From a4bb125bdad6fb4b69bd41e520b9d8aac9c4d177 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Wed, 5 Apr 2017 16:06:33 +0200
Subject: [PATCH] new ms run peptide store and msrun specific object
---
src/CMakeLists.txt | 6 +-
.../identificationdatasource.cpp | 6 +-
.../identificationdatasource.h | 8 +--
src/core/identificationgroup.cpp | 4 +-
src/core/identificationgroup.h | 8 +--
src/core/msrun.cpp | 63 +++++++++++++++++++
src/core/msrun.h | 59 +++++++++++++++++
src/core/peptidematch.cpp | 4 +-
src/core/peptidematch.h | 8 +--
src/core/project.cpp | 4 ++
src/core/project.h | 3 +
src/core/proteinmatch.cpp | 34 ++++------
src/core/proteinmatch.h | 17 ++---
src/grouping/groupinggroup.cpp | 4 +-
.../identificationgroupwidget.cpp | 2 +-
src/input/xpipsaxhandler.cpp | 18 +++---
src/input/xpipsaxhandler.h | 1 -
src/utils/identificationdatasourcestore.h | 1 -
src/utils/msrunstore.cpp | 57 +++++++++++++++++
src/utils/msrunstore.h | 49 +++++++++++++++
src/utils/readspectrum.cpp | 12 ++--
src/utils/readspectrum.h | 6 +-
22 files changed, 293 insertions(+), 81 deletions(-)
create mode 100644 src/core/msrun.cpp
create mode 100644 src/core/msrun.h
create mode 100644 src/utils/msrunstore.cpp
create mode 100644 src/utils/msrunstore.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 2be9885af..6d76e8269 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -55,14 +55,15 @@ configure_file (${CMAKE_SOURCE_DIR}/src/config.h.cmake ${CMAKE_SOURCE_DIR}/src/c
SET(CPP_FILES
core/automaticfilterparameters.cpp
core/identificationgroup.cpp
+ core/identification_sources/identificationdatasource.cpp
+ core/identification_sources/identificationxtandemfile.cpp
+ core/msrun.cpp
core/peptidematch.cpp
core/peptidextp.cpp
./core/project.cpp
core/proteinmatch.cpp
core/proteinxtp.cpp
core/sequencedatabase.cpp
- core/identification_sources/identificationdatasource.cpp
- core/identification_sources/identificationxtandemfile.cpp
files/xpipfile.cpp
grouping/groupingexperiment.cpp
grouping/groupinggroup.cpp
@@ -71,6 +72,7 @@ SET(CPP_FILES
input/xpipsaxhandler.cpp
utils/identificationdatasourcestore.cpp
utils/groupstore.cpp
+ utils/msrunstore.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 6341285c1..a90445286 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -56,15 +56,15 @@ const QString IdentificationDataSource::getSampleName () const {
return file.baseName();
}
-void IdentificationDataSource::setMsRunSp (pappso::MsRunIdSp ms_run_sp) {
+void IdentificationDataSource::setMsRunSp (MsRunSp ms_run_sp) {
_ms_run_sp = ms_run_sp;
}
-pappso::MsRunIdSp IdentificationDataSource::getMsRunSp () const {
+MsRunSp IdentificationDataSource::getMsRunSp () const {
return (_ms_run_sp);
}
pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const {
- pappso::SpectrumSp spectrum_sp = SpectrumStore::getSpectrumSpFromMsRunIdSp(_ms_run_sp, scan_number);
+ pappso::SpectrumSp spectrum_sp = SpectrumStore::getSpectrumSpFromMsRunSp(_ms_run_sp, scan_number);
return spectrum_sp;
}
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index eafcb169e..7f13e9593 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -24,9 +24,9 @@
#define IDENTIFICATIONDATASOURCE_H
-#include <pappsomspp/msrun/msrunid.h>
#include <pappsomspp/spectrum/spectrum.h>
#include <memory>
+#include "../msrun.h"
class IdentificationDataSource;
@@ -43,8 +43,8 @@ public:
const QString & getResourceName () const;
const QString getSampleName () const;
- void setMsRunSp (pappso::MsRunIdSp ms_run_sp);
- pappso::MsRunIdSp getMsRunSp () const;
+ void setMsRunSp (MsRunSp ms_run_sp);
+ MsRunSp getMsRunSp () const;
/** @brief get the spectrum with scan number
* */
virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const;
@@ -53,7 +53,7 @@ protected :
QString _resource_name;
private :
//static std::map<QString, pappso::MsRunIdSp> _map_msrunidsp;
