diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 4b3c3e3b7fec64f60a5c26a96e8c74261aa7b4f5..36ed21580d10cdc21d0da720c8fe8f2757c27f22 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -128,6 +128,9 @@ unsigned int IdentificationGroup::countProteinMatch(ValidationState state) const
void IdentificationGroup::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
qDebug() << "IdentificationGroup::updateAutomaticFilters begin" ;
+ for (IdentificationDataSource * p_identification_source_list:_id_source_list) {
+ p_identification_source_list->getPeptideEvidenceStore().updateAutomaticFilters(automatic_filter_parameters);
+ }
for (auto & p_protein_match : _protein_match_list) {
p_protein_match->updateAutomaticFilters(automatic_filter_parameters);
}
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 4f600217148e06263f02c09b9daba427c1651eea..c4a57c3a850f88d1108ac782f19171b18b67169b 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -33,6 +33,12 @@ PeptideMatch::PeptideMatch(const PeptideMatch & other) {
_p_peptide_evidence = other._p_peptide_evidence;
}
+bool PeptideMatch::operator==(const PeptideMatch & other) const {
+ if ((_p_peptide_evidence == other._p_peptide_evidence) && (_start == other._start)) {
+ return true;
+ }
+ return false;
+}
void PeptideMatch::setPeptideEvidenceSp(PeptideEvidenceSp sp_peptide_evidence) {
_p_peptide_evidence = sp_peptide_evidence.get();
}
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 1794efc211c2adf75b0789f1b07a91a4a9ad678b..4f18084ca68850346541f24114d6d41dc3622882 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -31,6 +31,8 @@ class PeptideMatch
public :
PeptideMatch();
PeptideMatch(const PeptideMatch & other);
+
+ bool operator==(const PeptideMatch & other) const;
/** @brief set start position of this peptide inside the protein sequence
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 37795b3f75c9c79644ff626689f9ea716533f076..0d2680d86f54317bddfba4ab00c1e90503f82f1e 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -51,13 +51,6 @@ ValidationState ProteinMatch::getValidationState() const {
}
return ValidationState::notValid;
}
-bool ProteinMatch::contains(PeptideMatch * peptide_match) const {
- if (peptide_match == nullptr) return false;
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match == peptide_match) return true;
- }
- return false;
-}
void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
//qDebug() <<"ProteinMatch::updateAutomaticFilters begin " ;
@@ -66,17 +59,13 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
bool cross_sample = automatic_filter_parameters.getFilterCrossSamplePeptideNumber();
if (cross_sample) {
- for (auto & p_peptide_match : _peptide_match_list) {
- p_peptide_match->updateAutomaticFilters(automatic_filter_parameters);
- }
number_of_valid_peptides= countSequenceLi(ValidationState::validAndChecked,nullptr);
}
else {
std::set<const MsRun *> msrun_set;
for (auto & p_peptide_match : _peptide_match_list) {
- p_peptide_match->updateAutomaticFilters(automatic_filter_parameters);
- if (p_peptide_match->isValidAndChecked()) {
- msrun_set.insert(p_peptide_match->getMsRunP());
+ if (p_peptide_match.getPeptideEvidence()->isValidAndChecked()) {
+ msrun_set.insert(p_peptide_match.getPeptideEvidence()->getMsRunP());
}
}
for (const MsRun * p_msrun : msrun_set) {
@@ -137,16 +126,17 @@ bool ProteinMatch::isGrouped() const {
void ProteinMatch::setChecked(bool arg1) {
_checked = arg1;
}
-void ProteinMatch::addPeptideMatchSp(PeptideMatchSp peptide_match) {
- _peptide_match_list.push_back(peptide_match.get());
+
+void ProteinMatch::addPeptideMatch(const PeptideMatch & peptide_match) {
+ _peptide_match_list.push_back(peptide_match);
}
-std::vector<PeptideMatch *> & ProteinMatch::getPeptideMatchList() {
+std::vector<PeptideMatch> & ProteinMatch::getPeptideMatchList() {
return _peptide_match_list;
}
-const std::vector<PeptideMatch *> & ProteinMatch::getPeptideMatchList() const {
+const std::vector<PeptideMatch> & ProteinMatch::getPeptideMatchList() const {
return _peptide_match_list;
}
@@ -156,9 +146,9 @@ void ProteinMatch::setGroupingExperiment(GroupingExperiment * p_grp_experiment)
_sp_grp_protein = p_grp_experiment->getGrpProteinSp(this);
for (auto & p_peptide_match : _peptide_match_list) {
- p_peptide_match->setGrpPeptideSp(nullptr);
- if (p_peptide_match->isValidAndChecked()) {
- p_peptide_match->setGrpPeptideSp(p_grp_experiment->setGrpPeptide(_sp_grp_protein, p_peptide_match));
+ p_peptide_match.getPeptideEvidence()->setGrpPeptideSp(nullptr);
+ if (p_peptide_match.getPeptideEvidence()->isValidAndChecked()) {
+ p_peptide_match.getPeptideEvidence()->setGrpPeptideSp(p_grp_experiment->setGrpPeptide(_sp_grp_protein, p_peptide_match.getPeptideEvidence()));
}
}
@@ -177,24 +167,24 @@ const pappso::GrpProteinSp & ProteinMatch::getGrpProteinSp() const {
void ProteinMatch::countPeptideMass(std::vector<pappso::GrpPeptide *> & count_peptide_mass, ValidationState state) const {
for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->getValidationState() >= state) {
- count_peptide_mass.push_back(p_peptide_match->getGrpPeptideSp().get());
+ if (p_peptide_match.getPeptideEvidence()->getValidationState() >= state) {
+ count_peptide_mass.push_back(p_peptide_match.getPeptideEvidence()->getGrpPeptideSp().get());
}
}
}
void ProteinMatch::countPeptideMassSample(std::vector<size_t> & count_peptide_mass_sample, ValidationState state) const {
for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->getValidationState() >= state) {
- count_peptide_mass_sample.push_back(p_peptide_match->getHashPeptideMassSample());
+ if (p_peptide_match.getPeptideEvidence()->getValidationState() >= state) {
+ count_peptide_mass_sample.push_back(p_peptide_match.getPeptideEvidence()->getHashPeptideMassSample());
}
}
}
-std::vector<PeptideMatch *> ProteinMatch::getPeptideMatchList(ValidationState state) const {
- std::vector<PeptideMatch *> peptide_match_list;
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->getValidationState() >= state) {
- peptide_match_list.push_back(p_peptide_match);
+std::vector<PeptideMatch> ProteinMatch::getPeptideMatchList(ValidationState state) const {
+ std::vector<PeptideMatch> peptide_match_list;
+ for (auto & peptide_match : _peptide_match_list) {
+ if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
+ peptide_match_list.push_back(peptide_match);
}
}
return peptide_match_list;
@@ -202,14 +192,15 @@ std::vector<PeptideMatch *> ProteinMatch::getPeptideMatchList(ValidationState st
unsigned int ProteinMatch::countSampleScan(ValidationState state, const MsRun * p_msrun_id) const {
std::vector<std::size_t> count_sample_scan;
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->getValidationState() >= state) {
+ for (auto & peptide_match : _peptide_match_list) {
