diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 7a1be53fac2af067b3de8160977edb59680069c0..0410712ba83af5ff6444aa8d5c2065a6a8468cd7 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -62,6 +62,7 @@ SET(CPP_FILES
core/tandem_run/tandemcondorprocess.cpp
core/tandem_run/tandemparameters.cpp
core/msrun.cpp
+ core/peptideevidence.cpp
core/peptidematch.cpp
core/peptidextp.cpp
core/project.cpp
@@ -106,7 +107,7 @@ SET(CPP_FILES
utils/identificationdatasourcestore.cpp
utils/groupstore.cpp
utils/msrunstore.cpp
- utils/peptidematchstore.cpp
+ utils/peptideevidencestore.cpp
utils/peptidestore.cpp
utils/proteinstore.cpp
utils/readspectrum.cpp
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index d300871d28df34d0eb05990bae4e3ecf099a790f..b06ae4d94787ea39499692b2251757826b4b4a60 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -44,8 +44,8 @@ IdentificationDataSource::~IdentificationDataSource()
}
-PeptideMatchStore & IdentificationDataSource::getPeptideMatchStore() {
- return _peptide_match_store;
+PeptideEvidenceStore & IdentificationDataSource::getPeptideEvidenceStore() {
+ return _peptide_evidence_store;
}
void IdentificationDataSource::setXmlId(const QString xmlid) {
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index de98f146b9960ebb3801bbf7ca5efca1ee0aee6b..f83588031bd4213c4d6126335632dd7b72fc1bcb 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -29,7 +29,7 @@
#include <QVariant>
#include "../msrun.h"
#include "../../utils/fastafilestore.h"
-#include "../../utils/peptidematchstore.h"
+#include "../../utils/peptideevidencestore.h"
class Project;
@@ -46,7 +46,7 @@ public:
~IdentificationDataSource();
bool operator==(const IdentificationDataSource& other) const;
- PeptideMatchStore & getPeptideMatchStore();
+ PeptideEvidenceStore & getPeptideEvidenceStore();
void setXmlId(const QString xmlid);
const QString & getXmlId() const;
@@ -122,7 +122,7 @@ private :
std::map<IdentificationEngineStatistics, QVariant> _param_stats;
std::vector<FastaFileSp> _fastafile_list;
- PeptideMatchStore _peptide_match_store;
+ PeptideEvidenceStore _peptide_evidence_store;
};
#endif // IDENTIFICATIONDATASOURCE_H
diff --git a/src/core/peptideevidence.cpp b/src/core/peptideevidence.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..c1669f2dc841fa492916897ca664280920a758b9
--- /dev/null
+++ b/src/core/peptideevidence.cpp
@@ -0,0 +1,217 @@
+/**
+ * \file utils/peptideevidence.cpp
+ * \date 18/11/2017
+ * \author Olivier Langella
+ * \brief peptide evidence : a peptide sequence + spectrum + identification engine evaluation (psm)
+ */
+
+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include "peptideevidence.h"
+#include <pappsomspp/pappsoexception.h>
+
+std::hash<std::string> PeptideEvidence::_hash_fn;
+
+PeptideEvidence::PeptideEvidence(MsRun * msrunid_sp, unsigned int scan) {
+ _msrunid_sp = msrunid_sp;
+ _scan = scan;
+
+ _hash_sample_scan = PeptideEvidence::_hash_fn (QString("%1 %2").arg(msrunid_sp->getXmlId()).arg(_scan).toStdString());
+}
+
+PeptideEvidence::PeptideEvidence(const PeptideEvidence & other): PeptideEvidence(other._msrunid_sp, other._scan) {
+ _hash_sample_scan = other._hash_sample_scan;
+ _sp_grp_peptide = other._sp_grp_peptide;
+ _peptide_sp = other._peptide_sp;
+ _rt = other._rt;
+ _evalue = other._evalue;
+ _exp_mass = other._exp_mass;
+ _start=other._start;
+ _charge= other._charge;
+ _p_identification_source = other._p_identification_source;
+ _params = other._params;
+ _checked = other._checked;
+ _proxy_valid = other._proxy_valid;
+
+}
+
+PeptideEvidenceSp PeptideEvidence::makePeptideEvidenceSp() const {
+ return std::make_shared<PeptideEvidence>(*this);
+}
+
+void PeptideEvidence::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