- pappso::MsRunIdSp _ms_run_sp = nullptr;
+ MsRunSp _ms_run_sp = nullptr;
};
#endif // IDENTIFICATIONDATASOURCE_H
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 406c49d31..75e8d1c63 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -52,10 +52,10 @@ void IdentificationGroup::updateAutomaticFilters(const AutomaticFilterParameters
void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
_protein_match_list.push_back(protein_match);
}
-void IdentificationGroup::addMsRunIdSp(pappso::MsRunIdSp ms_run_sp) {
+void IdentificationGroup::addMsRunSp(MsRunSp ms_run_sp) {
_ms_run_list.push_back(ms_run_sp);
}
-const std::vector<pappso::MsRunIdSp> & IdentificationGroup::getMsRunIdSpList() const {
+const std::vector<MsRunSp> & IdentificationGroup::getMsRunSpList() const {
return _ms_run_list;
}
std::vector<ProteinMatch *> & IdentificationGroup::getProteinMatchList() {
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index cc8f03a5f..587bde926 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -23,7 +23,7 @@
#include <memory>
#include <QFileInfo>
#include "proteinmatch.h"
-#include <pappsomspp/msrun/msrunid.h>
+#include "msrun.h"
#include "grouping/groupingexperiment.h"
#include "../utils/types.h"
@@ -45,7 +45,7 @@ public:
void addProteinMatch(ProteinMatch * protein_match);
std::vector<ProteinMatch *> & getProteinMatchList();
- void addMsRunIdSp(pappso::MsRunIdSp ms_run_sp);
+ void addMsRunSp(MsRunSp ms_run_sp);
/** @brief count valid proteins
* */
@@ -74,7 +74,7 @@ public:
void startGrouping (const GroupingType & grouping_type);
- const std::vector<pappso::MsRunIdSp> & getMsRunIdSpList() const;
+ const std::vector<MsRunSp> & getMsRunSpList() const;
/** @brief get tab name for qtabwidget
* */
@@ -88,7 +88,7 @@ private :
std::vector<ProteinMatch *> _protein_match_list;
- std::vector<pappso::MsRunIdSp> _ms_run_list;
+ std::vector<MsRunSp> _ms_run_list;
};
#endif // IDENTIFICATIONGROUP_H
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
new file mode 100644
index 000000000..f5685957b
--- /dev/null
+++ b/src/core/msrun.cpp
@@ -0,0 +1,63 @@
+/**
+ * \filed core/msrun.cpp
+ * \date 5/4/2017
+ * \author Olivier Langella
+ * \brief describes an MS run (chemical sample injected in a mass spectrometer)
+ */
+
+
+/*******************************************************************************
+* 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 "msrun.h"
+#include <QFileInfo>
+
+MsRun::MsRun(const QString & location) {
+ _xml_id = location;
+ _location = location;
+ QFileInfo fileinfo(location);
+ _name = fileinfo.baseName();
+}
+
+MsRun::MsRun(const MsRun& other) {
+ _xml_id = other._xml_id;
+ _location = other._location;
+ _name = other._name;
+}
+
+MsRun::~MsRun() {
+}
+
+
+void MsRun::setFilename(const QString filename) {
+ _location = filename;
+}
+void MsRun::setXmlId(const QString xmlid) {
+ _xml_id = xmlid;
+}
+const QString & MsRun::getXmlId() const {
+ return _xml_id;
+}
+const QString & MsRun::getFilename() const {
+ return _location;
+}
diff --git a/src/core/msrun.h b/src/core/msrun.h
new file mode 100644
index 000000000..5262b2bea
--- /dev/null
+++ b/src/core/msrun.h
@@ -0,0 +1,59 @@
+/**
+ * \filed core/msrun.h
+ * \date 5/4/2017
+ * \author Olivier Langella
+ * \brief describes an MS run (chemical sample injected in a mass spectrometer)
+ */
+
+
+/*******************************************************************************
+* 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 MSRUN_H
+#define MSRUN_H
+
+#include <memory>
+#include <QString>
+
+class MsRun;
+typedef std::shared_ptr<MsRun> MsRunSp;
+
+class MsRun
+{
+public:
+ MsRun(const QString & location);
+ MsRun(const MsRun& other);
+ ~MsRun();
+
+ void setFilename(const QString filename);
+ void setXmlId(const QString xmlid);
