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 35 of file grpexperiment.cpp.

36{
37 mp_monitor = p_monitor;
38}
GrpGroupingMonitorInterface * mp_monitor
Definition: grpexperiment.h:44

References mp_monitor.

◆ ~GrpExperiment()

GrpExperiment::~GrpExperiment ( )
virtual

Definition at line 40 of file grpexperiment.cpp.

41{
42}

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 50 of file grpexperiment.cpp.

51{
52 GrpPeptideSet peptide_set(sp_protein.get());
54}
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 58 of file grpexperiment.cpp.

59{
60 GrpPeptideSet peptide_set(sp_protein.get());
62}
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 201 of file grpexperiment.cpp.

203{
204 qDebug() << "GrpExperiment::addSubGroupSp begin "
205 << grpSubGroupSp.get()->getFirstAccession();
206
207 std::list<GrpGroupSp> new_group_list;
208 grp_map_peptide_to_group.getGroupList(grpSubGroupSp.get()->getPeptideSet(),
209 new_group_list);
210
211 if(new_group_list.size() == 0)
212 {
213 qDebug() << "GrpExperiment::addSubGroupSp create a new group";
214 // create a new group
215 GrpGroupSp sp_group = GrpGroup(grpSubGroupSp).makeGrpGroupSp();
216 // m_grpGroupSpList.push_back(sp_group);
217
218 grp_map_peptide_to_group.set(grpSubGroupSp.get()->getPeptideSet(),
219 sp_group);
220 }
221 else
222 {
223 qDebug() << "GrpExperiment::addSubGroupSp fusion groupList.size() "
224 << new_group_list.size();
225 // fusion group and add the subgroup
226 auto itGroup = new_group_list.begin();
227 GrpGroupSp p_keepGroup = *itGroup;
228 qDebug() << "GrpExperiment::addSubGroupSp "
229 "p_keepGroup->addSubGroupSp(grpSubGroupSp) "
230 << p_keepGroup.get();
231 p_keepGroup->addSubGroupSp(grpSubGroupSp);
232 grp_map_peptide_to_group.set(grpSubGroupSp.get()->getPeptideSet(),
233 p_keepGroup);
234
235 itGroup++;
236 while(itGroup != new_group_list.end())
237 {
238 qDebug()
239 << "GrpExperiment::addSubGroupSp p_keepGroup->addGroup(*itGroup) "
240 << itGroup->get();
241 p_keepGroup->addGroup(itGroup->get());
242 grp_map_peptide_to_group.set((*itGroup)->getGrpPeptideSet(),
243 p_keepGroup);
244
245 // m_grpGroupSpList.remove_if([itGroup](GrpGroupSp & groupSp) {
246 // return (itGroup->get() == groupSp.get()) ;
247 //});
248 itGroup++;
249 }
250 }
251
252 qDebug() << "GrpExperiment::addSubGroupSp end";
253}
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:39

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 65 of file grpexperiment.cpp.

66{
67 std::vector<GrpGroupSpConst> grp_list;
68 for(GrpGroupSp group : m_grpGroupSpList)
69 {
70 grp_list.push_back(group);
71 }
72 return grp_list;
73}
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 76 of file grpexperiment.cpp.

78{
79 GrpProtein grpProtein(accession, description);
80 auto insertedPair = m_mapProteins.insert(std::pair<QString, GrpProteinSp>(
81 accession, std::make_shared<GrpProtein>(grpProtein)));
82 if(insertedPair.second)
83 {
84 m_grpProteinList.push_back(insertedPair.first->second);
85 m_remainingGrpProteinList.push_back(insertedPair.first->second.get());
86 }
87 return (insertedPair.first->second);
88}
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 279 of file grpexperiment.cpp.

280{
281 std::vector<GrpProteinSpConst> grouped_protein_list;
283 {
284 throw PappsoException(
285 QObject::tr("unable to get grouped protein list before grouping"));
286 }
287 for(auto &&protein_sp : m_grpProteinList)
288 {
289 if(protein_sp.get()->getGroupNumber() > 0)
290 {
291 grouped_protein_list.push_back(protein_sp);
292 }
293 }
294 return grouped_protein_list;
295}

References m_grpProteinList, and m_isGroupingStarted.

◆ numbering()

void GrpExperiment::numbering ( )
private

Definition at line 256 of file grpexperiment.cpp.

257{
258 qDebug() << "GrpExperiment::numbering begin";
259 if(mp_monitor != nullptr)
261 for(auto &&group_sp : m_grpGroupSpList)
262 {
263 group_sp.get()->numbering();
264 }
265 m_grpGroupSpList.sort([](GrpGroupSp &first, GrpGroupSp &second) {
266 return ((*first.get()) < (*second.get()));
267 });
268 unsigned int i = 1;
269 for(auto &&group_sp : m_grpGroupSpList)
270 {
271 group_sp.get()->setGroupNumber(i);
272 i++;
273 }
274
275 qDebug() << "GrpExperiment::numbering end";
276}
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 298 of file grpexperiment.cpp.