+ const PeptideEvidence * p_peptide_evidence = peptide_match.getPeptideEvidence();
+ if (p_peptide_evidence->getValidationState() >= state) {
if(p_msrun_id == nullptr) {
- count_sample_scan.push_back(p_peptide_match->getHashSampleScan());
+ count_sample_scan.push_back(p_peptide_evidence->getHashSampleScan());
}
else {
- if (p_peptide_match->getMsRunP() == p_msrun_id) {
- count_sample_scan.push_back(p_peptide_match->getHashSampleScan());
+ if (p_peptide_evidence->getMsRunP() == p_msrun_id) {
+ count_sample_scan.push_back(p_peptide_evidence->getHashSampleScan());
}
}
}
@@ -220,8 +211,8 @@ unsigned int ProteinMatch::countSampleScan(ValidationState state, const MsRun *
}
unsigned int ProteinMatch::countPeptideMatch(ValidationState state) const {
- return std::count_if (_peptide_match_list.begin(), _peptide_match_list.end(), [state](const PeptideMatch * p_peptide_match) {
- if (p_peptide_match->getValidationState() >= state) {
+ return std::count_if (_peptide_match_list.begin(), _peptide_match_list.end(), [state](const PeptideMatch & peptide_match) {
+ if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
return true;
}
else {
@@ -232,17 +223,17 @@ unsigned int ProteinMatch::countPeptideMatch(ValidationState state) const {
size_t ProteinMatch::countSequenceLi(ValidationState state, const MsRun * p_msrun_id) const {
std::set<QString> sequence_list;
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->getValidationState() >= state) {
+ for (auto & peptide_match : _peptide_match_list) {
+ if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
if(p_msrun_id != nullptr) {
//within sample
- if (p_peptide_match->getMsRunP() == p_msrun_id) {
- sequence_list.insert(p_peptide_match->getPeptideXtpSp().get()->getSequenceLi());
+ if (peptide_match.getPeptideEvidence()->getMsRunP() == p_msrun_id) {
+ sequence_list.insert(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequenceLi());
}
}
else {
//overall samples
- sequence_list.insert(p_peptide_match->getPeptideXtpSp().get()->getSequenceLi());
+ sequence_list.insert(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequenceLi());
}
}
}
@@ -252,9 +243,9 @@ size_t ProteinMatch::countSequenceLi(ValidationState state, const MsRun * p_msru
unsigned int ProteinMatch::countDistinctMsSamples(ValidationState state) const {
std::set<QString> sequence_list;
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->getValidationState() >= state) {
- sequence_list.insert(QString("%1").arg(p_peptide_match->getMsRunP()->getXmlId()));
+ for (auto & peptide_match : _peptide_match_list) {
+ if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
+ sequence_list.insert(QString("%1").arg(peptide_match.getPeptideEvidence()->getMsRunP()->getXmlId()));
}
}
return sequence_list.size();
@@ -262,17 +253,17 @@ unsigned int ProteinMatch::countDistinctMsSamples(ValidationState state) const {
unsigned int ProteinMatch::countPeptideMassCharge(ValidationState state, const MsRun * sp_msrun_id) const {
std::set<QString> sequence_list;
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->getValidationState() >= state) {
+ for (auto & peptide_match : _peptide_match_list) {
+ if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
if(sp_msrun_id != nullptr) {
//within sample
- if (p_peptide_match->getMsRunP() == sp_msrun_id) {
- sequence_list.insert(QString("%1-%2-%3").arg(p_peptide_match->getPeptideXtpSp().get()->getNativePeptideP()->getSequenceLi()).arg(p_peptide_match->getPeptideXtpSp().get()->getNativePeptideP()->getMass()).arg(p_peptide_match->getCharge()));
+ if (peptide_match.getPeptideEvidence()->getMsRunP() == sp_msrun_id) {
+ sequence_list.insert(QString("%1-%2-%3").arg(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getNativePeptideP()->getSequenceLi()).arg(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getNativePeptideP()->getMass()).arg(peptide_match.getPeptideEvidence()->getCharge()));
}
}
else {
//overall samples
- sequence_list.insert(QString("%1-%2-%3").arg(p_peptide_match->getPeptideXtpSp().get()->getNativePeptideP()->getSequenceLi()).arg(p_peptide_match->getPeptideXtpSp().get()->getNativePeptideP()->getMass()).arg(p_peptide_match->getCharge()));
+ sequence_list.insert(QString("%1-%2-%3").arg(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getNativePeptideP()->getSequenceLi()).arg(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getNativePeptideP()->getMass()).arg(peptide_match.getPeptideEvidence()->getCharge()));
}
}
}
@@ -285,13 +276,13 @@ pappso::pappso_double ProteinMatch::getEvalue(const MsRun * sp_msrun_id) const {
pappso::pappso_double ProteinMatch::getLogEvalue(const MsRun * sp_msrun_id) const {
std::map<QString, pappso::pappso_double> map_sequence_evalue;
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->isValidAndChecked()) {
- QString sequence(p_peptide_match->getPeptideXtpSp().get()->getSequence());
- pappso::pappso_double evalue = p_peptide_match->getEvalue();
+ for (auto & peptide_match : _peptide_match_list) {
+ if (peptide_match.getPeptideEvidence()->isValidAndChecked()) {
+ QString sequence(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequence());
+ pappso::pappso_double evalue = peptide_match.getPeptideEvidence()->getEvalue();
if(sp_msrun_id != nullptr) {
//within sample
- if (p_peptide_match->getMsRunP() == sp_msrun_id) {
+ if (peptide_match.getPeptideEvidence()->getMsRunP() == sp_msrun_id) {
auto ret = map_sequence_evalue.insert(std::pair<QString, pappso::pappso_double>(sequence, evalue));
if (ret.second == false) {
if (ret.first->second > evalue) {//get best evalue for sequence
@@ -341,27 +332,29 @@ pappso::pappso_double ProteinMatch::getEmPAI(const MsRun * sp_msrun_id) const {
return value;
}
-const QString ProteinMatch::getHtmlSequence(PeptideMatch * peptide_match_to_locate) const
+const QString ProteinMatch::getHtmlSequence(PeptideEvidence * peptide_evidence_to_locate) const
{
size_t prot_size = _protein_sp.get()->size();
//qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << " " << _protein_sp.get()-//>getSequence();
if (prot_size == 0) return 0;
bool cover_bool[prot_size] = {false};
bool highlight_bool[prot_size] = {false};
- if (this->contains(peptide_match_to_locate)) {
- size_t size = peptide_match_to_locate->getPeptideXtpSp().get()->size();
- size_t offset = peptide_match_to_locate->getStart();
- if (offset >= 0) {
- for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
- highlight_bool[offset] = true;
+ for (auto & peptide_match : _peptide_match_list) {
+ if (peptide_match.getPeptideEvidence() == peptide_evidence_to_locate) {
+ size_t size = peptide_evidence_to_locate->getPeptideXtpSp().get()->size();
+ size_t offset = peptide_match.getStart();
+ if (offset >= 0) {
+ for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
+ highlight_bool[offset] = true;