+
+ const QString & getFilename() const;
+ const QString & getXmlId() const;
+private :
+ QString _xml_id;
+ QString _location;
+ QString _name;
+};
+
+#endif // MSRUN_H
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 12afc44b5..faba2b9a9 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -23,7 +23,7 @@
#include "peptidematch.h"
-PeptideMatch::PeptideMatch(pappso::MsRunIdSp msrunid_sp, unsigned int scan) {
+PeptideMatch::PeptideMatch(MsRun * msrunid_sp, unsigned int scan) {
_msrunid_sp = msrunid_sp;
_scan = scan;
}
@@ -109,7 +109,7 @@ const PeptideXtpSp & PeptideMatch::getPeptideXtpSp() const {
return _peptide_sp;
}
-const pappso::MsRunIdSp & PeptideMatch::getMsRunIdSp() const {
+const MsRun * PeptideMatch::getMsRunP() const {
return _msrunid_sp;
}
void PeptideMatch::setGrpPeptideSp(const pappso::GrpPeptideSp & sp_grp_peptide) {
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 3fd03a276..49c58b637 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -23,18 +23,18 @@
#ifndef PEPTIDEMATCH_H
#define PEPTIDEMATCH_H
-#include <pappsomspp/msrun/msrunid.h>
#include <pappsomspp/types.h>
#include "peptidextp.h"
#include "identification_sources/identificationdatasource.h"
#include "automaticfilterparameters.h"
+#include "msrun.h"
#include "../grouping/groupingexperiment.h"
class PeptideMatch
{
public :
- PeptideMatch(pappso::MsRunIdSp msrunid_sp, unsigned int scan);
+ PeptideMatch(MsRun * msrunid_sp, unsigned int scan);
void setRetentionTime(pappso::pappso_double rt);
void setEvalue(pappso::pappso_double evalue);
@@ -57,7 +57,7 @@ public :
bool isValidAndChecked() const;
bool isGrouped() const;
- const pappso::MsRunIdSp & getMsRunIdSp() const;
+ const MsRun * getMsRunP() const;
IdentificationDataSource* getIdentificationDataSource () const;
unsigned int getScan() const;
pappso::pappso_double getRetentionTime() const;
@@ -77,7 +77,7 @@ public :
pappso::mz getDeltaMass() const;
private :
- pappso::MsRunIdSp _msrunid_sp;
+ MsRun * _msrunid_sp;
unsigned int _scan;
pappso::GrpPeptideSp _sp_grp_peptide;
PeptideXtpSp _peptide_sp;
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 5b41ef2d9..b3fb2ea9f 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -44,6 +44,10 @@ std::vector<IdentificationGroup *> Project::getIdentificationGroupList() {
const GroupingType Project::getGroupingType() const {
return _grouping_type;
}
+
+MsRunStore & Project::getMsRunStore() {
+ return _msrun_store;
+}
PeptideStore & Project::getPeptideStore() {
return _peptide_store;
}
diff --git a/src/core/project.h b/src/core/project.h
index 9fcb09358..f00b2e41a 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -30,6 +30,7 @@
#include "../utils/peptidestore.h"
#include "../utils/proteinstore.h"
#include "../utils/identificationdatasourcestore.h"
+#include "../utils/msrunstore.h"
class Project;
typedef std::shared_ptr<Project> ProjectSp;
@@ -46,6 +47,7 @@ public:
ProjectSp makeProjectSp() const;
ProteinStore & getProteinStore();
PeptideStore & getPeptideStore();
+ MsRunStore & getMsRunStore();
IdentificationDataSourceStore & getIdentificationDataSourceStore();
void readXpipFile(QFileInfo xpip_source);
IdentificationGroup* newIdentificationGroup();
@@ -72,6 +74,7 @@ private :
ProteinStore _protein_store;
PeptideStore _peptide_store;
IdentificationDataSourceStore _identification_data_source_store;
+ MsRunStore _msrun_store;
};
#endif // PROJECT_H
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 091f7ac51..1b49536a9 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -22,7 +22,6 @@
******************************************************************************/
#include "proteinmatch.h"
-#include <pappsomspp/msrun/msrunid.h>
#include <pappsomspp/grouping/grpprotein.h>
#include <set>
@@ -66,14 +65,14 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
