From abeb33e9acd43d9f75ab0b677d13091d4ccc7a29 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Sun, 23 Apr 2017 14:36:26 +0200
Subject: [PATCH] better assign pointer first...
---
.../identificationdatasource.cpp | 5 ++-
.../identificationdatasource.h | 3 +-
src/core/project.cpp | 3 ++
src/core/project.h | 2 ++
src/core/proteinmatch.cpp | 6 ++--
src/files/fastafile.cpp | 15 +++-----
src/files/fastafile.h | 4 +--
src/gui/mainwindow.cpp | 3 ++
src/gui/project_view/projectwindow.cpp | 8 +++--
src/gui/project_view/projectwindow.h | 2 +-
src/input/xpipsaxhandler.cpp | 2 ++
src/input/xpipsaxhandler.h | 1 +
src/input/xtandemsaxhandler.cpp | 4 +--
src/utils/fastafilestore.cpp | 36 ++++++++++---------
src/utils/fastafilestore.h | 5 ++-
src/utils/identificationdatasourcestore.cpp | 14 --------
src/utils/identificationdatasourcestore.h | 2 --
17 files changed, 54 insertions(+), 61 deletions(-)
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index 4e377f01d..0e0780733 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -26,7 +26,6 @@
#include <QFileInfo>
#include "../../utils/readspectrum.h"
-FastaFileStore IdentificationDataSource::_fasta_file_store;
IdentificationDataSource::IdentificationDataSource(const QString resource_name)
{
@@ -83,8 +82,8 @@ pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_num
return spectrum_sp;
}
-void IdentificationDataSource::addFastaFile (FastaFile file) {
- _fastafile_list.push_back(IdentificationDataSource::_fasta_file_store.getInstance(file));
+void IdentificationDataSource::addFastaFile (FastaFileSp file) {
+ _fastafile_list.push_back(file);
}
const std::vector<FastaFileSp> & IdentificationDataSource::getFastaFileList() const {
qDebug()<< "IdentificationDataSource::getFastaFileList begin" << _fastafile_list.size();
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index f5a7d0e88..efb09f341 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -73,7 +73,7 @@ public:
/** \brief add Fastafile used by the identification engine
*/
- void addFastaFile (FastaFile file);
+ void addFastaFile (FastaFileSp file);
const std::vector<FastaFileSp> & getFastaFileList() const;
@@ -82,7 +82,6 @@ protected :
IdentificationEngine _engine = IdentificationEngine::unknown;
private :
//static std::map<QString, pappso::MsRunIdSp> _map_msrunidsp;
- static FastaFileStore _fasta_file_store;
QString _version;
MsRunSp _ms_run_sp = nullptr;
std::map<IdentificationEngineParam, QString> _params;
diff --git a/src/core/project.cpp b/src/core/project.cpp
index be9f6dde3..e4d78b800 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -65,6 +65,9 @@ const GroupingType Project::getGroupingType() const {
return _grouping_type;
}
+FastaFileStore & Project::getFastaFileStore() {
+ return _fasta_file_store;
+}
MsRunStore & Project::getMsRunStore() {
return _msrun_store;
}
diff --git a/src/core/project.h b/src/core/project.h
index 5f454f404..73a8b06b8 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -48,6 +48,7 @@ public:
ProteinStore & getProteinStore();
PeptideStore & getPeptideStore();
MsRunStore & getMsRunStore();
+ FastaFileStore & getFastaFileStore();
IdentificationDataSourceStore & getIdentificationDataSourceStore();
void readXpipFile(QFileInfo xpip_source);
IdentificationGroup* newIdentificationGroup();
@@ -83,6 +84,7 @@ private :
PeptideStore _peptide_store;
IdentificationDataSourceStore _identification_data_source_store;
MsRunStore _msrun_store;
+ FastaFileStore _fasta_file_store;
};
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 9265c6292..d44f1fe72 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -62,7 +62,7 @@ bool ProteinMatch::contains(PeptideMatch * peptide_match) const {
