From 675f375f1fe533289fafbc2473bbdb35ada60190 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 13 Nov 2018 14:50:01 +0100
Subject: [PATCH] look for sequence LI in protein list
---
src/gui/protein_list_view/protein_view.ui | 7 ++-
.../protein_list_view/proteinlistwindow.cpp | 45 ++++++++++++++-----
.../proteintableproxymodel.cpp | 15 ++++++-
3 files changed, 53 insertions(+), 14 deletions(-)
diff --git a/src/gui/protein_list_view/protein_view.ui b/src/gui/protein_list_view/protein_view.ui
index c1986229f..ada3765aa 100644
--- a/src/gui/protein_list_view/protein_view.ui
+++ b/src/gui/protein_list_view/protein_view.ui
@@ -96,7 +96,12 @@
</item>
<item>
<property name="text">
- <string>sequence</string>
+ <string extracomment="look for protein sequence containing this amino acid sequence.">sequence</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string extracomment="look for protein sequence containing these amino acids, but considering that L and I is the same.">sequence LI</string>
</property>
</item>
</widget>
diff --git a/src/gui/protein_list_view/proteinlistwindow.cpp b/src/gui/protein_list_view/proteinlistwindow.cpp
index 736483554..4a05e8cfc 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -47,7 +47,9 @@ ProteinListQactionColumn::ProteinListQactionColumn(ProteinListWindow *parent,
#if QT_VERSION >= 0x050000
// Qt5 code
- connect(this, &ProteinListQactionColumn::toggled, this,
+ connect(this,
+ &ProteinListQactionColumn::toggled,
+ this,
&ProteinListQactionColumn::doToggled);
#else
// Qt4 code
@@ -116,26 +118,41 @@ ProteinListWindow::ProteinListWindow(ProjectWindow *parent)
#if QT_VERSION >= 0x050000
// Qt5 code
- connect(_project_window, &ProjectWindow::identificationGroupGrouped, this,
+ connect(_project_window,
+ &ProjectWindow::identificationGroupGrouped,
+ this,
&ProteinListWindow::doIdentificationGroupGrouped);
- connect(this, &ProteinListWindow::proteinDataChanged, _protein_table_model_p,
+ connect(this,
+ &ProteinListWindow::proteinDataChanged,
+ _protein_table_model_p,
&ProteinTableModel::onProteinDataChanged);
- connect(ui->tableView, &QTableView::clicked, _p_proxy_model,
+ connect(ui->tableView,
+ &QTableView::clicked,
+ _p_proxy_model,
&ProteinTableProxyModel::onTableClicked);
- connect(ui->centralwidget, &QWidget::customContextMenuRequested, this,
+ connect(ui->centralwidget,
+ &QWidget::customContextMenuRequested,
+ this,
&ProteinListWindow::showContextMenu);
- connect(_protein_table_model_p, &ProteinTableModel::layoutChanged, this,
+ connect(_protein_table_model_p,
+ &ProteinTableModel::layoutChanged,
+ this,
&ProteinListWindow::updateStatusBar);
#else
// Qt4 code
connect(_project_window,
- SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
+ SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
+ this,
SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
- connect(this, SIGNAL(proteinDataChanged()), _protein_table_model_p,
+ connect(this,
+ SIGNAL(proteinDataChanged()),
+ _protein_table_model_p,
SLOT(onProteinDataChanged()));
- connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model,
+ connect(ui->tableView,
+ SIGNAL(clicked(const QModelIndex &)),
+ _p_proxy_model,
SLOT(onTableClicked(const QModelIndex &)));
// connect(ui->tableView, SIGNAL(doubleClicked(const QModelIndex &)),
// _p_proxy_model, SLOT(onTableDoubleClicked(const QModelIndex &)));
@@ -145,11 +162,15 @@ ProteinListWindow::ProteinListWindow(ProjectWindow *parent)
// connect( this, SIGNAL( focusReceived(bool) ),this,
// SLOT(doFocusReceived(bool)) );
- connect(ui->centralwidget, SIGNAL(customContextMenuRequested(const QPoint &)),
- this, SLOT(showContextMenu(const QPoint &)));
+ connect(ui->centralwidget,
+ SIGNAL(customContextMenuRequested(const QPoint &)),
+ this,
+ SLOT(showContextMenu(const QPoint &)));
// connect(_p_proxy_model, SIGNAL(layoutChanged()),
// this, SLOT(doProxyLayoutChanged()));
- connect(_protein_table_model_p, SIGNAL(layoutChanged()), this,
+ connect(_protein_table_model_p,
+ SIGNAL(layoutChanged()),
+ this,
SLOT(updateStatusBar()));
#endif
}
diff --git a/src/gui/protein_list_view/proteintableproxymodel.cpp b/src/gui/protein_list_view/proteintableproxymodel.cpp
index 7aa1d8ec3..336061c75 100644
--- a/src/gui/protein_list_view/proteintableproxymodel.cpp
+++ b/src/gui/protein_list_view/proteintableproxymodel.cpp
@@ -197,6 +197,18 @@ ProteinTableProxyModel::filterAcceptsRow(int source_row,
return false;
}
}
+ else if(_search_on == "sequence LI")
+ {
+ QString peptide_search_string =
+ QString(_protein_search_string).replace("L", "I");
+ QString protein_sequence_li =
+ QString(protein_match->getProteinXtpSp().get()->getSequence())
+ .replace("L", "I");
+ if(!protein_sequence_li.contains(peptide_search_string))
+ {
+ return false;
+ }
+ }
else if(_search_on == "peptide")
{
QString peptide_search_string =
@@ -366,7 +378,8 @@ ProteinTableProxyModel::data(const QModelIndex &index, int role) const
}
QVariant
-ProteinTableProxyModel::headerData(int section, Qt::Orientation orientation,
+ProteinTableProxyModel::headerData(int section,
+ Qt::Orientation orientation,
int role) const
{
int col = mapToSource(index(0, section)).column();
--
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