number_of_valid_peptides= countValidAndCheckedPeptide(nullptr);
}
else {
- std::set<const pappso::MsRunId *> msrun_set;
+ 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->getMsRunIdSp().get());
+ msrun_set.insert(p_peptide_match->getMsRunP());
}
}
- for (const pappso::MsRunId * p_msrun : msrun_set) {
+ for (const MsRun * p_msrun : msrun_set) {
unsigned int count = countValidAndCheckedPeptide(p_msrun);
if (count > number_of_valid_peptides) {
number_of_valid_peptides = count;
@@ -104,10 +103,6 @@ void ProteinMatch::setEvalue(pappso::pappso_double evalue) {
_evalue = evalue;
}
-pappso::pappso_double ProteinMatch::getEvalue() const {
- pappso::MsRunIdSp sp_msrun_id;
- return getEvalue(sp_msrun_id);
-}
void ProteinMatch::setProteinXtpSp(ProteinXtpSp protein_sp) {
_protein_sp = protein_sp;
}
@@ -195,13 +190,13 @@ size_t ProteinMatch::countUniqueSequence()const {
return sequence_list.size();
}
-unsigned int ProteinMatch::countValidAndCheckedPeptide(const pappso::MsRunId * p_msrun_id) const {
+unsigned int ProteinMatch::countValidAndCheckedPeptide(const MsRun * p_msrun_id) const {
std::set<QString> sequence_list;
for (auto & p_peptide_match : _peptide_match_list) {
if (p_peptide_match->isValidAndChecked()) {
if(p_msrun_id != nullptr) {
//within sample
- if (p_peptide_match->getMsRunIdSp().get() == p_msrun_id) {
+ if (p_peptide_match->getMsRunP() == p_msrun_id) {
sequence_list.insert(p_peptide_match->getPeptideXtpSp().get()->getSequenceLi());
}
}
@@ -215,13 +210,13 @@ unsigned int ProteinMatch::countValidAndCheckedPeptide(const pappso::MsRunId * p
return sequence_list.size();
}
-unsigned int ProteinMatch::countValidAndCheckedPeptideMassCharge(const pappso::MsRunIdSp & sp_msrun_id) const {
+unsigned int ProteinMatch::countValidAndCheckedPeptideMassCharge(const MsRun * sp_msrun_id) const {
std::set<QString> sequence_list;
for (auto & p_peptide_match : _peptide_match_list) {
if (p_peptide_match->isValidAndChecked()) {
- if(sp_msrun_id.get() != nullptr) {
+ if(sp_msrun_id != nullptr) {
//within sample
- if (p_peptide_match->getMsRunIdSp().get() == sp_msrun_id.get()) {
+ if (p_peptide_match->getMsRunP() == sp_msrun_id) {
sequence_list.insert(QString("%1-%2").arg(p_peptide_match->getPeptideXtpSp().get()->toAbsoluteString()).arg(p_peptide_match->getCharge()));
}
}
@@ -234,15 +229,15 @@ unsigned int ProteinMatch::countValidAndCheckedPeptideMassCharge(const pappso::M
return sequence_list.size();
}
-pappso::pappso_double ProteinMatch::getEvalue(const pappso::MsRunIdSp & sp_msrun_id) const {
+pappso::pappso_double ProteinMatch::getEvalue(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();
- if(sp_msrun_id.get() != nullptr) {
+ if(sp_msrun_id != nullptr) {
//within sample
- if (p_peptide_match->getMsRunIdSp().get() == sp_msrun_id.get()) {
+ if (p_peptide_match->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
@@ -274,12 +269,7 @@ pappso::pappso_double ProteinMatch::getEvalue(const pappso::MsRunIdSp & sp_msrun
}
-pappso::pappso_double ProteinMatch::getPAI() const {
- pappso::MsRunIdSp sp_msrun_id;
- return getPAI(sp_msrun_id);
-}
-
-pappso::pappso_double ProteinMatch::getPAI(const pappso::MsRunIdSp & sp_msrun_id) const {
+pappso::pappso_double ProteinMatch::getPAI(const MsRun * sp_msrun_id) const {
pappso::pappso_double PAI = (pappso::pappso_double) countValidAndCheckedPeptideMassCharge(sp_msrun_id) / (pappso::pappso_double) _protein_sp.get()->countTrypticPeptidesForPAI();
return PAI;
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index c26932481..dfce9d760 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -46,13 +46,9 @@ public:
const ProteinXtpSp & getProteinXtpSp() const;
void setEvalue(pappso::pappso_double evalue);
- /** @brief compute protein Evalue overall samples
- * */
- pappso::pappso_double getEvalue() const;