+ }
}
}
}
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->isValidAndChecked()) {
- size_t size = p_peptide_match->getPeptideXtpSp().get()->size();
- size_t offset = p_peptide_match->getStart();
+ for (auto & peptide_match : _peptide_match_list) {
+ if (peptide_match.getPeptideEvidence()->isValidAndChecked()) {
+ size_t size = peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->size();
+ size_t offset = peptide_match.getPeptideEvidence()->getStart();
if (offset >= 0) {
for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
cover_bool[offset] = true;
@@ -417,10 +410,10 @@ pappso::pappso_double ProteinMatch::getCoverage() const {
//qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << " " << _protein_sp.get()-//>getSequence();
if (prot_size == 0) return 0;
bool cover_bool[prot_size] = {false};
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->isValidAndChecked()) {
- size_t size = p_peptide_match->getPeptideXtpSp().get()->size();
- size_t offset = p_peptide_match->getStart();
+ for (auto & peptide_match : _peptide_match_list) {
+ if (peptide_match.getPeptideEvidence()->isValidAndChecked()) {
+ size_t size = peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->size();
+ size_t offset = peptide_match.getStart();
if (offset >= 0) {
for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
cover_bool[offset] = true;
@@ -452,14 +445,14 @@ void ProteinMatch::setGroupInstance(GroupStore & group_store) {
void ProteinMatch::collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->getValidationState() >= state) {
- pappso::pappso_double diff = p_peptide_match->getDeltaMass();
+ for (auto & peptide_match : _peptide_match_list) {
+ if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
+ pappso::pappso_double diff = peptide_match.getPeptideEvidence()->getDeltaMass();
if (unit == pappso::PrecisionUnit::ppm) {
while (diff < -0.5) {
diff = diff + pappso::DIFFC12C13;
}
- diff = (diff / p_peptide_match->getPeptideXtpSp().get()->getMz(1)) * pappso::ONEMILLION;
+ diff = (diff / peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getMz(1)) * pappso::ONEMILLION;
}
delta_list.push_back(diff);
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 4652c3edcbd02a97c07d2d8228b031a4d4ac33b8..e397ea51ada4e7317a505e8c3c8af765ead68686 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -61,7 +61,7 @@ public:
/** @brief get coverage sequence (html representation)
* @param peptide_match_to_locate pointer to optional peptide match to locate on protein sequence
**/
- const QString getHtmlSequence(PeptideMatch * peptide_match_to_locate = nullptr) const;
+ const QString getHtmlSequence(PeptideEvidence * peptide_evidence_to_locate = nullptr) const;
/** @brief compute Protein Abundance Index (PAI) within sample
* PAI computation (Rappsilber et al. 2002)
@@ -75,12 +75,12 @@ public:
void setProteinXtpSp(ProteinXtpSp protein_sp);
void addPeptideMatch(const PeptideMatch & peptide_match);
- std::vector<PeptideMatch *> & getPeptideMatchList();
- const std::vector<PeptideMatch *> & getPeptideMatchList() const;
+ std::vector<PeptideMatch> & getPeptideMatchList();
+ const std::vector<PeptideMatch> & getPeptideMatchList() const;
/** @brief get peptide match sublist with required validation state
* */
- std::vector<PeptideMatch *> getPeptideMatchList(ValidationState state) const;
+ std::vector<PeptideMatch> getPeptideMatchList(ValidationState state) const;
void setChecked(bool arg1);
bool isChecked() const;
@@ -113,10 +113,6 @@ public:
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
- /** @brief tells if this protein match contains this peptides
- */
- bool contains(PeptideMatch * peptide_match) const;
-
void collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
/** @brief count distinct sequence taking into account equivalence between Leucine and Isoleucine
@@ -152,7 +148,7 @@ private:
pappso::GrpProteinSp _sp_grp_protein;
GroupingGroupSp _sp_group;
- std::vector<PeptideMatch *> _peptide_match_list;
+ std::vector<PeptideMatch> _peptide_match_list;
ProteinXtpSp _protein_sp = nullptr;
/** @brief manually checked by user (true by default)
*/
diff --git a/src/grouping/groupingexperiment.h b/src/grouping/groupingexperiment.h
index bd974b4a7f3aed15296d849d2d401feea33af763..0910407c3bcce9cd02cfcfc0b030911b9fd22f6e 100644
--- a/src/grouping/groupingexperiment.h
+++ b/src/grouping/groupingexperiment.h
@@ -30,7 +30,7 @@
#define GROUPINGEXPERIMENT_H
class ProteinMatch;
-class PeptideMatch;
+class PeptideEvidence;
class GroupingExperiment
{
@@ -41,7 +41,7 @@ public:
static GroupingExperiment * newInstance(const GroupingType & grouping_type, WorkMonitorInterface * p_work_monitor);
virtual pappso::GrpProteinSp & getGrpProteinSp(ProteinMatch* p_protein_match) = 0;
- virtual pappso::GrpPeptideSp & setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) = 0;
+ virtual pappso::GrpPeptideSp & setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideEvidence * p_peptide_evidence) = 0;
virtual void addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) = 0;
virtual void startGrouping()= 0;
diff --git a/src/grouping/groupinggroup.cpp b/src/grouping/groupinggroup.cpp
index 806902120b70e40534d152ec2b511de9b6dcd49a..e3d85a0950dc72fbb9a6e17b64dea39c70570701 100644
--- a/src/grouping/groupinggroup.cpp
+++ b/src/grouping/groupinggroup.cpp
@@ -38,8 +38,8 @@ GroupingGroup::~GroupingGroup()
}
-const std::vector<std::pair<unsigned int, const PeptideMatch *>> & GroupingGroup::getPairSgNumberPeptideMatchList() const {
- return _pair_sg_number_peptide_match_list;
+const std::vector<std::pair<unsigned int, const PeptideEvidence *>> & GroupingGroup::getPairSgNumberPeptideEvidenceList() const {
+ return _pair_sg_number_peptide_evidence_list;
}
unsigned int GroupingGroup::getGroupNumber() const {
return _group_number;
@@ -50,19 +50,19 @@ unsigned int GroupingGroup::getNumberOfSubgroups() const {
const std::vector<const ProteinMatch *> & GroupingGroup::getProteinMatchList() const {
return _protein_match_list;
}
-std::vector<const PeptideMatch *> GroupingGroup::getPeptideMatchList() const {
- std::vector<const PeptideMatch *> peptide_match_list;
- for (auto && pair_peptide_match :_pair_sg_number_peptide_match_list) {
+std::vector<const PeptideEvidence *> GroupingGroup::getPeptideEvidenceList() const {
+ std::vector<const PeptideEvidence *> peptide_match_list;
+ for (auto && pair_peptide_match :_pair_sg_number_peptide_evidence_list) {
peptide_match_list.push_back(pair_peptide_match.second);
}
return peptide_match_list;
}
-const QStringList GroupingGroup::getSubgroupIdList(const PeptideMatch * p_peptide_match) const {
+const QStringList GroupingGroup::getSubgroupIdList(const PeptideEvidence * p_peptide_match) const {
std::set<unsigned int> subgroup_list;