+ _proxy_valid = false;
+
+ if (_evalue <= automatic_filter_parameters.getFilterPeptideEvalue()) {
+ _proxy_valid = true;
+ }
+}
+void PeptideEvidence::setRetentionTime(pappso::pappso_double rt) {
+ _rt = rt;
+}
+void PeptideEvidence::setEvalue(pappso::pappso_double evalue) {
+ _evalue = evalue;
+}
+
+/** \brief set specific parameter value
+ */
+void PeptideEvidence::setParam(PeptideMatchParam param, const QVariant& value) {
+ _params.insert(std::pair<PeptideMatchParam, QVariant>(param, value));
+}
+const QVariant PeptideEvidence::getParam(PeptideMatchParam param) const {
+ try {
+ return _params.at(param);
+ }
+ catch (std::out_of_range) {
+ return QVariant();
+ }
+}
+const std::map<PeptideMatchParam, QVariant> & PeptideEvidence::getParamList() const {
+ return _params;
+}
+
+std::size_t PeptideEvidence::getHashPeptideMassSample() const {
+ return PeptideEvidence::_hash_fn (QString("%1 %2").arg(_peptide_sp.get()->toAbsoluteString()).arg(_msrunid_sp->getXmlId()).toStdString());
+}
+
+std::size_t PeptideEvidence::getHashSampleScan() const {
+ return _hash_sample_scan;
+}
+pappso::pappso_double PeptideEvidence::getEvalue() const {
+ return _evalue;
+}
+pappso::pappso_double PeptideEvidence::getExperimentalMass() const {
+ return _exp_mass;
+}
+pappso::pappso_double PeptideEvidence::getExperimentalMz() const {
+ pappso::mz mz = _exp_mass;
+ for (unsigned int i=0; i < _charge; i++) {
+ mz+=pappso::MHPLUS;
+ }
+ mz = mz/_charge;
+ return mz;
+}
+void PeptideEvidence::setExperimentalMass(pappso::pappso_double exp_mass) {
+ _exp_mass =exp_mass;
+}
+void PeptideEvidence::setStart(unsigned int start) {
+ _start =start;
+}
+pappso::mz PeptideEvidence::getDeltaMass() const {
+ return (_peptide_sp.get()->getMz(1) - (_exp_mass+pappso::MHPLUS));
+}
+unsigned int PeptideEvidence::getStart() const {
+ return _start;
+}
+unsigned int PeptideEvidence::getStop() const {
+ return _start+_peptide_sp.get()->size();
+}
+
+bool PeptideEvidence::containsPosition(unsigned int position) const {
+ if (position < _start) {
+ return false;
+ }
+ if (position < getStop()) {
+ return true;
+ }
+ return false;
+
+}
+void PeptideEvidence::setCharge(unsigned int charge) {
+ _charge =charge;
+}
+
+void PeptideEvidence::setPeptideXtpSp (PeptideXtpSp peptide) {
+ _peptide_sp = peptide;
+}
+
+void PeptideEvidence::setChecked(bool arg1) {
+ _checked = arg1;
+}
+
+ValidationState PeptideEvidence::getValidationState() const {
+ if (isGrouped()) {
+ return ValidationState::grouped;
+ } else if (isValidAndChecked()) {
+ return ValidationState::validAndChecked;
+ } else if (isValid()) {
+ return ValidationState::valid;
+ }
+ return ValidationState::notValid;
+}
+
+bool PeptideEvidence::isValid() const {
+ return _proxy_valid;
+}
+bool PeptideEvidence::isChecked() const {
+ return _checked;
+}
+
+bool PeptideEvidence::isValidAndChecked() const {
+ return _proxy_valid && _checked;
+}
+
+bool PeptideEvidence::isGrouped() const {
+ if (_sp_grp_peptide.get() == nullptr) {
+ return false;
+ }
+ if (_sp_grp_peptide.get()->getGroupNumber() ==0) {
+ return false;
+ }
+ return true;
+}
+void PeptideEvidence::setIdentificationDataSource(IdentificationDataSource* identification_source) {
+ _p_identification_source = identification_source;
+}
+IdentificationDataSource* PeptideEvidence::getIdentificationDataSource () const {
+ return _p_identification_source;
+}
+unsigned int PeptideEvidence::getScan() const {
+ return _scan;
+}
+pappso::pappso_double PeptideEvidence::getRetentionTime() const {
+ return _rt;
+}
+unsigned int PeptideEvidence::getCharge() const {
+ return _charge;
+}
+
+const PeptideXtpSp & PeptideEvidence::getPeptideXtpSp() const {