-
/** @brief compute protein Evalue within samples
* */
- pappso::pappso_double getEvalue(const pappso::MsRunIdSp & sp_msrun_id) const;
+ pappso::pappso_double getEvalue(const MsRun * sp_msrun_id = nullptr) const;
/** @brief protein coverage overall samples
@@ -64,15 +60,10 @@ public:
**/
const QString getHtmlSequence(PeptideMatch * peptide_match_to_locate = nullptr) const;
- /** @brief compute Protein Abundance Index (PAI)
- * overall sample PAI computation (Rappsilber et al. 2002)
- * */
- pappso::pappso_double getPAI() const;
-
/** @brief compute Protein Abundance Index (PAI) within sample
* PAI computation (Rappsilber et al. 2002)
* */
- pappso::pappso_double getPAI(const pappso::MsRunIdSp & sp_msrun_id) const;
+ pappso::pappso_double getPAI(const MsRun * sp_msrun_id = nullptr) const;
void setProteinXtpSp(ProteinXtpSp protein_sp);
void addPeptideMatch(PeptideMatch * peptide_match);
@@ -114,8 +105,8 @@ protected :
void setGroupInstance(GroupStore & group_store);
private :
- unsigned int countValidAndCheckedPeptide(const pappso::MsRunId * p_msrun_id) const;
- unsigned int countValidAndCheckedPeptideMassCharge(const pappso::MsRunIdSp & sp_msrun_id) const;
+ unsigned int countValidAndCheckedPeptide(const MsRun * p_msrun_id) const;
+ unsigned int countValidAndCheckedPeptideMassCharge(const MsRun * sp_msrun_id) const;
private:
static QColor _color_peptide_background;
diff --git a/src/grouping/groupinggroup.cpp b/src/grouping/groupinggroup.cpp
index 702aea18b..b414e3208 100644
--- a/src/grouping/groupinggroup.cpp
+++ b/src/grouping/groupinggroup.cpp
@@ -81,14 +81,14 @@ std::size_t GroupingGroup::countSpecificSpectrum(const ProteinMatch * p_protein_
std::set<QString> spectrum_list_in;
for (auto && p_peptide_match :p_protein_match->getPeptideMatchList()) {
if (p_peptide_match->isValidAndChecked()) {
- spectrum_list_in.insert(QString("%1-%2").arg(p_peptide_match->getMsRunIdSp().get()->getXmlId()).arg(p_peptide_match->getScan()));
+ spectrum_list_in.insert(QString("%1-%2").arg(p_peptide_match->getMsRunP()->getXmlId()).arg(p_peptide_match->getScan()));
}
}
std::set<QString> spectrum_list_out;
unsigned int sg_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
for (auto && pair_peptide_match :_pair_sg_number_peptide_match_list) {
if (pair_peptide_match.first != sg_number) {
- spectrum_list_out.insert(QString("%1-%2").arg(pair_peptide_match.second->getMsRunIdSp().get()->getXmlId()).arg(pair_peptide_match.second->getScan()));
+ spectrum_list_out.insert(QString("%1-%2").arg(pair_peptide_match.second->getMsRunP()->getXmlId()).arg(pair_peptide_match.second->getScan()));
}
}
diff --git a/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp b/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
index 3ffc648df..8fb21db15 100644
--- a/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
+++ b/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
@@ -63,7 +63,7 @@ void IdentificationGroupWidget::doViewProteinList() {
void IdentificationGroupWidget::doIdentificationGroupGrouped(IdentificationGroup * p_identification_group) {
if (_p_identification_group == p_identification_group) {
- vector< pappso::MsRunIdSp > ms_run_list = _p_identification_group->getMsRunIdSpList();
+ vector< MsRunSp > ms_run_list = _p_identification_group->getMsRunSpList();
ui->sample_number_display->setText(QString("%1").arg(ms_run_list.size()));
ui->group_number_display->setText(QString("%1").arg(_p_identification_group->countGroup()));
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 09c5e2480..fc4057431 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -21,7 +21,6 @@
******************************************************************************/
#include "xpipsaxhandler.h"
-#include <pappsomspp/msrun/msrunid.h>
#include <pappsomspp/exception/exceptionnotfound.h>
#include <cmath>
#include "../utils/peptidestore.h"
@@ -181,14 +180,11 @@ bool XpipSaxHandler::startElement_modifs_mass(QXmlAttributes attributes) {
bool XpipSaxHandler::startElement_sample(QXmlAttributes attributes) {
qDebug() << "startElement_sample ";
- pappso::MsRunId ms_run;
- ms_run.setXmlId(attributes.value("value").simplified());
- ms_run.setFilename(attributes.value("value").simplified());
-
- pappso::MsRunIdSp msrunid_sp = ms_run.makeMsRunIdSp();
- _current_identification_group_p->addMsRunIdSp(msrunid_sp);
-
- _map_msrunid[ms_run.getXmlId()] = msrunid_sp;
+
+ MsRunSp ms_run = _p_project->getMsRunStore().getInstance(attributes.value("value").simplified());
+ ms_run.get()->setXmlId(attributes.value("value").simplified());
+ ms_run.get()->setFilename(attributes.value("value").simplified());
+ _current_identification_group_p->addMsRunSp(ms_run);
qDebug() << "startElement_sample end" ;
return true;
}
@@ -237,8 +233,8 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
//</modifs>
qDebug() << "startElement_peptide ";
_current_peptide_sp = PeptideXtp(attributes.value("sequence").simplified()).makePeptideXtpSp();
- pappso::MsRunIdSp ms_run_id = _map_msrunid[attributes.value("sample").simplified()];
- _p_peptide_match = new PeptideMatch(ms_run_id, attributes.value("scan").simplified().toUInt());
+ 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());
pappso::pappso_double exp_mass = attributes.value("mhplus_obser").simplified().toDouble() - pappso::MHPLUS;
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
index f3f0ed5c9..dc172caa0 100644
--- a/src/input/xpipsaxhandler.h
+++ b/src/input/xpipsaxhandler.h
@@ -87,7 +87,6 @@ private:
IdentificationGroup * _current_identification_group_p;
QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
- QMap<QString, pappso::MsRunIdSp> _map_msrunid;
};
#endif // XTANDEMRESULTSHANDLER_H
diff --git a/src/utils/identificationdatasourcestore.h b/src/utils/identificationdatasourcestore.h
index 60b2a6c22..cfef38ee8 100644
--- a/src/utils/identificationdatasourcestore.h
+++ b/src/utils/identificationdatasourcestore.h
@@ -40,7 +40,6 @@ public:
IdentificationDataSourceStore();
~IdentificationDataSourceStore();
IdentificationDataSourceSp getInstance(const QString & location);
- void clear();
private :
std::map<QString, IdentificationDataSourceSp> _map_identification_data_sources;
};
diff --git a/src/utils/msrunstore.cpp b/src/utils/msrunstore.cpp
new file mode 100644
index 000000000..1fee9ca9e
--- /dev/null
+++ b/src/utils/msrunstore.cpp
@@ -0,0 +1,57 @@
+/**
+ * \file utils/msrunstore.cpp
+ * \date 5/4/2017
+ * \author Olivier Langella
+ * \brief store unique version of msrun references (filename, sample name...)
+ */
+
+
+/*******************************************************************************
+* 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 "msrunstore.h"
+#include <pappsomspp/exception/exceptionnotfound.h>
+
+MsRunStore::MsRunStore()
+{
+
+}
+
+MsRunStore::~MsRunStore()
+{
+
+}
+
+MsRunSp MsRunStore::getInstance(const QString & location) {
+
+ std::map< QString, MsRunSp >::iterator it = _map_msrun.find(location);
+ if (it != _map_msrun.end()) {
+ return it->second;
+ }
+ else {
+ MsRunSp p_xtfile = std::make_shared<MsRun>(location);
+ _map_msrun.insert(std::pair< QString, MsRunSp >(location, p_xtfile));
+ return p_xtfile;
+
+ }
+ throw pappso::ExceptionNotFound(QObject::tr("Ms resource %1 not found").arg(location));
+}
diff --git a/src/utils/msrunstore.h b/src/utils/msrunstore.h
new file mode 100644
index 000000000..27e6df6f2
--- /dev/null
+++ b/src/utils/msrunstore.h
@@ -0,0 +1,49 @@
+/**
+ * \file utils/msrunstore.h
+ * \date 5/4/2017
+ * \author Olivier Langella
+ * \brief store unique version of msrun references (filename, sample name...)