pappso::GrpPeptide * p_grp_peptide = p_peptide_match->getGrpPeptideSp().get();
if (p_grp_peptide != nullptr) {
- for (auto && pair_peptide_match :_pair_sg_number_peptide_match_list) {
+ for (auto && pair_peptide_match :_pair_sg_number_peptide_evidence_list) {
if(pair_peptide_match.second->getGrpPeptideSp().get() == p_grp_peptide) {
subgroup_list.insert(pair_peptide_match.first);
}
@@ -78,11 +78,11 @@ const QStringList GroupingGroup::getSubgroupIdList(const PeptideMatch * p_peptid
}
-unsigned int GroupingGroup::countSubgroupPresence(const PeptideMatch * p_peptide_match) const {
+unsigned int GroupingGroup::countSubgroupPresence(const PeptideEvidence * p_peptide_evidence) const {
std::set<unsigned int> subgroup_list;
- pappso::GrpPeptide * p_grp_peptide = p_peptide_match->getGrpPeptideSp().get();
+ pappso::GrpPeptide * p_grp_peptide = p_peptide_evidence->getGrpPeptideSp().get();
if (p_grp_peptide != nullptr) {
- for (auto && pair_peptide_match :_pair_sg_number_peptide_match_list) {
+ for (auto && pair_peptide_match :_pair_sg_number_peptide_evidence_list) {
if(pair_peptide_match.second->getGrpPeptideSp().get() == p_grp_peptide) {
subgroup_list.insert(pair_peptide_match.first);
}
@@ -97,20 +97,20 @@ std::size_t GroupingGroup::countSpecificSampleScan(const ProteinMatch * p_protei
}
std::set<size_t> spectrum_list_in;
for (auto && p_peptide_match :p_protein_match->getPeptideMatchList()) {
- if (p_peptide_match->getValidationState() >= state) {
+ if (p_peptide_match.getPeptideEvidence()->getValidationState() >= state) {
if(p_msrun_id == nullptr) {
- spectrum_list_in.insert(p_peptide_match->getHashSampleScan());
+ spectrum_list_in.insert(p_peptide_match.getPeptideEvidence()->getHashSampleScan());
}
else {
- if (p_peptide_match->getMsRunP() == p_msrun_id) {
- spectrum_list_in.insert(p_peptide_match->getHashSampleScan());
+ if (p_peptide_match.getPeptideEvidence()->getMsRunP() == p_msrun_id) {
+ spectrum_list_in.insert(p_peptide_match.getPeptideEvidence()->getHashSampleScan());
}
}
}
}
std::set<size_t> spectrum_list_out;
unsigned int sg_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
- for (auto && pair_peptide_match :_pair_sg_number_peptide_match_list) {
+ for (auto && pair_peptide_match :_pair_sg_number_peptide_evidence_list) {
if (pair_peptide_match.first != sg_number) {
spectrum_list_out.insert(pair_peptide_match.second->getHashSampleScan());
}
@@ -132,20 +132,20 @@ std::size_t GroupingGroup::countSpecificSequenceLi(const ProteinMatch * p_protei
}
std::set<QString> sequence_list_in;
for (auto && p_peptide_match :p_protein_match->getPeptideMatchList()) {
- if (p_peptide_match->getValidationState() >= state) {
+ if (p_peptide_match.getPeptideEvidence()->getValidationState() >= state) {
if(p_msrun_id == nullptr) {
- sequence_list_in.insert(p_peptide_match->getPeptideXtpSp().get()->getSequenceLi());
+ sequence_list_in.insert(p_peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequenceLi());
}
else {
- if (p_peptide_match->getMsRunP() == p_msrun_id) {
- sequence_list_in.insert(p_peptide_match->getPeptideXtpSp().get()->getSequenceLi());
+ if (p_peptide_match.getPeptideEvidence()->getMsRunP() == p_msrun_id) {
+ sequence_list_in.insert(p_peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequenceLi());
}
}
}
}
std::set<QString> sequence_list_out;
unsigned int sg_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
- for (auto && pair_peptide_match :_pair_sg_number_peptide_match_list) {
+ for (auto && pair_peptide_match :_pair_sg_number_peptide_evidence_list) {
if (pair_peptide_match.first != sg_number) {
sequence_list_out.insert(pair_peptide_match.second->getPeptideXtpSp().get()->getSequenceLi());
}
@@ -183,9 +183,9 @@ void GroupingGroup::add(const ProteinMatch * p_protein_match) {
_number_of_subgroup++;
unsigned int sg_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
- for (auto && p_peptide_match :p_protein_match->getPeptideMatchList()) {
- if (p_peptide_match->isValidAndChecked()) {
- _pair_sg_number_peptide_match_list.push_back(std::pair<unsigned int, const PeptideMatch * >(sg_number, p_peptide_match));
+ for (auto && peptide_match :p_protein_match->getPeptideMatchList()) {
+ if (peptide_match.getPeptideEvidence()->isValidAndChecked()) {
+ _pair_sg_number_peptide_evidence_list.push_back(std::pair<unsigned int, const PeptideEvidence * >(sg_number, peptide_match.getPeptideEvidence()));
}
}
}
diff --git a/src/grouping/groupinggroup.h b/src/grouping/groupinggroup.h
index d351b18785fd20b907acfe2f76d80dcb1e534e97..1789a683b2c2facdefb5c75049565e8757c024b0 100644
--- a/src/grouping/groupinggroup.h
+++ b/src/grouping/groupinggroup.h
@@ -31,7 +31,7 @@
#include "../core/msrun.h"
class ProteinMatch;
-class PeptideMatch;
+class PeptideEvidence;
class GroupingGroup;
typedef std::shared_ptr<GroupingGroup> GroupingGroupSp;
@@ -57,11 +57,11 @@ public:
/** @brief count number of subgroups in which this peptide is present
* */
- unsigned int countSubgroupPresence(const PeptideMatch * p_peptide_match) const;
+ unsigned int countSubgroupPresence(const PeptideEvidence * p_peptide_evidence) const;
/** @brief subgroup identifier list in which this peptide is present
* */
- const QStringList getSubgroupIdList(const PeptideMatch * p_peptide_match) const;
+ const QStringList getSubgroupIdList(const PeptideEvidence * p_peptide_evidence) const;
/** @brief give the protein group id of the representant of a subgroup
* */
@@ -72,18 +72,18 @@ public:
* */
const std::vector<const ProteinMatch *> & getProteinMatchList() const;
- /** @brief get the list of peptide match included in this group
+ /** @brief get the list of peptide evidence included in this group
* warning : it only contains the first protein representant in one subgroup
* use a double loop with getProteinMatchList to scan every peptide match
* */
- std::vector<const PeptideMatch *> getPeptideMatchList() const;
+ std::vector<const PeptideEvidence *> getPeptideEvidenceList() const;
- const std::vector<std::pair<unsigned int, const PeptideMatch *>> & getPairSgNumberPeptideMatchList() const;
+ const std::vector<std::pair<unsigned int, const PeptideEvidence *>> & getPairSgNumberPeptideEvidenceList() const;
private :
unsigned int _group_number=0;
unsigned int _number_of_subgroup=0;
- std::vector<std::pair<unsigned int, const PeptideMatch *>> _pair_sg_number_peptide_match_list;
+ std::vector<std::pair<unsigned int, const PeptideEvidence *>> _pair_sg_number_peptide_evidence_list;
std::vector<const ProteinMatch *> _protein_match_list;
};
diff --git a/src/grouping/groupingpeptidemass.cpp b/src/grouping/groupingpeptidemass.cpp
index a1b47b2ffd6679f9a6756a0eeaebf4d6dadc0ff2..108f89fb9ae1ab06f9994e370e9cdf897956c4e0 100644
--- a/src/grouping/groupingpeptidemass.cpp
+++ b/src/grouping/groupingpeptidemass.cpp