+ //if (_sp_grp_peptide.get() == nullptr) {
+ // throw pappso::PappsoException(QObject::tr("Peptide is null in %1 %2").arg(_msrunid_sp->getXmlId()).arg(this->getScan()));
+ //}
+ return _peptide_sp;
+}
+
+const MsRun * PeptideEvidence::getMsRunP() const {
+ return _msrunid_sp;
+}
+void PeptideEvidence::setGrpPeptideSp(const pappso::GrpPeptideSp & sp_grp_peptide) {
+ _sp_grp_peptide =sp_grp_peptide;
+}
+
+const pappso::GrpPeptideSp & PeptideEvidence::getGrpPeptideSp() const {
+ return _sp_grp_peptide;
+}
+
diff --git a/src/core/peptideevidence.h b/src/core/peptideevidence.h
new file mode 100644
index 0000000000000000000000000000000000000000..6ecbb1a2d48fb9d589fb2740af49429f40e1b6f9
--- /dev/null
+++ b/src/core/peptideevidence.h
@@ -0,0 +1,159 @@
+/**
+ * \file utils/peptideevidence.h
+ * \date 18/11/2017
+ * \author Olivier Langella
+ * \brief peptide evidence : a peptide sequence + spectrum + identification engine evaluation (psm)
+ */
+
+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+#ifndef PEPTIDEEVIDENCE_H
+#define PEPTIDEEVIDENCE_H
+
+#include <pappsomspp/types.h>
+#include "peptidextp.h"
+#include "identification_sources/identificationdatasource.h"
+#include "automaticfilterparameters.h"
+#include "msrun.h"
+
+#include "../grouping/groupingexperiment.h"
+
+class PeptideEvidence;
+
+/** \brief shared pointer on a Peptide object
+ */
+typedef std::shared_ptr<PeptideEvidence> PeptideEvidenceSp;
+
+class PeptideEvidence
+{
+public :
+ PeptideEvidence(MsRun * msrunid_sp, unsigned int scan);
+ PeptideEvidence(const PeptideEvidence & other);
+ std::size_t getHashSampleScan() const;
+ std::size_t getHashPeptideMassSample() const;
+
+ PeptideEvidenceSp makePeptideEvidenceSp() const;
+
+ void setRetentionTime(pappso::pappso_double rt);
+ void setEvalue(pappso::pappso_double evalue);
+
+ /** @brief get experimental mass of this peptide
+ * @return the computed mass given the precursor measured mass and the deduced peptide charge
+ */
+ pappso::pappso_double getExperimentalMass() const;
+
+ /** @brief get experimental mz of this peptide
+ * @return the real mass measured (precuror mass) by the spectrometer
+ */
+ pappso::pappso_double getExperimentalMz() const;
+
+
+ /** @brief set experimental mass of this peptide
+ * @arg exp_mass the computed mass given the precursor measured mass and the deduced peptide charge
+ */
+ void setExperimentalMass(pappso::pappso_double exp_mass);
+
+
+
+ /** \brief set specific parameter value
+ */
+ virtual void setParam(PeptideMatchParam param, const QVariant& value);
+ /** \brief get specific parameter value
+ */
+ virtual const QVariant getParam(PeptideMatchParam param) const;
+
+ const std::map<PeptideMatchParam, QVariant> & getParamList() const;
+
+
+ /** @brief set start position of this peptide inside the protein sequence
+ * @param start position in the protein amino acid sequence (starts at 0)
+ * */
+ void setStart(unsigned int start);
+ /** @brief get start position of this peptide inside the protein sequence
+ * @return start position in the protein amino acid sequence (starts at 0)
+ * */
+ unsigned int getStart() const;
+ /** @brief get stop position of this peptide inside the protein sequence
+ * @return stop position in the protein amino acid sequence (starts at 0)
+ * */
+ unsigned int getStop() const;
+ void setCharge(unsigned int charge);
+ void setPeptideXtpSp (PeptideXtpSp peptide);
+ void setIdentificationDataSource(IdentificationDataSource* identification_source);
+ void setChecked(bool arg1);
+ bool isChecked() const;
+ bool isValid() const;
+ bool isValidAndChecked() const;
+ bool isGrouped() const;
+
+ const MsRun * getMsRunP() const;
+ IdentificationDataSource* getIdentificationDataSource () const;