299{
300 qDebug() << "GrpExperiment::removeNonInformativeSubGroups begin";
301 if(mp_monitor != nullptr)
303 m_grpGroupSpList.size());
304
305 std::list<GrpGroupSp> old_grp_group_sp_list(m_grpGroupSpList);
306 m_grpGroupSpList.clear();
307 auto it_group = old_grp_group_sp_list.begin();
308 while(it_group != old_grp_group_sp_list.end())
309 {
310 if(mp_monitor != nullptr)
312 if(it_group->get()->removeNonInformativeSubGroups())
313 {
314 // need to regroup it
315 GrpGroupSp old_group_sp = *it_group;
316 GrpMapPeptideToGroup grp_map_peptide_to_group;
317
318 std::list<GrpSubGroupSp> dispatch_sub_group_set =
319 old_group_sp.get()->getSubGroupSpList();
320 for(GrpSubGroupSp &grp_subgroup : dispatch_sub_group_set)
321 {
322 addSubGroupSp(grp_map_peptide_to_group, grp_subgroup);
323 }
324 grp_map_peptide_to_group.clear(m_grpGroupSpList);
325 }
326 else
327 {
328 qDebug() << "GrpExperiment::removeNonInformativeSubGroups no "
329 "removeNonInformativeSubGroups";
330 m_grpGroupSpList.push_back(*it_group);
331 }
332 it_group++;
333 }
334 if(mp_monitor != nullptr)
336 m_grpGroupSpList.size());
337
338 qDebug() << "GrpExperiment::removeNonInformativeSubGroups end";
339}
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 91 of file grpexperiment.cpp.

94{
95 proteinSp.get()->countPlus();
96 GrpPeptideSp sp_grppeptide =
97 std::make_shared<GrpPeptide>(GrpPeptide(sequence, mass));
98
99 auto insertedPair = m_mapPeptides.insert(
100 std::pair<QString, std::map<unsigned long, GrpPeptideSp>>(
101 sp_grppeptide.get()->m_sequence,
102 std::map<unsigned long, GrpPeptideSp>()));
103 auto secondInsertedPair =
104 insertedPair.first->second.insert(std::pair<unsigned long, GrpPeptideSp>(
105 (unsigned long)(mass * 100), sp_grppeptide));
106 if(secondInsertedPair.second)
107 {
108 m_grpPeptideList.push_back(secondInsertedPair.first->second);
109 }
110 proteinSp.get()->push_back(secondInsertedPair.first->second.get());
111 return (secondInsertedPair.first->second);
112}
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 44 of file grpexperiment.cpp.

References m_isRemoveNonInformativeSubgroups.

◆ startGrouping()

void GrpExperiment::startGrouping ( )

Definition at line 115 of file grpexperiment.cpp.

116{
117 qDebug() << "GrpExperiment::startGrouping begin";
118 if(mp_monitor != nullptr)
120 m_grpPeptideList.size());
121 m_isGroupingStarted = true;
122 m_mapPeptides.clear();
123 m_mapProteins.clear();
124 qDebug() << "GrpExperiment::startGrouping sort protein list "
125 "m_remainingGrpProteinList.size() "
127 // m_remainingGrpProteinList.sort();
128 // m_remainingGrpProteinList.unique();
129
131 {
132 // TODO clean protein list to remove contaminant peptides before grouping
133 }
134
135
136 GrpMapPeptideToGroup grp_map_peptide_to_group;
137 qDebug() << "GrpExperiment::startGrouping grouping begin";
138 for(auto p_grpProtein : m_remainingGrpProteinList)
139 {
140 p_grpProtein->strip();
141 if(p_grpProtein->m_count == 0)
142 {
143 // no peptides : do not group this protein
144 }
145 else
146 {
147 GrpSubGroupSp grpSubGroupSp =
148 GrpSubGroup(p_grpProtein).makeGrpSubGroupSp();
149
150 if(mp_monitor != nullptr)
152 this->addSubGroupSp(grp_map_peptide_to_group, grpSubGroupSp);
153 }
154 }
155 grp_map_peptide_to_group.clear(m_grpGroupSpList);
156 qDebug() << "GrpExperiment::startGrouping grouping end";
157
158 qDebug() << "GrpExperiment::startGrouping grouping m_grpGroupSpList.size() "
159 << m_grpGroupSpList.size();
160
162 {
164 }
165
166 // post grouping protein group removal
167 // remove any group containing contaminants
168 m_grpGroupSpList.remove_if([this](GrpGroupSp &groupSp) {
169 return (
170 groupSp.get()->containsAny(this->m_grpPostGroupingProteinListRemoval));
171 });
172
173
174 numbering();
175 if(mp_monitor != nullptr)
177 // GrpGroup(this, *m_remainingGrpProteinList.begin());
178 qDebug() << "GrpExperiment::startGrouping end";
179}
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: