From 7c319cbbd289c3f1798f33bcbddd725a25ca3268 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Sun, 23 Apr 2017 00:09:57 +0200
Subject: [PATCH] problem with fastafile
---
src/CMakeLists.txt | 3 +-
.../identificationdatasource.cpp | 8 ++-
.../identificationdatasource.h | 7 ++-
src/core/project.h | 1 +
src/files/fastafile.cpp | 18 ++++--
src/files/fastafile.h | 13 +++-
.../choosemodificationdialog.cpp | 48 +++++++-------
src/gui/project_view/project_view.ui | 25 +++++++-
src/gui/project_view/projectwindow.cpp | 23 +++++--
src/gui/project_view/projectwindow.h | 4 ++
src/utils/fastafilestore.cpp | 63 +++++++++++++++++++
src/utils/fastafilestore.h | 52 +++++++++++++++
src/utils/identificationdatasourcestore.cpp | 17 ++++-
src/utils/identificationdatasourcestore.h | 4 ++
14 files changed, 243 insertions(+), 43 deletions(-)
create mode 100644 src/utils/fastafilestore.cpp
create mode 100644 src/utils/fastafilestore.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index b18681860..885ed02d1 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -72,6 +72,7 @@ SET(CPP_FILES
output/masschroqml.cpp
output/ods/odsexport.cpp
output/ods/simplesheet.cpp
+ utils/fastafilestore.cpp
utils/identificationdatasourcestore.cpp
utils/groupstore.cpp
utils/msrunstore.cpp
@@ -109,7 +110,7 @@ SET(XTPCPP_SRCS
)
SET (GUI_UIS
- ./gui/choose_modification_dialog/choose_modification_dialog.uicpp
+ ./gui/choose_modification_dialog/choose_modification_dialog.ui
./gui/edit_label_methods/edit_label_methods.ui
./gui/edit_modifications/edit_modifications.ui
./gui/export_spreadsheet_dialog/export_spreadsheet_dialog.ui
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index dd06ce03a..4e377f01d 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -26,6 +26,8 @@
#include <QFileInfo>
#include "../../utils/readspectrum.h"
+FastaFileStore IdentificationDataSource::_fasta_file_store;
+
IdentificationDataSource::IdentificationDataSource(const QString resource_name)
{
_resource_name = resource_name;
@@ -82,5 +84,9 @@ pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_num
}
void IdentificationDataSource::addFastaFile (FastaFile file) {
- _fastafile_list.push_back(file);
+ _fastafile_list.push_back(IdentificationDataSource::_fasta_file_store.getInstance(file));
+}
+const std::vector<FastaFileSp> & IdentificationDataSource::getFastaFileList() const {
+ qDebug()<< "IdentificationDataSource::getFastaFileList begin" << _fastafile_list.size();
+ return _fastafile_list;
}
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index 3d4b51f2b..f5a7d0e88 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -27,7 +27,7 @@
#include <pappsomspp/spectrum/spectrum.h>
#include <memory>
#include "../msrun.h"
-#include "../../files/fastafile.h"
+#include "../../utils/fastafilestore.h"
class Project;
@@ -74,16 +74,19 @@ public:
/** \brief add Fastafile used by the identification engine
*/
void addFastaFile (FastaFile file);
+
+ const std::vector<FastaFileSp> & getFastaFileList() const;
protected :
QString _resource_name;
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;
- std::vector<FastaFile> _fastafile_list;
+ std::vector<FastaFileSp> _fastafile_list;
};
#endif // IDENTIFICATIONDATASOURCE_H
diff --git a/src/core/project.h b/src/core/project.h
index 544de7dc9..5f454f404 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -83,6 +83,7 @@ private :
PeptideStore _peptide_store;
IdentificationDataSourceStore _identification_data_source_store;
MsRunStore _msrun_store;
+
};
#endif // PROJECT_H
diff --git a/src/files/fastafile.cpp b/src/files/fastafile.cpp
index 26d4c8358..aa6694508 100644
--- a/src/files/fastafile.cpp
+++ b/src/files/fastafile.cpp
@@ -26,11 +26,6 @@
FastaFile::FastaFile(const QString & fasta_source) : _fasta_source(fasta_source)
{
-}
-
-FastaFile::FastaFile(const QUrl & fasta_source) : _fasta_source(fasta_source)
-{
-
}