+ unsigned int getScan() const;
+ pappso::pappso_double getRetentionTime() const;
+ unsigned int getCharge() const;
+ const PeptideXtpSp & getPeptideXtpSp() const;
+ pappso::pappso_double getEvalue() const;
+
+ void setGrpPeptideSp(const pappso::GrpPeptideSp & sp_grp_peptide);
+ const pappso::GrpPeptideSp & getGrpPeptideSp() const;
+
+ /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
+ * */
+ void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
+
+ /** @brief get delta between theoretical mhplus mass and mhplus experimental mass
+ * theoretical mhplus mass - mhplus experimental mass
+ */
+ pappso::mz getDeltaMass() const;
+
+ ValidationState getValidationState() const;
+
+ /** @brief tells if this peptide contains a protein position
+ * the position is the amino acid position on the protein sequence (starts from 0)
+ * */
+ bool containsPosition(unsigned int position) const;
+
+private :
+ static std::hash<std::string> _hash_fn;
+ MsRun * _msrunid_sp;
+ unsigned int _scan;
+ size_t _hash_sample_scan;
+ pappso::GrpPeptideSp _sp_grp_peptide;
+ PeptideXtpSp _peptide_sp;
+ pappso::pappso_double _rt;
+ pappso::pappso_double _evalue=0;
+ pappso::pappso_double _exp_mass;
+ unsigned int _start=0;
+ unsigned int _charge;
+ IdentificationDataSource* _p_identification_source = nullptr;
+ std::map<PeptideMatchParam, QVariant> _params;
+
+ /** @brief manually checked by user (true by default)
+ */
+ bool _checked = true;
+
+ /** @brief automatic filter result (false by default)
+ */
+ bool _proxy_valid = false;
+};
+#endif // PEPTIDEEVIDENCE_H
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index ad0938af0b99b32021fc746d6546510836caf011..4f600217148e06263f02c09b9daba427c1651eea 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -24,101 +24,32 @@
#include "peptidematch.h"
#include <pappsomspp/pappsoexception.h>
-std::hash<std::string> PeptideMatch::_hash_fn;
-PeptideMatch::PeptideMatch(MsRun * msrunid_sp, unsigned int scan) {
- _msrunid_sp = msrunid_sp;
- _scan = scan;
-
- _hash_sample_scan = PeptideMatch::_hash_fn (QString("%1 %2").arg(msrunid_sp->getXmlId()).arg(_scan).toStdString());
+PeptideMatch::PeptideMatch() {
}
-PeptideMatch::PeptideMatch(const PeptideMatch & other): PeptideMatch(other._msrunid_sp, other._scan) {
- _hash_sample_scan = other._hash_sample_scan;
- _sp_grp_peptide = other._sp_grp_peptide;
- _peptide_sp = other._peptide_sp;
- _rt = other._rt;
- _evalue = other._evalue;
- _exp_mass = other._exp_mass;
+PeptideMatch::PeptideMatch(const PeptideMatch & other) {
_start=other._start;
- _charge= other._charge;
- _p_identification_source = other._p_identification_source;
- _params = other._params;
- _checked = other._checked;
- _proxy_valid = other._proxy_valid;
-
-}
-
-PeptideMatchSp PeptideMatch::makePeptideMatchSp() const {
- return std::make_shared<PeptideMatch>(*this);
-}
-
-void PeptideMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
- _proxy_valid = false;
-
- if (_evalue <= automatic_filter_parameters.getFilterPeptideEvalue()) {
- _proxy_valid = true;
- }
-}
-void PeptideMatch::setRetentionTime(pappso::pappso_double rt) {
- _rt = rt;
-}
-void PeptideMatch::setEvalue(pappso::pappso_double evalue) {
- _evalue = evalue;
-}
-
-/** \brief set specific parameter value
- */
-void PeptideMatch::setParam(PeptideMatchParam param, const QVariant& value) {
- _params.insert(std::pair<PeptideMatchParam, QVariant>(param, value));
-}
-const QVariant PeptideMatch::getParam(PeptideMatchParam param) const {
- try {
- return _params.at(param);
- }
- catch (std::out_of_range) {
- return QVariant();
- }
-}
-const std::map<PeptideMatchParam, QVariant> & PeptideMatch::getParamList() const {
- return _params;
-}