}
void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
- qDebug() <<"ProteinMatch::updateAutomaticFilters begin " ;
+ //qDebug() <<"ProteinMatch::updateAutomaticFilters begin " ;
_proxy_valid = false;
unsigned int number_of_valid_peptides =0;
bool cross_sample = automatic_filter_parameters.getFilterCrossSamplePeptideNumber();
@@ -102,7 +102,7 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
}
}
}
- qDebug() <<"ProteinMatch::updateAutomaticFilters end " << number_of_valid_peptides ;
+ //qDebug() <<"ProteinMatch::updateAutomaticFilters end " << number_of_valid_peptides ;
}
const ProteinXtpSp & ProteinMatch::getProteinXtpSp() const {
@@ -213,7 +213,7 @@ unsigned int ProteinMatch::countSequenceLi(ValidationState state, const MsRun *
}
}
}
- qDebug() <<"ProteinMatch::countValidAndCheckedPeptide end " << sequence_list.size();
+ //qDebug() <<"ProteinMatch::countValidAndCheckedPeptide end " << sequence_list.size();
return sequence_list.size();
}
diff --git a/src/files/fastafile.cpp b/src/files/fastafile.cpp
index aa6694508..2ac6b0dac 100644
--- a/src/files/fastafile.cpp
+++ b/src/files/fastafile.cpp
@@ -27,7 +27,7 @@ FastaFile::FastaFile(const QString & fasta_source) : _fasta_source(fasta_source)
{
}
-FastaFile::FastaFile(const QFileInfo & fasta_source): _fasta_source(fasta_source.absoluteFilePath())
+FastaFile::FastaFile(const QFileInfo & fasta_source): _fasta_source(fasta_source)
{
}
FastaFile::FastaFile(const FastaFile & other) : _fasta_source(other._fasta_source)
@@ -39,15 +39,10 @@ FastaFile::~FastaFile()
}
-bool FastaFile::operator<( const FastaFile& other ) const
-{
- return (_fasta_source.absoluteFilePath() < other._fasta_source.absoluteFilePath());
-}
-bool FastaFile::operator==( const FastaFile& other ) const
-{
- return (_fasta_source == other._fasta_source);
-}
-
const QString FastaFile::getFilename() const {
return _fasta_source.fileName();
}
+
+const QString FastaFile::getAbsoluteFilePath() const {
+ return _fasta_source.absoluteFilePath();
+}
diff --git a/src/files/fastafile.h b/src/files/fastafile.h
index 263bf587d..1ba908272 100644
--- a/src/files/fastafile.h
+++ b/src/files/fastafile.h
@@ -38,10 +38,10 @@ public:
FastaFile(const FastaFile & other);
~FastaFile();
- bool operator<( const FastaFile& other ) const;
- bool operator==( const FastaFile& other ) const;
const QString getFilename() const;
+ const QString getAbsoluteFilePath() const;
+
private :
const QFileInfo _fasta_source;
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index b6b27e378..496fb71d9 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -219,7 +219,10 @@ void MainWindow::doProjectReady(ProjectSp project_sp) {
qDebug() << "MainWindow::doProjectReady begin";
try {
+ qDebug() << "MainWindow::doProjectReady begin a " << project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
_project_sp = project_sp;
+
+ qDebug() << "MainWindow::doProjectReady begin b " << _project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
doDisplayLoadingMessage(tr("grouping proteins"));
project_sp.get()->startGrouping();
doDisplayLoadingMessage(tr("grouping proteins finished"));
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 7e6294f1b..780eaa948 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -346,8 +346,12 @@ void ProjectWindow::doViewProteinList(IdentificationGroup* p_identification_grou
}
void ProjectWindow::setProjectSp(ProjectSp project_sp) {
+ qDebug() << "ProjectWindow::setProjectSp begin" ;
- _fastafile_list = _project_sp.get()->getIdentificationDataSourceStore().getFastaFileList();
+ _project_sp = project_sp;
+
+ qDebug() << "ProjectWindow::setProjectSp begin " << _project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
+ _fastafile_list = _project_sp.get()->getFastaFileStore().getFastaFileList();
for (FastaFileSp fasta_file : _fastafile_list ) {
@@ -384,8 +388,6 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
_peptide_detail_window_collection.clear();
_p_current_peptide_detail_window = nullptr;
- _project_sp = project_sp;
-
if (_p_identification_widget != nullptr) {
delete _p_identification_widget;
}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index 5d3882f18..daae90f48 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -105,7 +105,7 @@ private:
ProjectSp _project_sp;
QStandardItemModel * _p_fasta_str_li;
- std::set<FastaFileSp> _fastafile_list;
+ std::vector<FastaFileSp> _fastafile_list;
};
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index e925bd943..a8f9b20c5 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -215,6 +215,7 @@ bool XpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
</protein>
*/
_current_protein.setCompleteDescription(attributes.value("description"));
+ _current_fasta_file_sp = _p_project->getFastaFileStore().getInstance(FastaFile(attributes.value("URL")));
qDebug() << "startElement_protein end" ;
return true;
}
@@ -247,6 +248,7 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
if (p_identification_data_source->getMsRunSp().get() != ms_run_id.get()) {
throw pappso::PappsoException(QObject::tr("p_identification_data_source->getMsRunSp().get() != ms_run_id.get()"));
}
+ p_identification_data_source->addFastaFile(_current_fasta_file_sp);
_p_peptide_match->setChecked(false);
if (attributes.value("validate").simplified().toLower() == "true") {
_p_peptide_match->setChecked(true);
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
index dc172caa0..f7f3feeb8 100644
--- a/src/input/xpipsaxhandler.h
+++ b/src/input/xpipsaxhandler.h
@@ -85,6 +85,7 @@ private:
ProteinXtp _current_protein;
PeptideXtpSp _current_peptide_sp;
IdentificationGroup * _current_identification_group_p;
+ FastaFileSp _current_fasta_file_sp;
QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
};
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index e1649cf2f..58c59468c 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -449,8 +449,8 @@ bool XtandemSaxHandler::endElement_note() {
//<note label="list path, sequence source #1">/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta</note>
//<note label="list path, sequence source #2">/gorgone/pappso/formation/TD/Database/contaminants_standarts.fasta</note>
- if (_current_note_label.startsWith("list path, sequence source")) {
- _p_identification_data_source->addFastaFile(FastaFile(_current_text));
+ if (_current_note_label.startsWith("list path, sequence source #")) {
+ _p_identification_data_source->addFastaFile(_p_project->getFastaFileStore().getInstance( FastaFile(_current_text)));
}
/*
diff --git a/src/utils/fastafilestore.cpp b/src/utils/fastafilestore.cpp
index d07b8ba6b..ab5a58b4a 100644
--- a/src/utils/fastafilestore.cpp
+++ b/src/utils/fastafilestore.cpp
@@ -29,6 +29,7 @@
******************************************************************************/
#include "fastafilestore.h"
+#include <QDebug>
FastaFileStore::FastaFileStore()
{
@@ -40,24 +41,27 @@ FastaFileStore::~FastaFileStore()
}
FastaFileSp FastaFileStore::getInstance(const FastaFile & location) {
-
- std::map< FastaFile, FastaFileSp >::iterator it = _map_fastafile.find(location);
- if (it != _map_fastafile.end()) {
