diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 88bd6083345d7c12e5b442119ebe69150e869631..2be9885af9288d4ccbd49068ffd6d724f77a834f 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -29,8 +29,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
#sudo apt-get install libpappsomspp-dev
#FIND_PACKAGE( Pappsomspp REQUIRED )
- SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
-# SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
+# SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
+ SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
@@ -69,6 +69,7 @@ SET(CPP_FILES
grouping/groupingpeptidemass.cpp
gui/peptide_detail_view/spectrum_widget/spectrumpainter.cpp
input/xpipsaxhandler.cpp
+ utils/identificationdatasourcestore.cpp
utils/groupstore.cpp
utils/peptidestore.cpp
utils/proteinstore.cpp
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index dfaa29727dd18da29867a2854d6d69564b086933..6341285c15b97ea46f0a671244211bb6d3538cac 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -26,14 +26,6 @@
#include <QFileInfo>
#include "../../utils/readspectrum.h"
-
-IdentificationDataSource::MapIdentificationDataSources IdentificationDataSource::_map_identification_data_sources = []
-{
- MapIdentificationDataSources ret;
-
- return ret;
-}();
-
IdentificationDataSource::IdentificationDataSource(const QString resource_name)
{
_resource_name = resource_name;
@@ -55,31 +47,6 @@ bool IdentificationDataSource::operator==(const IdentificationDataSource& other)
}
-void IdentificationDataSource::clear() {
- _map_identification_data_sources.clear();
-}
-
-IdentificationDataSource * IdentificationDataSource::getInstance(const QString & location) {
-
- std::map< QString, IdentificationDataSource* >::iterator it = IdentificationDataSource::_map_identification_data_sources.find(location);
- if (it != IdentificationDataSource::_map_identification_data_sources.end()) {
- return it->second;
- }
- else {
- QFileInfo location_file(location);
- QString ext = location_file.suffix();
- //QString sample_name = location_file.baseName();
- if (ext.toLower() == "xml") {
- //X!Tandem result file
- IdentificationXtandemFile * p_xtfile = new IdentificationXtandemFile(location_file);
- _map_identification_data_sources.insert(std::pair< QString, IdentificationDataSource* >(location, p_xtfile));
- _map_identification_data_sources.insert(std::pair< QString, IdentificationDataSource* >(location_file.absoluteFilePath(), p_xtfile));
- return p_xtfile;
- }
- }
- throw pappso::PappsoException(QObject::tr("Identification resource %1 not recognized").arg(location));
-}
-
const QString & IdentificationDataSource::getResourceName () const {
return _resource_name;
}
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index 4205c18d35bb7e61ad942e52283b15a64a533a62..eafcb169ea4892786b084b2c6516f6837dba30f7 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -26,17 +26,16 @@
#include <pappsomspp/msrun/msrunid.h>
#include <pappsomspp/spectrum/spectrum.h>
-#include <map>
+#include <memory>
+class IdentificationDataSource;
+typedef std::shared_ptr<IdentificationDataSource> IdentificationDataSourceSp;
+
class IdentificationDataSource
{
public:
- using MapIdentificationDataSources = std::map<QString, IdentificationDataSource *>;
- static void clear();
- static IdentificationDataSource * getInstance(const QString & location);
-
IdentificationDataSource(const QString resource_name);
IdentificationDataSource(const IdentificationDataSource& other);
~IdentificationDataSource();
@@ -53,7 +52,6 @@ public:
protected :
QString _resource_name;
private :
- static MapIdentificationDataSources _map_identification_data_sources;
//static std::map<QString, pappso::MsRunIdSp> _map_msrunidsp;
pappso::MsRunIdSp _ms_run_sp = nullptr;
};
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 6139b6d20d64075dfb72a1f8a90b7d06d0919328..5b41ef2d9dee01253d0fb17f570f17278287da4c 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -42,7 +42,7 @@ std::vector<IdentificationGroup *> Project::getIdentificationGroupList() {
return _identification_goup_list;
}
const GroupingType Project::getGroupingType() const {
- return _grouping_type;
+ return _grouping_type;
}
PeptideStore & Project::getPeptideStore() {
return _peptide_store;
@@ -51,6 +51,10 @@ PeptideStore & Project::getPeptideStore() {
ProteinStore & Project::getProteinStore() {
return _protein_store;
}
+
+IdentificationDataSourceStore & Project::getIdentificationDataSourceStore() {
+ return _identification_data_source_store;
+}
const AutomaticFilterParameters & Project::getAutomaticFilterParameters() const {
return _automatic_filter_parameters;
}
@@ -101,7 +105,7 @@ void Project::readXpipFile(QFileInfo xpip_fileinfo) {
}
IdentificationGroup* Project::getCurrentIdentificationGroupP() const {
-
+
qDebug() << "Project::getCurrentIdentificationGroupP begin " << _p_current_identification_group;
return _p_current_identification_group;
}
diff --git a/src/core/project.h b/src/core/project.h