+ _p_peptide_evidence = other._p_peptide_evidence;
-std::size_t PeptideMatch::getHashPeptideMassSample() const {
- return PeptideMatch::_hash_fn (QString("%1 %2").arg(_peptide_sp.get()->toAbsoluteString()).arg(_msrunid_sp->getXmlId()).toStdString());
}
-
-std::size_t PeptideMatch::getHashSampleScan() const {
- return _hash_sample_scan;
+void PeptideMatch::setPeptideEvidenceSp(PeptideEvidenceSp sp_peptide_evidence) {
+ _p_peptide_evidence = sp_peptide_evidence.get();
}
-pappso::pappso_double PeptideMatch::getEvalue() const {
- return _evalue;
-}
-pappso::pappso_double PeptideMatch::getExperimentalMass() const {
- return _exp_mass;
-}
-pappso::pappso_double PeptideMatch::getExperimentalMz() const {
- pappso::mz mz = _exp_mass;
- for (unsigned int i=0; i < _charge; i++) {
- mz+=pappso::MHPLUS;
- }
- mz = mz/_charge;
- return mz;
+const PeptideEvidence * PeptideMatch::getPeptideEvidence() const {
+ return _p_peptide_evidence;
}
-void PeptideMatch::setExperimentalMass(pappso::pappso_double exp_mass) {
- _exp_mass =exp_mass;
+PeptideEvidence * PeptideMatch::getPeptideEvidence() {
+ return _p_peptide_evidence;
}
void PeptideMatch::setStart(unsigned int start) {
_start =start;
}
-pappso::mz PeptideMatch::getDeltaMass() const {
- return (_peptide_sp.get()->getMz(1) - (_exp_mass+pappso::MHPLUS));
-}
unsigned int PeptideMatch::getStart() const {
return _start;
}
unsigned int PeptideMatch::getStop() const {
- return _start+_peptide_sp.get()->size();
+ return _start+_p_peptide_evidence->getPeptideXtpSp().get()->size();
}
bool PeptideMatch::containsPosition(unsigned int position) const {
@@ -131,79 +62,3 @@ bool PeptideMatch::containsPosition(unsigned int position) const {
return false;
}
-void PeptideMatch::setCharge(unsigned int charge) {
- _charge =charge;
-}
-
-void PeptideMatch::setPeptideXtpSp (PeptideXtpSp peptide) {
- _peptide_sp = peptide;
-}
-
-void PeptideMatch::setChecked(bool arg1) {
- _checked = arg1;
-}
-
-ValidationState PeptideMatch::getValidationState() const {
- if (isGrouped()) {
- return ValidationState::grouped;
- } else if (isValidAndChecked()) {
- return ValidationState::validAndChecked;
- } else if (isValid()) {
- return ValidationState::valid;
- }
- return ValidationState::notValid;
-}
-
-bool PeptideMatch::isValid() const {
- return _proxy_valid;
-}
-bool PeptideMatch::isChecked() const {
- return _checked;
-}
-
-bool PeptideMatch::isValidAndChecked() const {
- return _proxy_valid && _checked;
-}
-
-bool PeptideMatch::isGrouped() const {
- if (_sp_grp_peptide.get() == nullptr) {
- return false;
- }
- if (_sp_grp_peptide.get()->getGroupNumber() ==0) {
- return false;
- }
- return true;
-}
-void PeptideMatch::setIdentificationDataSource(IdentificationDataSource* identification_source) {
- _p_identification_source = identification_source;
-}
-IdentificationDataSource* PeptideMatch::getIdentificationDataSource () const {
- return _p_identification_source;
-}
-unsigned int PeptideMatch::getScan() const {
- return _scan;
-}
-pappso::pappso_double PeptideMatch::getRetentionTime() const {
- return _rt;
-}
-unsigned int PeptideMatch::getCharge() const {
- return _charge;
-}
-
-const PeptideXtpSp & PeptideMatch::getPeptideXtpSp() const {
- //if (_sp_grp_peptide.get() == nullptr) {
- // throw pappso::PappsoException(QObject::tr("Peptide is null in %1 %2").arg(_msrunid_sp->getXmlId()).arg(this->getScan()));
- //}
- return _peptide_sp;
-}
-
-const MsRun * PeptideMatch::getMsRunP() const {
- return _msrunid_sp;
-}
-void PeptideMatch::setGrpPeptideSp(const pappso::GrpPeptideSp & sp_grp_peptide) {
- _sp_grp_peptide =sp_grp_peptide;
-}
-
-const pappso::GrpPeptideSp & PeptideMatch::getGrpPeptideSp() const {
- return _sp_grp_peptide;
-}