- return it->second;
- }
- else {
- FastaFileSp p_xtfile = std::make_shared<FastaFile>(location);
- _map_fastafile.insert(std::pair< FastaFile, FastaFileSp >(location, p_xtfile));
- return p_xtfile;
-
+qDebug() << "FastaFileStore::getInstance() begin ";
+qDebug() << "FastaFileStore::getInstance() begin "<< location.getAbsoluteFilePath();
+ std::vector<FastaFileSp>::iterator it = _map_fastafile.begin();
+ std::vector<FastaFileSp>::iterator itend = _map_fastafile.end();
+ while (it != itend) {
+ if (it->get()->getAbsoluteFilePath() == location.getAbsoluteFilePath()) {
+
+qDebug() << "FastaFileStore::getInstance() end b "<< it->get()->getAbsoluteFilePath();
+ return *it;
+ }
+ it++;
}
+ FastaFileSp fastafile_sp = std::make_shared<FastaFile>(location);
+ _map_fastafile.push_back(fastafile_sp);
+ qDebug() << "FastaFileStore::getFastaFileList() end a " << _map_fastafile.size();
+ return fastafile_sp;
}
-std::vector<FastaFileSp> FastaFileStore::getFastaFileList() const {
- std::vector<FastaFileSp> msrun_list;
- for (auto & msrun_pair :_map_fastafile) {
- msrun_list.push_back(msrun_pair.second);
- }
- return msrun_list;
+const std::vector<FastaFileSp> & FastaFileStore::getFastaFileList() const {
+ qDebug() << "FastaFileStore::getFastaFileList() begin" ;
+ qDebug() << "FastaFileStore::getFastaFileList() begin" << _map_fastafile.size();
+ return _map_fastafile;
}
diff --git a/src/utils/fastafilestore.h b/src/utils/fastafilestore.h
index a5cca3cc0..af3e877b3 100644
--- a/src/utils/fastafilestore.h
+++ b/src/utils/fastafilestore.h
@@ -31,7 +31,6 @@
#ifndef FASTAFILESTORE_H
#define FASTAFILESTORE_H
-#include <map>
#include <vector>
#include "../files/fastafile.h"
@@ -43,9 +42,9 @@ public:
FastaFileSp getInstance(const FastaFile & fastafile);
- std::vector<FastaFileSp> getFastaFileList() const;
+ const std::vector<FastaFileSp> & getFastaFileList() const;
private:
- std::map<FastaFile, FastaFileSp> _map_fastafile;
+ std::vector<FastaFileSp> _map_fastafile;
};
diff --git a/src/utils/identificationdatasourcestore.cpp b/src/utils/identificationdatasourcestore.cpp
index 003800f78..012e65c8c 100644
--- a/src/utils/identificationdatasourcestore.cpp
+++ b/src/utils/identificationdatasourcestore.cpp
@@ -63,17 +63,3 @@ qDebug() << " " << _map_identification_data_sources.size();
}
throw pappso::PappsoException(QObject::tr("Identification resource %1 not recognized").arg(location));
}
-
-std::set<FastaFileSp> IdentificationDataSourceStore::getFastaFileList() const {
- qDebug()<< "IdentificationDataSourceStore::getFastaFileList begin ";
- std::set<FastaFileSp> list_fasta_set;
- /*
- for (auto pair_ident:_map_identification_data_sources) {
- qDebug()<< "IdentificationDataSourceStore::getFastaFileList 1";
- std::vector<FastaFileSp> idfastalist = pair_ident.second.get()->getFastaFileList();
- list_fasta_set.insert(idfastalist.begin(), idfastalist.end());
- }
- */
- qDebug()<< "IdentificationDataSourceStore::getFastaFileList end";
- return list_fasta_set;
-}
diff --git a/src/utils/identificationdatasourcestore.h b/src/utils/identificationdatasourcestore.h
index 3262a49eb..e634800fb 100644
--- a/src/utils/identificationdatasourcestore.h
+++ b/src/utils/identificationdatasourcestore.h
@@ -42,8 +42,6 @@ public:
IdentificationDataSourceStore();
~IdentificationDataSourceStore();
IdentificationDataSourceSp getInstance(const QString & location);
-
- std::set<FastaFileSp> getFastaFileList() const;
private :
std::map<QString, IdentificationDataSourceSp> _map_identification_data_sources;
};
--
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