From 496505bed58ca7ecb04ca1d7c87add9fec2d8fb4 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 19 May 2017 23:35:49 +0200
Subject: [PATCH] select contaminant database
---
src/files/fastafile.cpp | 35 +++++++++++++++++++++++++-
src/files/fastafile.h | 5 ++++
src/gui/project_view/projectwindow.cpp | 16 ++++++++++--
src/input/xpipsaxhandler.cpp | 1 +
src/utils/fastafilestore.cpp | 4 +--
src/utils/proteinstore.cpp | 9 +++++++
src/utils/proteinstore.h | 4 +++
7 files changed, 69 insertions(+), 5 deletions(-)
diff --git a/src/files/fastafile.cpp b/src/files/fastafile.cpp
index 2ac6b0da..688eb2c3 100644
--- a/src/files/fastafile.cpp
+++ b/src/files/fastafile.cpp
@@ -22,10 +22,29 @@
******************************************************************************/
#include "fastafile.h"
+#include <pappsomspp/fasta/fastareader.h>
+#include <QStringList>
+#include <QDebug>
+
+class AccessionContaminantReader: public pappso::FastaHandlerInterface {
+public:
+ AccessionContaminantReader (ProteinStore & protein_store) :_protein_store(protein_store) {
+ };
+
+ void setSequence(const QString& description, const QString& sequence) override {
+ //qDebug() << "PeptideReader::setSequence " << description << " " <<sequence;
+ QStringList descr_split = description.simplified().split(" ");
+ QString accession = descr_split.at(0);
+ _protein_store.setContaminantAccession(accession);
+ };
+private:
+ ProteinStore & _protein_store;
+};
+
FastaFile::FastaFile(const QString & fasta_source) : _fasta_source(fasta_source)
{
-
+ qDebug() << "FastaFile::FastaFile "<< fasta_source;
}
FastaFile::FastaFile(const QFileInfo & fasta_source): _fasta_source(fasta_source)
{
@@ -46,3 +65,17 @@ const QString FastaFile::getFilename() const {
const QString FastaFile::getAbsoluteFilePath() const {
return _fasta_source.absoluteFilePath();
}
+void FastaFile::setContaminants(ProteinStore & protein_store) const {
+
+ if (_fasta_source.exists()) {
+ AccessionContaminantReader accession_reader(protein_store);
+ pappso::FastaReader reader(accession_reader);
+ QFile fasta_file(_fasta_source.absoluteFilePath());
+ fasta_file.open(QIODevice::ReadOnly);
+ reader.parse(&fasta_file);
+ fasta_file.close();
+ }
+ else {
+ qDebug() << "FastaFile::setContaminants "<< _fasta_source.absoluteFilePath() << " does not exists";
+ }
+}
diff --git a/src/files/fastafile.h b/src/files/fastafile.h
index 1ba90827..1c424741 100644
--- a/src/files/fastafile.h
+++ b/src/files/fastafile.h
@@ -26,6 +26,7 @@
#include <QFileInfo>
#include <memory>
+#include "../utils/proteinstore.h"
class FastaFile;
typedef std::shared_ptr<FastaFile> FastaFileSp;
@@ -41,6 +42,10 @@ public:
const QString getFilename() const;
const QString getAbsoluteFilePath() const;
+
+ /** @brief read fasta file and set accessions as contaminants
+ * */
+ void setContaminants(ProteinStore & protein_store) const;
private :
const QFileInfo _fasta_source;
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 1b0dd5cd..cb8ade14 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -51,6 +51,8 @@ ProjectWindow::ProjectWindow(MainWindow *parent):
_p_fasta_str_li = new QStandardItemModel();
ui->decoy_database_listview->setModel(_p_fasta_str_li);
ui->contaminant_database_listview->setModel(_p_fasta_str_li);
+ QItemSelectionModel * selection_model = ui->contaminant_database_listview->selectionModel();
+ ui->contaminant_database_listview->setSelectionMode(QAbstractItemView::MultiSelection);
_p_automatic_filter_widget = new AutomaticFilterWidget(this);
ui->filter_parameter_layout->addWidget(_p_automatic_filter_widget);