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 2f28bfe01659eb88122fe2077126c64f3236bb20..1794efc211c2adf75b0789f1b07a91a4a9ad678b 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -23,59 +23,14 @@
#ifndef PEPTIDEMATCH_H
#define PEPTIDEMATCH_H
-#include <pappsomspp/types.h>
-#include "peptidextp.h"
-#include "identification_sources/identificationdatasource.h"
-#include "automaticfilterparameters.h"
-#include "msrun.h"
+#include "peptideevidence.h"
-#include "../grouping/groupingexperiment.h"
-
-class PeptideMatch;
-
-/** \brief shared pointer on a Peptide object
- */
-typedef std::shared_ptr<PeptideMatch> PeptideMatchSp;
class PeptideMatch
{
public :
- PeptideMatch(MsRun * msrunid_sp, unsigned int scan);
+ PeptideMatch();
PeptideMatch(const PeptideMatch & other);
- std::size_t getHashSampleScan() const;
- std::size_t getHashPeptideMassSample() const;
-
- PeptideMatchSp makePeptideMatchSp() const;
-
- void setRetentionTime(pappso::pappso_double rt);
- void setEvalue(pappso::pappso_double evalue);
-
- /** @brief get experimental mass of this peptide
- * @return the computed mass given the precursor measured mass and the deduced peptide charge
- */
- pappso::pappso_double getExperimentalMass() const;
-
- /** @brief get experimental mz of this peptide
- * @return the real mass measured (precuror mass) by the spectrometer
- */
- pappso::pappso_double getExperimentalMz() const;
-
-
- /** @brief set experimental mass of this peptide
- * @arg exp_mass the computed mass given the precursor measured mass and the deduced peptide charge
- */
- void setExperimentalMass(pappso::pappso_double exp_mass);
-
-
-
- /** \brief set specific parameter value
- */
- virtual void setParam(PeptideMatchParam param, const QVariant& value);
- /** \brief get specific parameter value
- */
- virtual const QVariant getParam(PeptideMatchParam param) const;
-
- const std::map<PeptideMatchParam, QVariant> & getParamList() const;
/** @brief set start position of this peptide inside the protein sequence
@@ -90,64 +45,19 @@ public :
* @return stop position in the protein amino acid sequence (starts at 0)
* */
unsigned int getStop() const;
- void setCharge(unsigned int charge);
- void setPeptideXtpSp (PeptideXtpSp peptide);
- void setIdentificationDataSource(IdentificationDataSource* identification_source);
- void setChecked(bool arg1);
- bool isChecked() const;
- bool isValid() const;
- bool isValidAndChecked() const;
- bool isGrouped() const;
-
- const MsRun * getMsRunP() const;
- IdentificationDataSource* getIdentificationDataSource () const;
- unsigned int getScan() const;
- pappso::pappso_double getRetentionTime() const;
- unsigned int getCharge() const;
- const PeptideXtpSp & getPeptideXtpSp() const;
- pappso::pappso_double getEvalue() const;
-
- void setGrpPeptideSp(const pappso::GrpPeptideSp & sp_grp_peptide);
- const pappso::GrpPeptideSp & getGrpPeptideSp() const;
-
- /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
- * */
- void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
-
- /** @brief get delta between theoretical mhplus mass and mhplus experimental mass
- * theoretical mhplus mass - mhplus experimental mass
- */
- pappso::mz getDeltaMass() const;
-
- ValidationState getValidationState() const;
/** @brief tells if this peptide contains a protein position
* the position is the amino acid position on the protein sequence (starts from 0)
* */
bool containsPosition(unsigned int position) const;
+
+ void setPeptideEvidenceSp(PeptideEvidenceSp sp_peptide_evidence);
+ const PeptideEvidence * getPeptideEvidence() const;
+ PeptideEvidence * getPeptideEvidence();
private :
- static std::hash<std::string> _hash_fn;
- MsRun * _msrunid_sp;
- unsigned int _scan;