index 880ac3e383bb019b09aea894b0b364d79f726d95..9fcb09358473e6fdc8292d9971c8ed6569e7c65e 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -29,6 +29,7 @@
#include "../utils/types.h"
#include "../utils/peptidestore.h"
#include "../utils/proteinstore.h"
+#include "../utils/identificationdatasourcestore.h"
class Project;
typedef std::shared_ptr<Project> ProjectSp;
@@ -45,6 +46,7 @@ public:
ProjectSp makeProjectSp() const;
ProteinStore & getProteinStore();
PeptideStore & getPeptideStore();
+ IdentificationDataSourceStore & getIdentificationDataSourceStore();
void readXpipFile(QFileInfo xpip_source);
IdentificationGroup* newIdentificationGroup();
IdentificationGroup* getCurrentIdentificationGroupP() const;
@@ -69,6 +71,7 @@ private :
ProteinStore _protein_store;
PeptideStore _peptide_store;
+ IdentificationDataSourceStore _identification_data_source_store;
};
#endif // PROJECT_H
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 6033fe6f5058681a1b058740ce95599593ed4a74..09c5e24807928e0654efb41a96ec1f2e7b9ec836 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -248,7 +248,7 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
_p_peptide_match->setCharge(attributes.value("charge").simplified().toUInt());
- IdentificationDataSource* p_identification_data_source = IdentificationDataSource::getInstance(attributes.value("sample_file").simplified());
+ IdentificationDataSource* p_identification_data_source = _p_project->getIdentificationDataSourceStore().getInstance(attributes.value("sample_file").simplified()).get();
_p_peptide_match->setIdentificationDataSource( p_identification_data_source);
if (p_identification_data_source->getMsRunSp().get() == nullptr) {
p_identification_data_source->setMsRunSp(ms_run_id);
@@ -340,7 +340,6 @@ bool XpipSaxHandler::endDocument() {
}
bool XpipSaxHandler::startDocument() {
- IdentificationDataSource::clear();
return true;
}
diff --git a/src/utils/identificationdatasourcestore.cpp b/src/utils/identificationdatasourcestore.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..04e37584f6c21368d278f256613b7b3f83768dd3
--- /dev/null
+++ b/src/utils/identificationdatasourcestore.cpp
@@ -0,0 +1,64 @@
+/**
+ * \file utils/identificationdatasourcestore.cpp
+ * \date 5/4/2017
+ * \author Olivier Langella
+ * \brief store unique version of identification data sources (output files from identification engines)
+ */
+
+
+/*******************************************************************************
+* 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 "identificationdatasourcestore.h"
+#include "../core/identification_sources/identificationxtandemfile.h"
+#include <pappsomspp/pappsoexception.h>
+
+IdentificationDataSourceStore::IdentificationDataSourceStore()
+{
+
+}
+
+IdentificationDataSourceStore::~IdentificationDataSourceStore()
+{
+
+}
+
+IdentificationDataSourceSp IdentificationDataSourceStore::getInstance(const QString & location) {
+
+ std::map< QString, IdentificationDataSourceSp >::iterator it = _map_identification_data_sources.find(location);
+ if (it != _map_identification_data_sources.end()) {
+ return it->second;
+ }
+ else {
+ QFileInfo location_file(location);
+ QString ext = location_file.suffix();
+ //QString sample_name = location_file.baseName();
+ if (ext.toLower() == "xml") {
+ //X!Tandem result file
+ IdentificationDataSourceSp p_xtfile = std::make_shared<IdentificationXtandemFile>(location_file);
+ _map_identification_data_sources.insert(std::pair< QString, IdentificationDataSourceSp >(location, p_xtfile));
+ _map_identification_data_sources.insert(std::pair< QString, IdentificationDataSourceSp >(location_file.absoluteFilePath(), p_xtfile));
+ return p_xtfile;
+ }
+ }
+ throw pappso::PappsoException(QObject::tr("Identification resource %1 not recognized").arg(location));
+}
diff --git a/src/utils/identificationdatasourcestore.h b/src/utils/identificationdatasourcestore.h
new file mode 100644
index 0000000000000000000000000000000000000000..60b2a6c22238ba1a141effbb94f40eea671e8749
--- /dev/null
+++ b/src/utils/identificationdatasourcestore.h
@@ -0,0 +1,48 @@
+/**
+ * \file utils/identificationdatasourcestore.h
+ * \date 5/4/2017
+ * \author Olivier Langella
+ * \brief store unique version of identification data sources (output files from identification engines)
+ */
+
+
+/*******************************************************************************
+* 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 IDENTIFICATIONDATASOURCESTORE_H
+#define IDENTIFICATIONDATASOURCESTORE_H
+
+#include <map>
+#include "../core/identification_sources/identificationdatasource.h"
+
+class IdentificationDataSourceStore
+{
+public:
+ IdentificationDataSourceStore();
+ ~IdentificationDataSourceStore();
+ IdentificationDataSourceSp getInstance(const QString & location);
+ void clear();
+private :
+ std::map<QString, IdentificationDataSourceSp> _map_identification_data_sources;
+};
+
+#endif // IDENTIFICATIONDATASOURCESTORE_H