31 #include "../pappsoexception.h"
64 std::vector<GrpGroupSpConst>
67 std::vector<GrpGroupSpConst> grp_list;
70 grp_list.push_back(group);
77 const QString &description)
80 auto insertedPair =
m_mapProteins.insert(std::pair<QString, GrpProteinSp>(
81 accession, std::make_shared<GrpProtein>(grpProtein)));
82 if(insertedPair.second)
87 return (insertedPair.first->second);
92 const QString &sequence,
95 proteinSp.get()->countPlus();
97 std::make_shared<GrpPeptide>(
GrpPeptide(sequence, mass));
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)
110 proteinSp.get()->push_back(secondInsertedPair.first->second.get());
111 return (secondInsertedPair.first->second);
117 qDebug() <<
"GrpExperiment::startGrouping begin";
124 qDebug() <<
"GrpExperiment::startGrouping sort protein list "
125 "m_remainingGrpProteinList.size() "
137 qDebug() <<
"GrpExperiment::startGrouping grouping begin";
140 p_grpProtein->strip();
141 if(p_grpProtein->m_count == 0)
152 this->
addSubGroupSp(grp_map_peptide_to_group, grpSubGroupSp);
156 qDebug() <<
"GrpExperiment::startGrouping grouping end";
158 qDebug() <<
"GrpExperiment::startGrouping grouping m_grpGroupSpList.size() "
170 groupSp.get()->containsAny(this->m_grpPostGroupingProteinListRemoval));
178 qDebug() <<
"GrpExperiment::startGrouping end";
193 return testGroupSp.get()->containsAny(_peptide_set);
204 qDebug() <<
"GrpExperiment::addSubGroupSp begin "
205 << grpSubGroupSp.get()->getFirstAccession();
207 std::list<GrpGroupSp> new_group_list;
208 grp_map_peptide_to_group.
getGroupList(grpSubGroupSp.get()->getPeptideSet(),
211 if(new_group_list.size() == 0)
213 qDebug() <<
"GrpExperiment::addSubGroupSp create a new group";
218 grp_map_peptide_to_group.
set(grpSubGroupSp.get()->getPeptideSet(),
223 qDebug() <<
"GrpExperiment::addSubGroupSp fusion groupList.size() "
224 << new_group_list.size();
226 auto itGroup = new_group_list.begin();
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(),
236 while(itGroup != new_group_list.end())
239 <<
"GrpExperiment::addSubGroupSp p_keepGroup->addGroup(*itGroup) "
241 p_keepGroup->addGroup(itGroup->get());
242 grp_map_peptide_to_group.
set((*itGroup)->getGrpPeptideSet(),
252 qDebug() <<
"GrpExperiment::addSubGroupSp end";
258 qDebug() <<
"GrpExperiment::numbering begin";
263 group_sp.get()->numbering();
266 return ((*first.get()) < (*second.get()));
271 group_sp.get()->setGroupNumber(i);
275 qDebug() <<
"GrpExperiment::numbering end";
278 std::vector<GrpProteinSpConst>
281 std::vector<GrpProteinSpConst> grouped_protein_list;
285 QObject::tr(
"unable to get grouped protein list before grouping"));
289 if(protein_sp.get()->getGroupNumber() > 0)
291 grouped_protein_list.push_back(protein_sp);
294 return grouped_protein_list;
300 qDebug() <<
"GrpExperiment::removeNonInformativeSubGroups begin";
307 auto it_group = old_grp_group_sp_list.begin();
308 while(it_group != old_grp_group_sp_list.end())
312 if(it_group->get()->removeNonInformativeSubGroups())
318 std::list<GrpSubGroupSp> dispatch_sub_group_set =
319 old_group_sp.get()->getSubGroupSpList();
328 qDebug() <<
"GrpExperiment::removeNonInformativeSubGroups no "
329 "removeNonInformativeSubGroups";
338 qDebug() <<
"GrpExperiment::removeNonInformativeSubGroups end";
void addSubGroupSp(GrpMapPeptideToGroup &grp_map_peptide_to_group, GrpSubGroupSp &grpSubGroupSp) const
std::list< GrpGroupSp > m_grpGroupSpList
GrpPeptideSp & setGrpPeptide(const GrpProteinSp &proteinSp, const QString &sequence, pappso_double mass)
GrpGroupingMonitorInterface * mp_monitor
void removeNonInformativeSubGroups()
GrpProteinSp & getGrpProteinSp(const QString &acc, const QString &description)
void addPostGroupingGrpProteinSpRemoval(GrpProteinSp sp_protein)
protein to remove with its entire group after grouping is completed typically : to use with protein c...
bool m_isRemoveNonInformativeSubgroups
std::list< GrpPeptideSp > m_grpPeptideList
std::vector< GrpGroupSpConst > getGrpGroupSpList() const
void setRemoveNonInformativeSubgroups(bool ok)
GrpPeptideSet m_grpPreGroupingProteinListRemoval
GrpExperiment(GrpGroupingMonitorInterface *p_monitor)
void addPreGroupingGrpProteinSpRemoval(GrpProteinSp sp_protein)
protein peptides to remove before grouping typically : remove protein contaminants in special metapro...
std::map< QString, std::map< unsigned long, GrpPeptideSp > > m_mapPeptides
std::list< GrpProteinSp > m_grpProteinList
GrpPeptideSet m_grpPostGroupingProteinListRemoval
std::list< GrpProtein * > m_remainingGrpProteinList
std::vector< GrpProteinSpConst > getGrpProteinSpList() const
std::map< QString, GrpProteinSp > m_mapProteins
GrpGroupSp makeGrpGroupSp()
virtual void removingNonInformativeSubGroupsInGroup()=0
virtual void startNumberingAllGroups(std::size_t total_number_group)=0
virtual void startRemovingNonInformativeSubGroupsInAllGroups(std::size_t total_number_group)=0
virtual void stopGrouping()=0
virtual void startGrouping(std::size_t total_number_protein, std::size_t total_number_peptide)=0
virtual void groupingProtein()=0
virtual void stopRemovingNonInformativeSubGroupsInAllGroups(std::size_t total_number_group)=0
void clear(std::list< GrpGroupSp > &grp_group_list)
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
unsigned int size() const
void addAll(const GrpPeptideSet &peptideSet)
GrpSubGroupSp makeGrpSubGroupSp()
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< GrpProtein > GrpProteinSp
std::shared_ptr< GrpSubGroup > GrpSubGroupSp
std::shared_ptr< GrpPeptide > GrpPeptideSp
double pappso_double
A type definition for doubles.
std::shared_ptr< GrpGroup > GrpGroupSp
bool operator()(const GrpGroupSp &testGroupSp)
GrpPeptideSet _peptide_set
ContainsAny(const GrpPeptideSet &peptide_set)