+ */
+
+
+/*******************************************************************************
+* 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 MSRUNSTORE_H
+#define MSRUNSTORE_H
+
+#include <QString>
+#include <map>
+#include "../core/msrun.h"
+
+class MsRunStore
+{
+public:
+ MsRunStore();
+ ~MsRunStore();
+
+ MsRunSp getInstance(const QString & location);
+private:
+ std::map<QString, MsRunSp> _map_msrun;
+};
+
+#endif // MSRUNSTORE_H
diff --git a/src/utils/readspectrum.cpp b/src/utils/readspectrum.cpp
index 0d6d8c33c..5708eb5c6 100644
--- a/src/utils/readspectrum.cpp
+++ b/src/utils/readspectrum.cpp
@@ -221,13 +221,13 @@ Spectrum readSpectrum(const QString & filename, unsigned int scan_num, unsigned
}
-std::map<pappso::MsRunIdSp, pwiz::msdata::MSDataFile *> create_map()
+std::map<MsRunSp, pwiz::msdata::MSDataFile *> create_map()
{
- std::map<pappso::MsRunIdSp, pwiz::msdata::MSDataFile *> m;
+ std::map<MsRunSp, pwiz::msdata::MSDataFile *> m;
return m;
}
-std::map<pappso::MsRunIdSp, pwiz::msdata::MSDataFile *> SpectrumStore::_map_msrun_msdatafile = create_map();
+std::map<MsRunSp, pwiz::msdata::MSDataFile *> SpectrumStore::_map_msrun_msdatafile = create_map();
const QString SpectrumStore::findMzFile(const QString &filename) {
@@ -262,10 +262,10 @@ const QString SpectrumStore::findMzFile(const QString &filename) {
return QString();
}
-pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunIdSp(pappso::MsRunIdSp msrun, unsigned int scan_num) {
+pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRunSp msrun, unsigned int scan_num) {
pappso::SpectrumSp spectrum;
pwiz::msdata::MSDataFile * p_msdatafile = nullptr;
- std::map<pappso::MsRunIdSp, pwiz::msdata::MSDataFile *>::iterator it_msdata = _map_msrun_msdatafile.find(msrun);
+ std::map<MsRunSp, pwiz::msdata::MSDataFile *>::iterator it_msdata = _map_msrun_msdatafile.find(msrun);
if (it_msdata == _map_msrun_msdatafile.end()) {
//not found
@@ -276,7 +276,7 @@ pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunIdSp(pappso::MsRunIdSp m
//return spectrum;
}
p_msdatafile = getPwizMSDataFile(mz_file);
- _map_msrun_msdatafile.insert(std::pair<pappso::MsRunIdSp, pwiz::msdata::MSDataFile *>(msrun, p_msdatafile));
+ _map_msrun_msdatafile.insert(std::pair<MsRunSp, pwiz::msdata::MSDataFile *>(msrun, p_msdatafile));
}
else {
p_msdatafile =it_msdata->second;
diff --git a/src/utils/readspectrum.h b/src/utils/readspectrum.h
index 919f7bd80..89eee5bf7 100644
--- a/src/utils/readspectrum.h
+++ b/src/utils/readspectrum.h
@@ -26,9 +26,9 @@
#include <QString>
#include <pappsomspp/spectrum/spectrum.h>
-#include <pappsomspp/msrun/msrunid.h>
#include <pwiz/data/msdata/MSDataFile.hpp>
#include <map>
+#include "../core/msrun.h"
pappso::Spectrum readSpectrum(const QString & filename, unsigned int scan_num,unsigned int & precursor_charge_state);
@@ -38,10 +38,10 @@ pappso::SpectrumSp getSpectrumSpFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_
class SpectrumStore {
public:
- static pappso::SpectrumSp getSpectrumSpFromMsRunIdSp(pappso::MsRunIdSp msrun, unsigned int scan_num);
+ static pappso::SpectrumSp getSpectrumSpFromMsRunSp(MsRunSp msrun, unsigned int scan_num);
private:
static const QString findMzFile(const QString &filename);
private:
- static std::map<pappso::MsRunIdSp, pwiz::msdata::MSDataFile *> _map_msrun_msdatafile;
+ static std::map<MsRunSp, pwiz::msdata::MSDataFile *> _map_msrun_msdatafile;
};
#endif // READSPECTRUM_H
--
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