )
private

Definition at line 258 of file grpexperiment.cpp.

259 {
260  qDebug() << "GrpExperiment::numbering begin";
261  if(mp_monitor != nullptr)
263  for(auto &&group_sp : m_grpGroupSpList)
264  {
265  group_sp.get()->numbering();
266  }
267  m_grpGroupSpList.sort([](GrpGroupSp &first, GrpGroupSp &second) {
268  return ((*first.get()) < (*second.get()));
269  });
270  unsigned int i = 1;
271  for(auto &&group_sp : m_grpGroupSpList)
272  {
273  group_sp.get()->setGroupNumber(i);
274  i++;
275  }
276 
277  qDebug() << "GrpExperiment::numbering end";
278 }
virtual void startNumberingAllGroups(std::size_t total_number_group)=0

References m_grpGroupSpList, mp_monitor, and pappso::GrpGroupingMonitorInterface::startNumberingAllGroups().

Referenced by startGrouping().

◆ removeNonInformativeSubGroups()

void GrpExperiment::removeNonInformativeSubGroups ( )
private

Definition at line 300 of file grpexperiment.cpp.

301 {
302  qDebug() << "GrpExperiment::removeNonInformativeSubGroups begin";
303  if(mp_monitor != nullptr)
305  m_grpGroupSpList.size());
306 
307  std::list<GrpGroupSp> old_grp_group_sp_list(m_grpGroupSpList);
308  m_grpGroupSpList.clear();
309  auto it_group = old_grp_group_sp_list.begin();
310  while(it_group != old_grp_group_sp_list.end())
311  {
312  if(mp_monitor != nullptr)
314  if(it_group->get()->removeNonInformativeSubGroups())
315  {
316  // need to regroup it
317  GrpGroupSp old_group_sp = *it_group;
318  GrpMapPeptideToGroup grp_map_peptide_to_group;
319 
320  std::list<GrpSubGroupSp> dispatch_sub_group_set =
321  old_group_sp.get()->getSubGroupSpList();
322  for(GrpSubGroupSp &grp_subgroup : dispatch_sub_group_set)
323  {
324  addSubGroupSp(grp_map_peptide_to_group, grp_subgroup);
325  }
326  grp_map_peptide_to_group.clear(m_grpGroupSpList);
327  }
328  else
329  {
330  qDebug() << "GrpExperiment::removeNonInformativeSubGroups no "
331  "removeNonInformativeSubGroups";
332  m_grpGroupSpList.push_back(*it_group);
333  }
334  it_group++;
335  }
336  if(mp_monitor != nullptr)
338  m_grpGroupSpList.size());
339 
340  qDebug() << "GrpExperiment::removeNonInformativeSubGroups end";
341 }
void addSubGroupSp(GrpMapPeptideToGroup &grp_map_peptide_to_group, GrpSubGroupSp &grpSubGroupSp) const
virtual void removingNonInformativeSubGroupsInGroup()=0
virtual void startRemovingNonInformativeSubGroupsInAllGroups(std::size_t total_number_group)=0
virtual void stopRemovingNonInformativeSubGroupsInAllGroups(std::size_t total_number_group)=0
void clear(std::list< GrpGroupSp > &grp_group_list)
std::shared_ptr< GrpSubGroup > GrpSubGroupSp
Definition: grpsubgroup.h:39

References addSubGroupSp(), pappso::GrpMapPeptideToGroup::clear(), m_grpGroupSpList, mp_monitor, pappso::GrpGroupingMonitorInterface::removingNonInformativeSubGroupsInGroup(), pappso::GrpGroupingMonitorInterface::startRemovingNonInformativeSubGroupsInAllGroups(), and pappso::GrpGroupingMonitorInterface::stopRemovingNonInformativeSubGroupsInAllGroups().

Referenced by startGrouping().

◆ setGrpPeptide()

GrpPeptideSp & GrpExperiment::setGrpPeptide ( const GrpProteinSp proteinSp,
const QString &  sequence,
pappso_double  mass 
)

Definition at line 93 of file grpexperiment.cpp.

96 {
97  proteinSp.get()->countPlus();
98  GrpPeptideSp sp_grppeptide =
99  std::make_shared<GrpPeptide>(GrpPeptide(sequence, mass));
100 
101  auto insertedPair = m_mapPeptides.insert(
102  std::pair<QString, std::map<unsigned long, GrpPeptideSp>>(
103  sp_grppeptide.get()->m_sequence,
104  std::map<unsigned long, GrpPeptideSp>()));
105  auto secondInsertedPair =
106  insertedPair.first->second.insert(std::pair<unsigned long, GrpPeptideSp>(
107  (unsigned long)(mass * 100), sp_grppeptide));
108  if(secondInsertedPair.second)
109  {
110  m_grpPeptideList.push_back(secondInsertedPair.first->second);
111  }
112  proteinSp.get()->push_back(secondInsertedPair.first->second.get());
113  return (secondInsertedPair.first->second);
114 }
std::list< GrpPeptideSp > m_grpPeptideList
Definition: grpexperiment.h:49
std::map< QString, std::map< unsigned long, GrpPeptideSp > > m_mapPeptides
Definition: grpexperiment.h:47
std::shared_ptr< GrpPeptide > GrpPeptideSp
Definition: grppeptide.h:40

References m_grpPeptideList, and m_mapPeptides.

◆ setRemoveNonInformativeSubgroups()

void GrpExperiment::setRemoveNonInformativeSubgroups ( bool  ok)

Definition at line 46 of file grpexperiment.cpp.

47 {
49 }
bool m_isRemoveNonInformativeSubgroups
Definition: grpexperiment.h:45

References m_isRemoveNonInformativeSubgroups.

◆ startGrouping()

void GrpExperiment::startGrouping ( )

Definition at line 117 of file grpexperiment.cpp.

118 {
119  qDebug() << "GrpExperiment::startGrouping begin";
120  if(mp_monitor != nullptr)
122  m_grpPeptideList.size());
123  m_isGroupingStarted = true;
124  m_mapPeptides.clear();
125  m_mapProteins.clear();
126  qDebug() << "GrpExperiment::startGrouping sort protein list "
127  "m_remainingGrpProteinList.size() "
128  << m_remainingGrpProteinList.size();
129  // m_remainingGrpProteinList.sort();
130  // m_remainingGrpProteinList.unique();
131 
133  {
134  // TODO clean protein list to remove contaminant peptides before grouping
135  }
136 
137 
138  GrpMapPeptideToGroup grp_map_peptide_to_group;
139  qDebug() << "GrpExperiment::startGrouping grouping begin";
140  for(auto p_grpProtein : m_remainingGrpProteinList)
141  {
142  p_grpProtein->strip();
143  if(p_grpProtein->m_count == 0)
144  {
145  // no peptides : do not group this protein
146  }
147  else
148  {
149  GrpSubGroupSp grpSubGroupSp =
150  GrpSubGroup(p_grpProtein).makeGrpSubGroupSp();
151 
152  if(mp_monitor != nullptr)
154  this->addSubGroupSp(grp_map_peptide_to_group, grpSubGroupSp);
155  }
156  }
157  grp_map_peptide_to_group.clear(m_grpGroupSpList);
158  qDebug() << "GrpExperiment::startGrouping grouping end";
159 
160  qDebug() << "GrpExperiment::startGrouping grouping m_grpGroupSpList.size() "
161  << m_grpGroupSpList.size();
162 
164  {
166  }
167 
168  // post grouping protein group removal
169  // remove any group containing contaminants
170  m_grpGroupSpList.remove_if([this](GrpGroupSp &groupSp) {
171  return (
172  groupSp.get()->containsAny(this->m_grpPostGroupingProteinListRemoval));
173  });
174 
175 
176  numbering();
177  if(mp_monitor != nullptr)
179  // GrpGroup(this, *m_remainingGrpProteinList.begin());
180  qDebug() << "GrpExperiment::startGrouping end";
181 }
virtual void startGrouping(std::size_t total_number_protein, std::size_t total_number_peptide)=0
unsigned int size() const
Definition: grppeptideset.h:54
GrpSubGroupSp makeGrpSubGroupSp()

References addSubGroupSp(), pappso::GrpMapPeptideToGroup::clear(), pappso::GrpGroupingMonitorInterface::groupingProtein(), m_grpGroupSpList, m_grpPeptideList, m_grpPreGroupingProteinListRemoval, m_isGroupingStarted, m_isRemoveNonInformativeSubgroups, m_mapPeptides, m_mapProteins, m_remainingGrpProteinList, pappso::GrpSubGroup::makeGrpSubGroupSp(), mp_monitor, numbering(), removeNonInformativeSubGroups(), pappso::GrpPeptideSet::size(), pappso::GrpGroupingMonitorInterface::startGrouping(), and pappso::GrpGroupingMonitorInterface::stopGrouping().

Member Data Documentation

◆ m_grpGroupSpList

std::list<GrpGroupSp> pappso::GrpExperiment::m_grpGroupSpList
private

◆ m_grpPeptideList

std::list<GrpPeptideSp> pappso::GrpExperiment::m_grpPeptideList
private

Definition at line 49 of file grpexperiment.h.

Referenced by setGrpPeptide(), and startGrouping().

◆ m_grpPostGroupingProteinListRemoval

GrpPeptideSet pappso::GrpExperiment::m_grpPostGroupingProteinListRemoval
private

Definition at line 54 of file grpexperiment.h.

Referenced by addPostGroupingGrpProteinSpRemoval().

◆ m_grpPreGroupingProteinListRemoval

GrpPeptideSet pappso::GrpExperiment::m_grpPreGroupingProteinListRemoval
private

Definition at line 56 of file grpexperiment.h.

Referenced by addPreGroupingGrpProteinSpRemoval(), and startGrouping().

◆ m_grpProteinList

std::list<GrpProteinSp> pappso::GrpExperiment::m_grpProteinList
private

Definition at line 50 of file grpexperiment.h.

Referenced by getGrpProteinSp(), and getGrpProteinSpList().

◆ m_isGroupingStarted

bool pappso::GrpExperiment::m_isGroupingStarted = false
private

Definition at line 51 of file grpexperiment.h.

Referenced by getGrpProteinSpList(), and startGrouping().

◆ m_isRemoveNonInformativeSubgroups

bool pappso::GrpExperiment::m_isRemoveNonInformativeSubgroups = true
private

Definition at line 45 of file grpexperiment.h.

Referenced by setRemoveNonInformativeSubgroups(), and startGrouping().

◆ m_mapPeptides

std::map<QString, std::map<unsigned long, GrpPeptideSp> > pappso::GrpExperiment::m_mapPeptides
private

Definition at line 47 of file grpexperiment.h.

Referenced by setGrpPeptide(), and startGrouping().

◆ m_mapProteins

std::map<QString, GrpProteinSp> pappso::GrpExperiment::m_mapProteins
private

Definition at line 46 of file grpexperiment.h.

Referenced by getGrpProteinSp(), and startGrouping().

◆ m_remainingGrpProteinList

std::list<GrpProtein *> pappso::GrpExperiment::m_remainingGrpProteinList
private

Definition at line 52 of file grpexperiment.h.

Referenced by getGrpProteinSp(), and startGrouping().

◆ mp_monitor

GrpGroupingMonitorInterface* pappso::GrpExperiment::mp_monitor = nullptr
private

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