@@ -78,9 +78,9 @@ GroupingPeptideMass::~GroupingPeptideMass()
pappso::GrpProteinSp & GroupingPeptideMass::getGrpProteinSp(ProteinMatch* p_protein_match) {
return _p_grp_experiment->getGrpProteinSp(p_protein_match->getProteinXtpSp().get()->getAccession(),p_protein_match->getProteinXtpSp().get()->getDescription());
}
-pappso::GrpPeptideSp & GroupingPeptideMass::setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) {
+pappso::GrpPeptideSp & GroupingPeptideMass::setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideEvidence * p_peptide_evidence) {
- return _p_grp_experiment->setGrpPeptide(proteinSp,p_peptide_match->getPeptideXtpSp().get()->getSequence(), p_peptide_match->getPeptideXtpSp().get()->getGroupingMass());
+ return _p_grp_experiment->setGrpPeptide(proteinSp,p_peptide_evidence->getPeptideXtpSp().get()->getSequence(), p_peptide_evidence->getPeptideXtpSp().get()->getGroupingMass());
}
void GroupingPeptideMass::startGrouping() {
diff --git a/src/grouping/groupingpeptidemass.h b/src/grouping/groupingpeptidemass.h
index 5f64a54c9548dbbd4e67fca04f87a624f07f7008..a1d1d4e4136cab76cfba42cb8e1e99ea87899bea 100644
--- a/src/grouping/groupingpeptidemass.h
+++ b/src/grouping/groupingpeptidemass.h
@@ -35,7 +35,7 @@ public:
virtual ~GroupingPeptideMass();
virtual pappso::GrpProteinSp & getGrpProteinSp(ProteinMatch* p_protein_match) override;
- virtual pappso::GrpPeptideSp & setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) override;
+ virtual pappso::GrpPeptideSp & setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideEvidence * p_peptide_evidence) override;
virtual void addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) override;
virtual void startGrouping() override;
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index 2e0dbe225bd926ce170c04ab2ed5ae87dae27827..524c75f68c4ea245f108ce67560078e9903c5e22 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/src/grouping/ptm/ptmgroupingexperiment.cpp
@@ -123,9 +123,9 @@ void PtmGroupingExperiment::addProteinMatch(const ProteinMatch* p_protein_match)
for (unsigned int position : ptm_position_list) {
ptm_island_list.push_back(std::make_shared<PtmIsland>(p_protein_match, position));
}
- for (PeptideMatch * p_peptide_match: p_protein_match->getPeptideMatchList(_peptide_validation_state)) {
+ for (PeptideMatch & peptide_match: p_protein_match->getPeptideMatchList(_peptide_validation_state)) {
for (PtmIslandSp ptm_island_sp:ptm_island_list) {
- ptm_island_sp.get()->addPeptideMatch(p_peptide_match);
+ ptm_island_sp.get()->addPeptideMatch(peptide_match);
}
}
@@ -153,30 +153,30 @@ std::vector< PtmIslandSp > PtmGroupingExperiment::mergePeptideMatchPtmIslandList
}
-unsigned int PtmGroupingExperiment::countPeptideMatchPtm(const PeptideMatch* p_peptide_match)const {
+unsigned int PtmGroupingExperiment::countPeptideMatchPtm(const PeptideMatch & peptide_match)const {
unsigned int number=0;
for (const ModificationAndAa & modification: _modification_list) {
if (modification.aa_list.size() == 0) {
- number += p_peptide_match->getPeptideXtpSp().get()->getNumberOfModification(modification.modification);
+ number += peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getNumberOfModification(modification.modification);
}
else {
- number += p_peptide_match->getPeptideXtpSp().get()->countModificationOnAa(modification.modification, modification.aa_list);
+ number += peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->countModificationOnAa(modification.modification, modification.aa_list);
}
}
return number;
}
-std::vector<unsigned int> PtmGroupingExperiment::getPtmPositions(const PeptideMatch * p_peptide_match) const {
+std::vector<unsigned int> PtmGroupingExperiment::getPtmPositions(const PeptideMatch & peptide_match) const {
std::vector<unsigned int> position_list;
for (const ModificationAndAa & modification: _modification_list) {
if (modification.aa_list.size() == 0) {
- for (unsigned int position : p_peptide_match->getPeptideXtpSp().get()->getModificationPositionList(modification.modification)) {
+ for (unsigned int position : peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getModificationPositionList(modification.modification)) {
position_list.push_back(position);
}
}
else {
- for (unsigned int position : p_peptide_match->getPeptideXtpSp().get()->getModificationPositionList(modification.modification, modification.aa_list)) {
+ for (unsigned int position : peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getModificationPositionList(modification.modification, modification.aa_list)) {
position_list.push_back(position);
}
}
@@ -191,9 +191,9 @@ std::vector<unsigned int> PtmGroupingExperiment::getPtmPositions(const PeptideMa
std::vector<unsigned int> PtmGroupingExperiment::getPtmPositions(const ProteinMatch * protein_match) const {
std::vector<unsigned int> position_list;
- for (const PeptideMatch * p_peptide_match: protein_match->getPeptideMatchList(_peptide_validation_state)) {
- unsigned int start = p_peptide_match->getStart();
- std::vector<unsigned int> positionb_list = this->getPtmPositions(p_peptide_match);
+ for (const PeptideMatch & peptide_match: protein_match->getPeptideMatchList(_peptide_validation_state)) {
+ unsigned int start = peptide_match.getStart();
+ std::vector<unsigned int> positionb_list = this->getPtmPositions(peptide_match);
for (unsigned int position: positionb_list) {
position_list.push_back(start+position);
}
diff --git a/src/grouping/ptm/ptmgroupingexperiment.h b/src/grouping/ptm/ptmgroupingexperiment.h
index 61ab3c26e0946fed1f8e3dd8b0b786a36c1c4403..abbdf2c6c3e0025637d9c841e1ab31d9203c7e72 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.h
+++ b/src/grouping/ptm/ptmgroupingexperiment.h
@@ -58,8 +58,8 @@ public:
const std::vector<PtmIslandSp> & getPtmIslandList() const;
/** @brief count number of modifications in a PeptideMatch
* */
- unsigned int countPeptideMatchPtm(const PeptideMatch* p_peptide_match)const;
- std::vector<unsigned int> getPtmPositions(const PeptideMatch * p_peptide_match) const;
+ unsigned int countPeptideMatchPtm(const PeptideMatch & peptide_match)const;
+ std::vector<unsigned int> getPtmPositions(const PeptideMatch & peptide_match) const;
private:
std::vector<unsigned int> getPtmPositions(const ProteinMatch * protein_match) const;
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index 767c52a420a857e7832fa8fef3d10feee7cc5e1d..51d41937c73aa1a633f8450da42a326bb0a9888e 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/src/grouping/ptm/ptmisland.cpp
@@ -59,7 +59,7 @@ unsigned int PtmIsland::countSampleScanMultiPtm(const PtmGroupingExperiment * p_
std::set<std::size_t> sample_scan_list;
for (auto & p_peptide_match : _peptide_match_list) {
if (p_ptm_grouping_experiment->countPeptideMatchPtm(p_peptide_match) > 1) {