- size_t _hash_sample_scan;
- pappso::GrpPeptideSp _sp_grp_peptide;
- PeptideXtpSp _peptide_sp;
- pappso::pappso_double _rt;
- pappso::pappso_double _evalue=0;
- pappso::pappso_double _exp_mass;
unsigned int _start=0;
- unsigned int _charge;
- IdentificationDataSource* _p_identification_source = nullptr;
- std::map<PeptideMatchParam, QVariant> _params;
-
- /** @brief manually checked by user (true by default)
- */
- bool _checked = true;
-
- /** @brief automatic filter result (false by default)
- */
- bool _proxy_valid = false;
+ PeptideEvidence * _p_peptide_evidence=nullptr;
};
#endif // PEPTIDEMATCH_H
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index e4d0c66065d289ef68f1ac2aba57858097a6724e..4652c3edcbd02a97c07d2d8228b031a4d4ac33b8 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -74,7 +74,7 @@ public:
pappso::pappso_double getEmPAI(const MsRun * sp_msrun_id = nullptr) const;
void setProteinXtpSp(ProteinXtpSp protein_sp);
- void addPeptideMatchSp(PeptideMatchSp peptide_match);
+ void addPeptideMatch(const PeptideMatch & peptide_match);
std::vector<PeptideMatch *> & getPeptideMatchList();
const std::vector<PeptideMatch *> & getPeptideMatchList() const;
diff --git a/src/utils/peptidematchstore.cpp b/src/utils/peptideevidencestore.cpp
similarity index 79%
rename from src/utils/peptidematchstore.cpp
rename to src/utils/peptideevidencestore.cpp
index f2fbef9d23db3c0af8acd1d69ada99f871fe7c2e..1de93d17124eb44d42a6db76ab282597805592a6 100644
--- a/src/utils/peptidematchstore.cpp
+++ b/src/utils/peptideevidencestore.cpp
@@ -1,11 +1,12 @@
/**
- * \file utils/peptidematchstore.cpp
+ * \file utils/peptideevidencestore.cpp
* \date 18/11/2017
* \author Olivier Langella
- * \brief store unique instances of peptide match
+ * \brief store unique instances of peptide evidences
*/
+
/*******************************************************************************
* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
*
@@ -28,9 +29,9 @@
* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
******************************************************************************/
-#include "peptidematchstore.h"
+#include "peptideevidencestore.h"
-#include "../core/peptidematch.h"
+#include "../core/peptideevidence.h"
-std::shared_ptr<PeptideMatch> & PeptideMatchStore::getInstance(const PeptideMatch * p_peptide_match) {
+std::shared_ptr<PeptideEvidence> & PeptideEvidenceStore::getInstance(const PeptideEvidence * p_peptide_evidence) {
}
diff --git a/src/utils/peptidematchstore.h b/src/utils/peptideevidencestore.h
similarity index 77%
rename from src/utils/peptidematchstore.h
rename to src/utils/peptideevidencestore.h
index 912f17382144844351dfd6b709a3e771d31c200b..14727d03def2d7c807f3efba4ae10b202715cc5b 100644
--- a/src/utils/peptidematchstore.h
+++ b/src/utils/peptideevidencestore.h
@@ -1,8 +1,8 @@
/**
- * \file utils/peptidematchstore.h
+ * \file utils/peptideevidencestore.h
* \date 18/11/2017
* \author Olivier Langella
- * \brief store unique instances of peptide match
+ * \brief store unique instances of peptide evidences
*/
@@ -28,17 +28,17 @@
* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
******************************************************************************/
-#ifndef PEPTIDEMATCHSTORE_H
-#define PEPTIDEMATCHSTORE_H
+#ifndef PEPTIDEEVIDENCESTORE_H
+#define PEPTIDEEVIDENCESTORE_H
#include <memory>
-class PeptideMatch;
+class PeptideEvidence;
-class PeptideMatchStore
+class PeptideEvidenceStore
{
public:
- std::shared_ptr<PeptideMatch> & getInstance(const PeptideMatch * p_peptide_match);
+ std::shared_ptr<PeptideEvidence> & getInstance(const PeptideEvidence * p_peptide_evidence);
};
-#endif // PEPTIDEMATCHSTORE_H
+#endif // PEPTIDEEVIDENCESTORE_H