FastaFile::FastaFile(const QFileInfo & fasta_source): _fasta_source(fasta_source.absoluteFilePath())
{
@@ -43,3 +38,16 @@ 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();
+}
diff --git a/src/files/fastafile.h b/src/files/fastafile.h
index 3e3c90a39..263bf587d 100644
--- a/src/files/fastafile.h
+++ b/src/files/fastafile.h
@@ -24,19 +24,26 @@
#ifndef FASTAFILE_H
#define FASTAFILE_H
-#include <QUrl>
#include <QFileInfo>
+#include <memory>
+
+class FastaFile;
+typedef std::shared_ptr<FastaFile> FastaFileSp;
+
class FastaFile
{
public:
FastaFile(const QString & fasta_source);
- FastaFile(const QUrl & fasta_source);
FastaFile(const QFileInfo & fasta_source);
FastaFile(const FastaFile & other);
~FastaFile();
+ bool operator<( const FastaFile& other ) const;
+ bool operator==( const FastaFile& other ) const;
+
+ const QString getFilename() const;
private :
- const QUrl _fasta_source;
+ const QFileInfo _fasta_source;
};
diff --git a/src/gui/choose_modification_dialog/choosemodificationdialog.cpp b/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
index fc0c9bc5a..e8a889206 100644
--- a/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
+++ b/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
@@ -44,7 +44,7 @@ ChooseModificationDialog::ChooseModificationDialog(QWidget * parent):
_p_modification_str_li = new QStandardItemModel();
ui->modification_listview->setModel(_p_modification_str_li);
//param.setFilterCrossSamplePeptideNumber(settings.value("automatic_filter/cross_sample", "true").toBool());
-
+
#if QT_VERSION >= 0x050000
// Qt5 code
/*
@@ -68,27 +68,27 @@ ChooseModificationDialog::~ChooseModificationDialog()
}
void ChooseModificationDialog::setMassRange(const pappso::MassRange & massrange) {
-
- qDebug() << "ChooseModificationDialog::setMassRange " << massrange.toString();
- _selected_modification = nullptr;
+
+ qDebug() << "ChooseModificationDialog::setMassRange " << massrange.toString();
+ _selected_modification = nullptr;
_p_modification_str_li->removeRows(0,_p_modification_str_li->rowCount());
- pappso::FilterOboPsiModSink term_list;
-
- pappso::OboPsiModHandlerInterface * last_men_standing = &term_list;
- pappso::FilterOboPsiModTermDiffMono * p_filter_mass = nullptr;
- //FilterOboPsiModTermLabel * p_filter_label = nullptr;
- //FilterOboPsiModTermName * p_filter_name = nullptr;
-
- p_filter_mass = new pappso::FilterOboPsiModTermDiffMono(*last_men_standing, massrange);
- pappso::OboPsiMod psimodb(*p_filter_mass);
- for (pappso::OboPsiModTerm term : term_list.getOboPsiModTermList() ) {
-
- QStandardItem *item;
- item = new QStandardItem(QString("[%1] %2").arg(term._accession).arg(term._name));
- item->setEditable(false);
- _p_modification_str_li->appendRow(item);
- item->setData(QVariant(QString("%1").arg(term._accession)),Qt::UserRole);
- }
+ pappso::FilterOboPsiModSink term_list;
+
+ pappso::OboPsiModHandlerInterface * last_men_standing = &term_list;
+ pappso::FilterOboPsiModTermDiffMono * p_filter_mass = nullptr;
+ //FilterOboPsiModTermLabel * p_filter_label = nullptr;
+ //FilterOboPsiModTermName * p_filter_name = nullptr;
+
+ p_filter_mass = new pappso::FilterOboPsiModTermDiffMono(*last_men_standing, massrange);
+ pappso::OboPsiMod psimodb(*p_filter_mass);
+ for (pappso::OboPsiModTerm term : term_list.getOboPsiModTermList() ) {
+
+ QStandardItem *item;
+ item = new QStandardItem(QString("[%1] %2").arg(term._accession).arg(term._name));
+ item->setEditable(false);
+ _p_modification_str_li->appendRow(item);
+ item->setData(QVariant(QString("%1").arg(term._accession)),Qt::UserRole);
+ }
}
@@ -108,6 +108,6 @@ void ChooseModificationDialog::ItemClicked (QModelIndex index )
_selected_modification = modification;
}
- pappso::AaModificationP ChooseModificationDialog::getSelectedModification()const {
- return _selected_modification;
- }
+pappso::AaModificationP ChooseModificationDialog::getSelectedModification()const {