- sample_scan_list.insert(p_peptide_match->getHashSampleScan());
+ sample_scan_list.insert(p_peptide_match.getPeptideEvidence()->getHashSampleScan());
}
}
return sample_scan_list.size();
@@ -67,8 +67,8 @@ unsigned int PtmIsland::countSampleScanMultiPtm(const PtmGroupingExperiment * p_
unsigned int PtmIsland::countSequence() const {
std::set<QString> sequence_list;
- for (auto & p_peptide_match : _peptide_match_list) {
- sequence_list.insert(p_peptide_match->getPeptideXtpSp().get()->getSequence());
+ for (auto & peptide_match : _peptide_match_list) {
+ sequence_list.insert(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequence());
}
//qDebug() <<"ProteinMatch::countValidAndCheckedPeptide end " << sequence_list.size();
return sequence_list.size();
@@ -97,8 +97,8 @@ const ProteinMatch * PtmIsland::getProteinMatch() const {
}
std::vector<std::size_t> PtmIsland::getSampleScanSet() const {
std::vector<std::size_t> sample_scan_set;
- for (const PeptideMatch * p_peptide_match:_peptide_match_list) {
- sample_scan_set.push_back(p_peptide_match->getHashSampleScan());
+ for (const PeptideMatch & peptide_match:_peptide_match_list) {
+ sample_scan_set.push_back(peptide_match.getPeptideEvidence()->getHashSampleScan());
}
std::sort(sample_scan_set.begin(), sample_scan_set.end());
@@ -112,20 +112,20 @@ bool PtmIsland::containsPeptideMatch(const PeptideMatch* peptide_match) const {
});
}
-void PtmIsland::addPeptideMatch(PeptideMatch* p_peptide_match) {
+void PtmIsland::addPeptideMatch(const PeptideMatch & peptide_match) {
if (_position_list.size()==1) {
unsigned int position = _position_list[0];
- if (p_peptide_match->containsPosition(position)) {
+ if (peptide_match.containsPosition(position)) {
if (_peptide_match_list.size() == 0) {
- _protein_start = p_peptide_match->getStart();
+ _protein_start = peptide_match.getStart();
+ }
+ _peptide_match_list.push_back(peptide_match);
+ if (peptide_match.getStart() < _protein_start) {
+ _protein_start = peptide_match.getStart();
+ }
+ if (peptide_match.getStop() > _protein_stop) {
+ _protein_stop = peptide_match.getStop();
}
- _peptide_match_list.push_back(p_peptide_match);
- if (p_peptide_match->getStart() < _protein_start) {
- _protein_start = p_peptide_match->getStart();
- }
- if (p_peptide_match->getStop() > _protein_stop) {
- _protein_stop = p_peptide_match->getStop();
- }
}
}
else {
@@ -155,17 +155,17 @@ bool PtmIsland::merge(PtmIslandSp ptm_island_sp) {
_position_list.erase(std::unique(_position_list.begin(), _position_list.end()), _position_list.end());
- std::vector<PeptideMatch *>::const_iterator it_result = std::max_element(_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch * a, const PeptideMatch * b)
+ std::vector<PeptideMatch>::const_iterator it_result = std::max_element(_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch & a, const PeptideMatch & b)
{
- return (a->getStop() < b->getStop());
+ return (a.getStop() < b.getStop());
});
- _protein_stop = (*it_result)->getStop();
+ _protein_stop = it_result->getStop();
- it_result = std::min_element(_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch * a, const PeptideMatch * b)
+ it_result = std::min_element(_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch & a, const PeptideMatch & b)
{
- return a->getStart() < b->getStart();
+ return a.getStart() < b.getStart();
});
- _protein_start = (*it_result)->getStart();
+ _protein_start = it_result->getStart();
return true;
}
}
@@ -173,17 +173,17 @@ bool PtmIsland::merge(PtmIslandSp ptm_island_sp) {
std::vector<PtmSampleScanSp> PtmIsland::getPtmSampleScanSpList() const {
qDebug() << "PtmIsland::getPtmSampleScanSpList begin" ;
std::vector<PtmSampleScanSp> sample_scan_list;
- for (PeptideMatch * p_peptide_match:_peptide_match_list) {
-
+ for (const PeptideMatch & peptide_match:_peptide_match_list) {
+
std::vector<PtmSampleScanSp>::iterator it_ptm = sample_scan_list.begin();
std::vector<PtmSampleScanSp>::iterator it_ptm_end = sample_scan_list.end();
- while ((it_ptm != it_ptm_end) && (it_ptm->get()->add(p_peptide_match) == false)) {
+ while ((it_ptm != it_ptm_end) && (it_ptm->get()->add(peptide_match) == false)) {
//peptide added
it_ptm++;
}
if (it_ptm == it_ptm_end) {
//peptide NOT added
- sample_scan_list.push_back(std::make_shared<PtmSampleScan>(p_peptide_match));
+ sample_scan_list.push_back(std::make_shared<PtmSampleScan>(peptide_match));
}
}
diff --git a/src/grouping/ptm/ptmisland.h b/src/grouping/ptm/ptmisland.h
index 845ae3429729faa5719acc0c95dc51708e8f0d0b..d00537ec886f2537058fc2f8a0e3a81d29daf966 100644
--- a/src/grouping/ptm/ptmisland.h
+++ b/src/grouping/ptm/ptmisland.h
@@ -50,7 +50,7 @@ public:
PtmIsland(const ProteinMatch* p_protein_match, unsigned int position);
PtmIsland(const PtmIsland & other);
~PtmIsland();
- void addPeptideMatch(PeptideMatch* p_peptide_match);
+ void addPeptideMatch(const PeptideMatch & peptide_match);
/** @brief merge with the given ptm island if there is at least one common peptide match
* */
@@ -77,7 +77,7 @@ public:
private:
const ProteinMatch * _protein_match_p;
- std::vector<PeptideMatch *> _peptide_match_list;
+ std::vector<PeptideMatch> _peptide_match_list;
//std::vector<std::size_t> _sample_scan_set;
std::vector<unsigned int> _position_list;
unsigned int _protein_stop=0;
diff --git a/src/grouping/ptm/ptmsamplescan.cpp b/src/grouping/ptm/ptmsamplescan.cpp
index 361108102695b1aee25ae2cfe3e107fb5093c5c9..71a1abb5727c332bc51c17ac535a80b05d7708f4 100644
--- a/src/grouping/ptm/ptmsamplescan.cpp
+++ b/src/grouping/ptm/ptmsamplescan.cpp
@@ -36,8 +36,8 @@ QColor PtmSampleScan::_color_other_best = QColor("#ff7878");
QColor PtmSampleScan::_color_no_best = QColor("yellow");
-PtmSampleScan::PtmSampleScan(PeptideMatch * p_peptide_match) {
- _peptide_match_list.push_back(p_peptide_match);
+PtmSampleScan::PtmSampleScan(const PeptideMatch & peptide_match) {
+ _peptide_match_list.push_back(peptide_match);
}
PtmSampleScan::PtmSampleScan(const PtmSampleScan& other) {
@@ -45,24 +45,24 @@ PtmSampleScan::PtmSampleScan(const PtmSampleScan& other) {
PtmSampleScan::~PtmSampleScan() {
}
-const PeptideMatch * PtmSampleScan::getRepresentativePeptideMatch() const {
+const PeptideMatch & PtmSampleScan::getRepresentativePeptideMatch() const {
return _peptide_match_list[0];
}
-bool PtmSampleScan::add(PeptideMatch * p_peptide_match) {
- if(getRepresentativePeptideMatch()->getHashSampleScan() != p_peptide_match->getHashSampleScan()) {
+bool PtmSampleScan::add(const PeptideMatch & peptide_match) {
+ if(getRepresentativePeptideMatch().getPeptideEvidence()->getHashSampleScan() != peptide_match.getPeptideEvidence()->getHashSampleScan()) {
return false;
}
- if(getRepresentativePeptideMatch()->getPeptideXtpSp().get()->getSequence() != p_peptide_match->getPeptideXtpSp().get()->getSequence()) {