@@ -236,7 +238,17 @@ void ProjectWindow::doAutomaticFilterParametersChanged(AutomaticFilterParameters
showWaitingMessage(tr("Updating filters"));
doDisplayLoadingMessage(tr("tagging contaminant proteins"));
- _project_sp.get()->getProteinStore().setRegexpContaminantPattern(ui->contaminant_protein_regexp_line_edit->text());
+ QModelIndexList index_list = ui->contaminant_database_listview->selectionModel()->selectedIndexes();
+ if (index_list.size() > 0) {
+ _project_sp.get()->getProteinStore().clearContaminants();
+ for (QModelIndex index :index_list) {
+ FastaFile fasta_file (_p_fasta_str_li->itemFromIndex(index)->data(Qt::UserRole).toString());
+ fasta_file.setContaminants(_project_sp.get()->getProteinStore());
+ }
+ }
+ else {
+ _project_sp.get()->getProteinStore().setRegexpContaminantPattern(ui->contaminant_protein_regexp_line_edit->text());
+ }
doDisplayLoadingMessage(tr("updating filters"));
_project_sp.get()->updateAutomaticFilters(parameters);
@@ -380,7 +392,7 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
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);
+ item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
}
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 739fc8ac..f6d4affe 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -142,6 +142,7 @@ bool XpipSaxHandler::startElement_filter_params(QXmlAttributes attributes) {
if (attributes.value("filter_to_all").simplified() == "true") {
_automatic_filter_parameters.setFilterCrossSamplePeptideNumber(true);
}
+ _p_project->getFastaFileStore().getInstance(FastaFile(attributes.value("database_filter")));
qDebug() << "startElement_filter_params end" ;
return true;
}
diff --git a/src/utils/fastafilestore.cpp b/src/utils/fastafilestore.cpp
index ab5a58b4..ddafcd3c 100644
--- a/src/utils/fastafilestore.cpp
+++ b/src/utils/fastafilestore.cpp
@@ -46,9 +46,9 @@ qDebug() << "FastaFileStore::getInstance() begin "<< location.getAbsoluteFilePat
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()) {
+ if (it->get()->getFilename() == location.getFilename()) {
-qDebug() << "FastaFileStore::getInstance() end b "<< it->get()->getAbsoluteFilePath();
+qDebug() << "FastaFileStore::getInstance() end b "<< it->get()->getFilename();
return *it;
}
it++;
diff --git a/src/utils/proteinstore.cpp b/src/utils/proteinstore.cpp
index 6cf29b59..4bf6eb4a 100644
--- a/src/utils/proteinstore.cpp
+++ b/src/utils/proteinstore.cpp
@@ -72,6 +72,15 @@ void ProteinStore::setRegexpDecoyPattern(const QString & pattern) {
}
+void ProteinStore::clearContaminants() {
+ for (std::pair<const QString, ProteinXtpSp> & acc_protein :_map_accession_protein_list) {
+ acc_protein.second.get()->setIsContaminant(false);
+ }
+}
+
+void ProteinStore::setContaminantAccession(QString accession) {
+ _map_accession_protein_list.at(accession).get()->setIsContaminant(true);
+}
ProteinXtpSp & ProteinStore::getInstance(ProteinXtpSp & peptide_in) {
std::pair<std::map< QString, ProteinXtpSp>::iterator,bool> ret = _map_accession_protein_list.insert(std::pair<QString, ProteinXtpSp>(peptide_in.get()->getAccession(),peptide_in));
diff --git a/src/utils/proteinstore.h b/src/utils/proteinstore.h
index 2208156c..c6632503 100644
--- a/src/utils/proteinstore.h
+++ b/src/utils/proteinstore.h
@@ -53,6 +53,10 @@ public:
void setRegexpContaminantPattern(const QString & pattern);
QRegExp getRegexpContaminant() const;
+
+ void clearContaminants();
+
+ void setContaminantAccession(QString accession);
private :
void setProteinInformations(ProteinXtpSp & protein_in);
--
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