+ return _selected_modification;
+}
diff --git a/src/gui/project_view/project_view.ui b/src/gui/project_view/project_view.ui
index bcff87cae..f45e0bde2 100644
--- a/src/gui/project_view/project_view.ui
+++ b/src/gui/project_view/project_view.ui
@@ -20,8 +20,11 @@
<property name="enabled">
<bool>true</bool>
</property>
+ <property name="toolTip">
+ <string/>
+ </property>
<property name="currentIndex">
- <number>0</number>
+ <number>2</number>
</property>
<widget class="QWidget" name="identifications">
<attribute name="title">
@@ -64,6 +67,9 @@
</layout>
</widget>
<widget class="QWidget" name="fdr">
+ <property name="toolTip">
+ <string/>
+ </property>
<attribute name="title">
<string>FDR</string>
</attribute>
@@ -72,6 +78,9 @@
<layout class="QVBoxLayout" name="verticalLayout_2">
<item>
<widget class="QGroupBox" name="groupBox_3">
+ <property name="toolTip">
+ <string/>
+ </property>
<property name="title">
<string>FDR</string>
</property>
@@ -85,6 +94,9 @@
</item>
<item row="0" column="1">
<widget class="QLabel" name="peptide_fdr_label">
+ <property name="toolTip">
+ <string>FDR is computed using peptides tagged as "decoy" on all valid peptides (check filter parameters)</string>
+ </property>
<property name="text">
<string>0 %</string>
</property>
@@ -99,6 +111,9 @@
</item>
<item row="1" column="1">
<widget class="QLabel" name="protein_fdr_label">
+ <property name="toolTip">
+ <string>FDR is computed using proteins tagged as "decoy" on all valid proteins (check filter parameters)</string>
+ </property>
<property name="text">
<string>0 %</string>
</property>
@@ -114,7 +129,7 @@
</property>
<layout class="QVBoxLayout" name="verticalLayout_3">
<item>
- <widget class="QListWidget" name="decoy_database_list_widget"/>
+ <widget class="QListView" name="decoy_database_listview"/>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout">
@@ -188,6 +203,9 @@
</layout>
</widget>
<widget class="QWidget" name="mass_precision">
+ <property name="toolTip">
+ <string/>
+ </property>
<attribute name="title">
<string>Mass precision</string>
</attribute>
@@ -250,6 +268,9 @@
</item>
<item row="3" column="1">
<widget class="QLabel" name="mass_precision_sd_label">
+ <property name="toolTip">
+ <string>Mass deviation is computed on all valid and checked proteins but not decoy</string>
+ </property>
<property name="text">
<string>0</string>
</property>
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 92fc2c536..48254de5c 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -43,6 +43,9 @@ ProjectWindow::ProjectWindow(MainWindow *parent):
main_window = parent;
ui->setupUi(this);
+ _p_fasta_str_li = new QStandardItemModel();
+ ui->decoy_database_listview->setModel(_p_fasta_str_li);
+
_p_automatic_filter_widget = new AutomaticFilterWidget(this);
ui->filter_parameter_layout->addWidget(_p_automatic_filter_widget);
@@ -206,7 +209,7 @@ void ProjectWindow::refresh() {
computeFdr(ValidationState::valid);
computeMassPrecision(ValidationState::validAndChecked);
qDebug() << "ProjectWindow::refresh end ";
-
+
}
void ProjectWindow::doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters) {
qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged begin ";
@@ -341,7 +344,20 @@ void ProjectWindow::doViewProteinList(IdentificationGroup* p_identification_grou
}
void ProjectWindow::setProjectSp(ProjectSp project_sp) {
+
+ _fastafile_list = _project_sp.get()->getIdentificationDataSourceStore().getFastaFileList();
+
+ /*
+ for (FastaFileSp fasta_file : _fastafile_list ) {
+ QStandardItem *item;
+ item = new QStandardItem(QString("%1").arg(fasta_file.get()->getFilename()));
+ item->setEditable(false);
+ _p_fasta_str_li->appendRow(item);
+ item->setData(QVariant(QString("%1").arg(fasta_file.get()->getFilename())),Qt::UserRole);
+ }
+ */
+
for (auto && p_window :_peptide_list_window_collection) {
delete p_window;
}