+ if(getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->getSequence() != peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequence()) {
return false;
}
- if(getRepresentativePeptideMatch()->getPeptideXtpSp().get()->getMass() != p_peptide_match->getPeptideXtpSp().get()->getMass()) {
+ if(getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->getMass() != peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getMass()) {
return false;
}
- _peptide_match_list.push_back(p_peptide_match);
+ _peptide_match_list.push_back(peptide_match);
//sort list
- std::sort(_peptide_match_list.begin(),_peptide_match_list.end(),[](const PeptideMatch * first, const PeptideMatch * second) {
- return (first->getEvalue() < second->getEvalue()) ;
+ std::sort(_peptide_match_list.begin(),_peptide_match_list.end(),[](const PeptideMatch & first, const PeptideMatch & second) {
+ return (first.getPeptideEvidence()->getEvalue() < second.getPeptideEvidence()->getEvalue()) ;
});
return true;
@@ -75,8 +75,8 @@ std::vector<unsigned int> PtmSampleScan::getBestPtmPositionList(const PtmGroupin
std::vector<unsigned int> PtmSampleScan::getObservedPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const {
std::vector<unsigned int> position_list;
- for (const PeptideMatch * p_peptide_match: _peptide_match_list) {
- std::vector<unsigned int> positionb_list = p_ptm_grouping_experiment->getPtmPositions(p_peptide_match);
+ for (const PeptideMatch & peptide_match: _peptide_match_list) {
+ std::vector<unsigned int> positionb_list = p_ptm_grouping_experiment->getPtmPositions(peptide_match);
for (unsigned int position: positionb_list) {
position_list.push_back(position);
}
@@ -89,24 +89,24 @@ std::vector<unsigned int> PtmSampleScan::getObservedPtmPositionList(const PtmGro
const QString PtmSampleScan::getHtmlSequence(const PtmGroupingExperiment * p_ptm_grouping_experiment) const
{
- const PeptideMatch * p_representative_peptide = getRepresentativePeptideMatch();
- size_t pep_size = p_representative_peptide->getPeptideXtpSp().get()->size();
+ const PeptideMatch & representative_peptide = getRepresentativePeptideMatch();
+ size_t pep_size = representative_peptide.getPeptideEvidence()->getPeptideXtpSp().get()->size();
//qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << " " << _protein_sp.get()-//>getSequence();
if (pep_size == 0) return 0;
bool best_bool[pep_size] = {false};
bool other_best_bool[pep_size] = {false};
bool nobest_bool[pep_size] = {false};
- double best_evalue = p_representative_peptide->getEvalue();
+ double best_evalue = representative_peptide.getPeptideEvidence()->getEvalue();
- for (auto & p_peptide_match : _peptide_match_list) {
+ for (auto & peptide_match : _peptide_match_list) {
bool is_best= false;
- if (p_peptide_match->getEvalue() == best_evalue) {
+ if (peptide_match.getPeptideEvidence()->getEvalue() == best_evalue) {
is_best= true;
}
- std::vector<unsigned int> position_list = p_ptm_grouping_experiment->getPtmPositions(p_peptide_match);
+ std::vector<unsigned int> position_list = p_ptm_grouping_experiment->getPtmPositions(peptide_match);
for (unsigned int position :position_list) {
- if (p_representative_peptide == p_peptide_match) {
+ if (representative_peptide == peptide_match) {
best_bool[position] = true;
}
else if (is_best) {
@@ -117,7 +117,7 @@ const QString PtmSampleScan::getHtmlSequence(const PtmGroupingExperiment * p_ptm
}
}
}
- QString sequence = p_representative_peptide->getPeptideXtpSp().get()->getSequence();
+ QString sequence = representative_peptide.getPeptideEvidence()->getPeptideXtpSp().get()->getSequence();
QString sequence_html;
for (unsigned int i=0; i < pep_size; i++) {
if (best_bool[i]) {
@@ -136,6 +136,6 @@ const QString PtmSampleScan::getHtmlSequence(const PtmGroupingExperiment * p_ptm
return sequence_html;
}
-const std::vector<PeptideMatch *> & PtmSampleScan::getPeptideMatchList() const {
+const std::vector<PeptideMatch> & PtmSampleScan::getPeptideMatchList() const {
return _peptide_match_list;
}
diff --git a/src/grouping/ptm/ptmsamplescan.h b/src/grouping/ptm/ptmsamplescan.h
index 3533ff92dad010a82af0493d2094b7d34d0ce455..3ff57ed59f3e779f735990b6947b4e180f13a259 100644
--- a/src/grouping/ptm/ptmsamplescan.h
+++ b/src/grouping/ptm/ptmsamplescan.h
@@ -44,19 +44,19 @@ typedef std::shared_ptr<PtmSampleScan> PtmSampleScanSp;
class PtmSampleScan
{
public:
- PtmSampleScan(PeptideMatch * p_peptide_match);
+ PtmSampleScan(const PeptideMatch & peptide_match);
PtmSampleScan(const PtmSampleScan& other);
~PtmSampleScan();
- const PeptideMatch * getRepresentativePeptideMatch() const;
- bool add(PeptideMatch * p_peptide_match);
+ const PeptideMatch & getRepresentativePeptideMatch() const;
+ bool add(const PeptideMatch & peptide_match);
std::vector<unsigned int> getBestPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
std::vector<unsigned int> getObservedPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
const QString getHtmlSequence(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
- const std::vector<PeptideMatch *> & getPeptideMatchList() const;
+ const std::vector<PeptideMatch> & getPeptideMatchList() const;
private:
- std::vector<PeptideMatch *> _peptide_match_list;
+ std::vector<PeptideMatch> _peptide_match_list;
static QColor _color_best;
static QColor _color_other_best;
static QColor _color_no_best;
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index bfa3a3097e1d9357a1b82be22504b64314b2fbc9..78d69dacf58ed84777523945d6551b836324aa7f 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -239,28 +239,29 @@ void IdentificationPwizReader::read(
//<cvParam accession="MS:1001331" cvRef="PSI-MS" value="24.275219" name="X!Tandem:hyperscore"/>
// </SpectrumIdentificationItem>
for ( pwiz::identdata::SpectrumIdentificationItemPtr spid_item : spectrum_ptr.get()->spectrumIdentificationItem) {
- PeptideMatch * p_peptide_match = new PeptideMatch(_sp_msrun.get(), scan);
- p_peptide_match->setRetentionTime(rt.toDouble());
- p_peptide_match->setCharge(spid_item->chargeState);
+ PeptideEvidence * p_peptide_evidence = new PeptideEvidence(_sp_msrun.get(), scan);
+ p_peptide_evidence->setRetentionTime(rt.toDouble());
+ p_peptide_evidence->setCharge(spid_item->chargeState);
pappso::pappso_double exp_mass = spid_item->experimentalMassToCharge * ((double) spid_item->chargeState) - (((double) spid_item->chargeState) * pappso::MHPLUS);
- p_peptide_match->setExperimentalMass(exp_mass);
- p_peptide_match->setIdentificationDataSource( p_identification_data_source);
+ p_peptide_evidence->setExperimentalMass(exp_mass);
+ p_peptide_evidence->setIdentificationDataSource( p_identification_data_source);
- p_peptide_match->setChecked(true);
+ p_peptide_evidence->setChecked(true);
QVariant evalue = getQVariantDoubleParam(spid_item.get(), pwiz::cv::MS_X_Tandem_expect);
