From acb5d43688011389e09a3d78c2e17410225ca022 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sat, 18 Nov 2017 11:21:43 +0100
Subject: [PATCH] WIP: new peptide match store object
---
src/CMakeLists.txt | 1 +
.../identificationdatasource.cpp | 5 ++-
.../identificationdatasource.h | 5 +++
src/core/peptidematch.cpp | 4 ++
src/core/peptidematch.h | 6 ++-
src/core/proteinmatch.cpp | 10 ++---
src/core/proteinmatch.h | 2 +-
src/input/identificationpwizreader.cpp | 5 ++-
src/input/xpipsaxhandler.cpp | 4 +-
src/input/xtandemsaxhandler.cpp | 6 ++-
src/utils/peptidematchstore.cpp | 36 +++++++++++++++
src/utils/peptidematchstore.h | 44 +++++++++++++++++++
12 files changed, 113 insertions(+), 15 deletions(-)
create mode 100644 src/utils/peptidematchstore.cpp
create mode 100644 src/utils/peptidematchstore.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index f7b3c632b..7a1be53fa 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -106,6 +106,7 @@ SET(CPP_FILES
utils/identificationdatasourcestore.cpp
utils/groupstore.cpp
utils/msrunstore.cpp
+ utils/peptidematchstore.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 ca74c0739..d300871d2 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -27,7 +27,6 @@
#include <QFileInfo>
#include "../../utils/readspectrum.h"
-
IdentificationDataSource::IdentificationDataSource(const QString resource_name)
{
_resource_name = resource_name;
@@ -45,6 +44,10 @@ IdentificationDataSource::~IdentificationDataSource()
}
+PeptideMatchStore & IdentificationDataSource::getPeptideMatchStore() {
+ return _peptide_match_store;
+}
+
void IdentificationDataSource::setXmlId(const QString xmlid) {
_xml_id = xmlid;
}
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index 7d23ac482..de98f146b 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -29,12 +29,14 @@
#include <QVariant>
#include "../msrun.h"
#include "../../utils/fastafilestore.h"
+#include "../../utils/peptidematchstore.h"
class Project;
class IdentificationDataSource;
typedef std::shared_ptr<IdentificationDataSource> IdentificationDataSourceSp;
+
class IdentificationDataSource
{
public:
@@ -44,6 +46,7 @@ public:
~IdentificationDataSource();
bool operator==(const IdentificationDataSource& other) const;
+ PeptideMatchStore & getPeptideMatchStore();
void setXmlId(const QString xmlid);
const QString & getXmlId() const;
@@ -118,6 +121,8 @@ private :
std::map<IdentificationEngineParam, QVariant> _params;
std::map<IdentificationEngineStatistics, QVariant> _param_stats;
std::vector<FastaFileSp> _fastafile_list;
+
+ PeptideMatchStore _peptide_match_store;
};
#endif // IDENTIFICATIONDATASOURCE_H
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 4e51d36a7..ad0938af0 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -49,6 +49,10 @@ PeptideMatch::PeptideMatch(const PeptideMatch & other): PeptideMatch(other._msru
}
+PeptideMatchSp PeptideMatch::makePeptideMatchSp() const {
+ return std::make_shared<PeptideMatch>(*this);
+}
+
void PeptideMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
_proxy_valid = false;
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 2ae750d44..2f28bfe01 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -45,6 +45,8 @@ public :
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);
@@ -72,7 +74,7 @@ public :
/** \brief get specific parameter value
*/
virtual const QVariant getParam(PeptideMatchParam param) const;
-
+
const std::map<PeptideMatchParam, QVariant> & getParamList() const;
@@ -118,7 +120,7 @@ public :
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)
* */
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 4400d062c..37795b3f7 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -39,12 +39,8 @@ ProteinMatch::ProteinMatch()
ProteinMatch::~ProteinMatch()
{
- auto it = _peptide_match_list.begin();
- while (it != _peptide_match_list.end()) {
- delete (*it);
- it++;
- }
}
+
ValidationState ProteinMatch::getValidationState() const {
if (isGrouped()) {
return ValidationState::grouped;
@@ -141,8 +137,8 @@ bool ProteinMatch::isGrouped() const {
void ProteinMatch::setChecked(bool arg1) {
_checked = arg1;
}
-void ProteinMatch::addPeptideMatch(PeptideMatch * peptide_match) {
- _peptide_match_list.push_back(peptide_match);
+void ProteinMatch::addPeptideMatchSp(PeptideMatchSp peptide_match) {
+ _peptide_match_list.push_back(peptide_match.get());
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 01717dd4e..e4d0c6606 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 addPeptideMatch(PeptideMatch * peptide_match);
+ void addPeptideMatchSp(PeptideMatchSp peptide_match);
std::vector<PeptideMatch *> & getPeptideMatchList();
const std::vector<PeptideMatch *> & getPeptideMatchList() const;
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index 3f271316b..bfa3a3097 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -278,7 +278,10 @@ void IdentificationPwizReader::read(
}
ProteinMatch * protein_match_p = it->second;
- protein_match_p->addPeptideMatch(p_peptide_match_from_evidence);
+ 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);
}
delete p_peptide_match;
}
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index a5b4cd840..9c580c962 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -279,7 +279,6 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
if (attributes.value("validate").simplified().toLower() == "true") {
_p_peptide_match->setChecked(true);
}
- _p_protein_match->addPeptideMatch(_p_peptide_match);
qDebug() << "startElement_peptide end" ;
return true;
}
@@ -296,10 +295,11 @@ bool XpipSaxHandler::startElement_modif(QXmlAttributes attributes) {
}
bool XpipSaxHandler::endElement_peptide() {
qDebug() << "endElement_peptide ";
-
PeptideXtpSp peptide_const = PeptideXtp(*(_current_peptide_sp.get())).makePeptideXtpSp();
peptide_const = _p_project->getPeptideStore().getInstance(peptide_const);
_p_peptide_match->setPeptideXtpSp(peptide_const);
+ _p_protein_match->addPeptideMatchSp(_p_peptide_match->getIdentificationDataSource()->getPeptideMatchStore().getInstance(_p_peptide_match));
+ delete _p_peptide_match;
return true;
}
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index 396dba158..d1cdd2fcd 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -303,7 +303,6 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
_p_peptide_match->setIdentificationDataSource( _p_identification_data_source);
_p_peptide_match->setChecked(true);
- _p_protein_match->addPeptideMatch(_p_peptide_match);
@@ -331,6 +330,11 @@ bool XtandemSaxHandler::endElement_domain() {
_current_peptide_sp = _p_project->getPeptideStore().getInstance(_current_peptide_sp);
_p_peptide_match->setPeptideXtpSp(_current_peptide_sp);
+
+
+ _p_protein_match->addPeptideMatchSp(_p_peptide_match->getIdentificationDataSource()->getPeptideMatchStore().getInstance(_p_peptide_match));
+
+ delete _p_peptide_match;
return is_ok;
}
bool XtandemSaxHandler::endElement_note() {
diff --git a/src/utils/peptidematchstore.cpp b/src/utils/peptidematchstore.cpp
new file mode 100644
index 000000000..f2fbef9d2
--- /dev/null
+++ b/src/utils/peptidematchstore.cpp
@@ -0,0 +1,36 @@
+/**
+ * \file utils/peptidematchstore.cpp
+ * \date 18/11/2017
+ * \author Olivier Langella
+ * \brief store unique instances of peptide match
+ */
+
+
+/*******************************************************************************
+* 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 "peptidematchstore.h"
+
+#include "../core/peptidematch.h"
+
+std::shared_ptr<PeptideMatch> & PeptideMatchStore::getInstance(const PeptideMatch * p_peptide_match) {
+}
diff --git a/src/utils/peptidematchstore.h b/src/utils/peptidematchstore.h
new file mode 100644
index 000000000..912f17382
--- /dev/null
+++ b/src/utils/peptidematchstore.h
@@ -0,0 +1,44 @@
+/**
+ * \file utils/peptidematchstore.h
+ * \date 18/11/2017
+ * \author Olivier Langella
+ * \brief store unique instances of peptide match
+ */
+
+
+/*******************************************************************************
+* 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 PEPTIDEMATCHSTORE_H
+#define PEPTIDEMATCHSTORE_H
+
+#include <memory>
+
+class PeptideMatch;
+
+class PeptideMatchStore
+{
+public:
+ std::shared_ptr<PeptideMatch> & getInstance(const PeptideMatch * p_peptide_match);
+};
+
+#endif // PEPTIDEMATCHSTORE_H
--
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