@@ -402,9 +418,8 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
ui->decoy_protein_regexp_line_edit->setText(_project_sp.get()->getProteinStore().getRegexpDecoy().pattern());
ui->contaminant_protein_regexp_line_edit->setText(_project_sp.get()->getProteinStore().getRegexpContaminant().pattern());
- computeFdr(ValidationState::grouped);
-
- computeMassPrecision(ValidationState::validAndChecked);
+
+ refresh();
this->setEnabled(true);
}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index a2c680802..02144ec1d 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -25,6 +25,7 @@
#define PROJECTWINDOW_H
#include <QMainWindow>
+#include <set>
#include "../../core/project.h"
#include "../edit_label_methods/editlabelmethods.h"
#include "../edit_modifications/editmodifications.h"
@@ -102,6 +103,9 @@ private:
EditLabelMethods * _p_edit_label_methods = nullptr;
ProjectSp _project_sp;
+
+ QStandardItemModel * _p_fasta_str_li;
+ std::set<FastaFileSp> _fastafile_list;
};
diff --git a/src/utils/fastafilestore.cpp b/src/utils/fastafilestore.cpp
new file mode 100644
index 000000000..d07b8ba6b
--- /dev/null
+++ b/src/utils/fastafilestore.cpp
@@ -0,0 +1,63 @@
+/**
+ * \file utils/fastafiletore.cpp
+ * \date 22/4/2017
+ * \author Olivier Langella
+ * \brief store unique version of fastafile
+ */
+
+
+/*******************************************************************************
+* 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 "fastafilestore.h"
+FastaFileStore::FastaFileStore()
+{
+
+}
+
+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;
+
+ }
+}
+
+
+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;
+}
diff --git a/src/utils/fastafilestore.h b/src/utils/fastafilestore.h
new file mode 100644
index 000000000..a5cca3cc0
--- /dev/null
+++ b/src/utils/fastafilestore.h
@@ -0,0 +1,52 @@
+/**
+ * \file utils/fastafiletore.h
+ * \date 22/4/2017
+ * \author Olivier Langella
+ * \brief store unique version of fastafile
+ */
+
+
+/*******************************************************************************
+* 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 FASTAFILESTORE_H
+#define FASTAFILESTORE_H
+
+#include <map>
+#include <vector>
+#include "../files/fastafile.h"
+
+class FastaFileStore
+{
+public:
+ FastaFileStore();
+ ~FastaFileStore();
+
+ FastaFileSp getInstance(const FastaFile & fastafile);
+
+ std::vector<FastaFileSp> getFastaFileList() const;
+private:
+ std::map<FastaFile, FastaFileSp> _map_fastafile;
+};
+
+
+#endif // FASTAFILESTORE_H
diff --git a/src/utils/identificationdatasourcestore.cpp b/src/utils/identificationdatasourcestore.cpp
index 04e37584f..003800f78 100644
--- a/src/utils/identificationdatasourcestore.cpp
+++ b/src/utils/identificationdatasourcestore.cpp
@@ -43,7 +43,8 @@ IdentificationDataSourceStore::~IdentificationDataSourceStore()
}
IdentificationDataSourceSp IdentificationDataSourceStore::getInstance(const QString & location) {
-
+qDebug() << "IdentificationDataSourceStore::getInstance begin " << location;
+qDebug() << " " << _map_identification_data_sources.size();
std::map< QString, IdentificationDataSourceSp >::iterator it = _map_identification_data_sources.find(location);
if (it != _map_identification_data_sources.end()) {
return it->second;
@@ -62,3 +63,17 @@ IdentificationDataSourceSp IdentificationDataSourceStore::getInstance(const QStr
}
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 cfef38ee8..3262a49eb 100644
--- a/src/utils/identificationdatasourcestore.h
+++ b/src/utils/identificationdatasourcestore.h
@@ -32,7 +32,9 @@
#define IDENTIFICATIONDATASOURCESTORE_H
#include <map>
+#include <set>
#include "../core/identification_sources/identificationdatasource.h"
+#include "../files/fastafile.h"
class IdentificationDataSourceStore
{
@@ -40,6 +42,8 @@ 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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