if (!evalue.isNull())
{
- p_peptide_match->setEvalue(evalue.toDouble());
+ p_peptide_evidence->setEvalue(evalue.toDouble());
}
QVariant hyperscore = getQVariantDoubleParam(spid_item.get(), pwiz::cv::MS_X_Tandem_hyperscore);
if (!hyperscore.isNull())
{
- p_peptide_match->setParam(PeptideMatchParam::tandem_hyperscore, hyperscore);
+ p_peptide_evidence->setParam(PeptideMatchParam::tandem_hyperscore, hyperscore);
}
+
for ( pwiz::identdata::PeptideEvidencePtr peptide_evidence_sp : spid_item.get()->peptideEvidencePtr) {
- PeptideMatch * p_peptide_match_from_evidence = new PeptideMatch(*p_peptide_match);
- p_peptide_match_from_evidence->setStart(peptide_evidence_sp.get()->start);
+ PeptideMatch peptide_match;
+ peptide_match.setStart(peptide_evidence_sp.get()->start);
auto it_pep = map_id2peptide.find(QString::fromStdString(peptide_evidence_sp.get()->peptidePtr.get()->id));
@@ -270,7 +271,12 @@ void IdentificationPwizReader::read(
.arg(QString::fromStdString(spid_item.get()->id))
);
}
- p_peptide_match_from_evidence->setPeptideXtpSp(it_pep->second);
+
+
+ p_peptide_evidence->setPeptideXtpSp(it_pep->second);
+ PeptideEvidenceSp peptide_evidence_sp = p_identification_data_source->getPeptideEvidenceStore().getInstance(p_peptide_evidence);
+
+ peptide_match.setPeptideEvidenceSp(peptide_evidence_sp);
auto it = map_id2protein.find(QString::fromStdString(peptide_evidence_sp.get()->dbSequencePtr.get()->id));
if (it == map_id2protein.end()) {
@@ -278,12 +284,10 @@ void IdentificationPwizReader::read(
}
ProteinMatch * protein_match_p = it->second;
- protein_match_p->addPeptideMatchSp(p_peptide_match_from_evidence->getIdentificationDataSource()->getPeptideMatchStore().getInstance(p_peptide_match_from_evidence));
-
- delete p_peptide_match_from_evidence;
- //protein_match_p->addPeptideMatch(p_peptide_match_from_evidence);
+ protein_match_p->addPeptideMatch(peptide_match);
}
- delete p_peptide_match;
+
+ delete p_peptide_evidence;
}
}
}
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 9c580c9629effb049f9d4f13b2927c534ace4775..94fcd0345258253dbbdffa8377b32cbd46c25400 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -256,17 +256,17 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
qDebug() << "startElement_peptide ";
_current_peptide_sp = PeptideXtp(attributes.value("sequence").simplified()).makePeptideXtpSp();
MsRunSp ms_run_id = _p_project->getMsRunStore().getInstance(attributes.value("sample").simplified());
- _p_peptide_match = new PeptideMatch(ms_run_id.get(), attributes.value("scan").simplified().toUInt());
- _p_peptide_match->setRetentionTime(attributes.value("RT").simplified().toDouble());
- _p_peptide_match->setEvalue(attributes.value("evalue").simplified().toDouble());
+ _p_peptide_evidence = new PeptideEvidence(ms_run_id.get(), attributes.value("scan").simplified().toUInt());
+ _p_peptide_evidence->setRetentionTime(attributes.value("RT").simplified().toDouble());
+ _p_peptide_evidence->setEvalue(attributes.value("evalue").simplified().toDouble());
pappso::pappso_double exp_mass = attributes.value("mhplus_obser").simplified().toDouble() - pappso::MHPLUS;
- _p_peptide_match->setExperimentalMass(exp_mass);
- _p_peptide_match->setStart(attributes.value("start").simplified().toUInt()-1);
- _p_peptide_match->setCharge(attributes.value("charge").simplified().toUInt());
- _p_peptide_match->setParam(PeptideMatchParam::tandem_hyperscore, QVariant( attributes.value("hypercorr").toDouble()));
+ _p_peptide_evidence->setExperimentalMass(exp_mass);
+ _p_peptide_evidence->setStart(attributes.value("start").simplified().toUInt()-1);
+ _p_peptide_evidence->setCharge(attributes.value("charge").simplified().toUInt());
+ _p_peptide_evidence->setParam(PeptideMatchParam::tandem_hyperscore, QVariant( attributes.value("hypercorr").toDouble()));
IdentificationDataSource* p_identification_data_source = _p_project->getIdentificationDataSourceStore().getInstance(attributes.value("sample_file").simplified()).get();
- _p_peptide_match->setIdentificationDataSource( p_identification_data_source);
+ _p_peptide_evidence->setIdentificationDataSource( p_identification_data_source);
if (p_identification_data_source->getMsRunSp().get() == nullptr) {
p_identification_data_source->setMsRunSp(ms_run_id);
}
@@ -275,9 +275,9 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
}
_current_identification_group_p->addIdentificationDataSourceP(p_identification_data_source);
p_identification_data_source->addFastaFile(_current_fasta_file_sp);
- _p_peptide_match->setChecked(false);
+ _p_peptide_evidence->setChecked(false);
if (attributes.value("validate").simplified().toLower() == "true") {
- _p_peptide_match->setChecked(true);
+ _p_peptide_evidence->setChecked(true);
}
qDebug() << "startElement_peptide end" ;
return true;
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
index ebf326e7a0a76f66c1594eb4189ace41993506bd..29b75cf8738d9653ecc06c9a1c552c25f5d080aa 100644
--- a/src/input/xpipsaxhandler.h
+++ b/src/input/xpipsaxhandler.h
@@ -84,7 +84,7 @@ private:
Project * _p_project;
ProteinMatch * _p_protein_match;
- PeptideMatch * _p_peptide_match;
+ PeptideEvidence * _p_peptide_evidence;
ProteinXtp _current_protein;
PeptideXtpSp _current_peptide_sp;
IdentificationGroup * _current_identification_group_p;
diff --git a/src/utils/peptideevidencestore.cpp b/src/utils/peptideevidencestore.cpp
index 1de93d17124eb44d42a6db76ab282597805592a6..ad3110da70e086a616a99432b619e152e063d4fd 100644
--- a/src/utils/peptideevidencestore.cpp
+++ b/src/utils/peptideevidencestore.cpp
@@ -35,3 +35,12 @@
std::shared_ptr<PeptideEvidence> & PeptideEvidenceStore::getInstance(const PeptideEvidence * p_peptide_evidence) {
}
+
+void PeptideEvidenceStore::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
+ qDebug() << "PeptideEvidenceStore::updateAutomaticFilters begin" ;
+ for (PeptideEvidenceSp & peptide_evidence_sp:_peptide_evidence_list) {
+ peptide_evidence_sp.get()->updateAutomaticFilters(automatic_filter_parameters);
+ }
+ qDebug() << "PeptideEvidenceStore::updateAutomaticFilters end" ;
+
+}
diff --git a/src/utils/peptideevidencestore.h b/src/utils/peptideevidencestore.h
index 14727d03def2d7c807f3efba4ae10b202715cc5b..32d7895b3c5d4a6d2c845f60769bac6f8c4e8b41 100644
--- a/src/utils/peptideevidencestore.h
+++ b/src/utils/peptideevidencestore.h
@@ -32,6 +32,7 @@
#define PEPTIDEEVIDENCESTORE_H
#include <memory>
+#include "../core/automaticfilterparameters.h"
class PeptideEvidence;
@@ -39,6 +40,9 @@ class PeptideEvidenceStore
{
public:
std::shared_ptr<PeptideEvidence> & getInstance(const PeptideEvidence * p_peptide_evidence);
+ void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
+private:
+ std::vector<std::shared_ptr<PeptideEvidence>> _peptide_evidence_list;
};
#endif // PEPTIDEEVIDENCESTORE_H