diff --git a/modules/gui/src/CMakeLists.txt b/modules/gui/src/CMakeLists.txt
index da9df49e3eb9f6886b5a0eea4bd10e5fa813c213..ea38cf4c0ad9fe88403b10777f51bfd2d16813bf 100644
--- a/modules/gui/src/CMakeLists.txt
+++ b/modules/gui/src/CMakeLists.txt
@@ -31,6 +31,7 @@ seq_text_painter.hh
sequence_delegate.hh
sequence_model.hh
sequence_row.hh
+sequence_search_bar.hh
sequence_table_view.hh
sequence_viewer.hh
tick_painter.hh
@@ -220,6 +221,7 @@ sequence/seq_text_painter.cc
sequence/sequence_delegate.cc
sequence/sequence_model.cc
sequence/sequence_row.cc
+sequence/sequence_search_bar.cc
sequence/sequence_table_view.cc
sequence/sequence_viewer.cc
sequence/tick_painter.cc
@@ -351,6 +353,7 @@ sequence/seq_text_painter.hh
sequence/sequence_delegate.hh
sequence/sequence_model.hh
sequence/sequence_row.hh
+sequence/sequence_search_bar.hh
sequence/sequence_table_view.hh
sequence/sequence_viewer.hh
sequence/tick_painter.hh
diff --git a/modules/gui/src/sequence/sequence_model.cc b/modules/gui/src/sequence/sequence_model.cc
index ddac0e2a8db67446cb5bb75f32d699cf7a8c2c96..a44cf3a95c68ee1e6d9aec181ff539c14785810c 100644
--- a/modules/gui/src/sequence/sequence_model.cc
+++ b/modules/gui/src/sequence/sequence_model.cc
@@ -179,6 +179,25 @@ QModelIndexList SequenceModel::GetModelIndexes(gfx::EntityP& entity, const mol::
return list;
}
+QModelIndexList SequenceModel::GetModelIndexes(const QString& subject, const QString& sequence_name)
+{
+ QModelIndexList list;
+ for (int i = 0; i<objects_.size(); i++){
+ ViewObject* object = objects_[i];
+ QMap<int, QList<int> > indexes = object->GetIndexesForSubject(subject,sequence_name);
+ QMapIterator< int, QList<int> > i(indexes);
+ while (i.hasNext()) {
+ i.next();
+ int row = this->GetGlobalRow(object, i.key());
+ const QList<int>& index_list = i.value();
+ for(int i=0; i<index_list.size(); i++){
+ list.append(this->index(row,index_list[i]));
+ }
+ }
+ }
+ return list;
+}
+
void SequenceModel::SelectionChanged(const QItemSelection& sel, const QItemSelection& desel)
{
QMap<int,QPair<QSet<int>,QSet<int> > > sel_map;
diff --git a/modules/gui/src/sequence/sequence_model.hh b/modules/gui/src/sequence/sequence_model.hh
index 1c8b27f6fca5cf94f9eefff0bd938025870b2180..ea42f348fbb0df21d0d590c1f990f7c4bff7545c 100644
--- a/modules/gui/src/sequence/sequence_model.hh
+++ b/modules/gui/src/sequence/sequence_model.hh
@@ -50,6 +50,8 @@ public:
void RemoveGfxEntity(gfx::EntityP& entity);
QModelIndexList GetModelIndexes(gfx::EntityP& entity, const mol::EntityView& view);
+ QModelIndexList GetModelIndexes(const QString& subject, const QString& sequence_name=QString());
+
int GetGlobalRow(ViewObject* obj, int row) const;
diff --git a/modules/gui/src/sequence/sequence_search_bar.cc b/modules/gui/src/sequence/sequence_search_bar.cc
new file mode 100644
index 0000000000000000000000000000000000000000..9ae88675e2468dbe5083cbb642df653fd563c67a
--- /dev/null
+++ b/modules/gui/src/sequence/sequence_search_bar.cc
@@ -0,0 +1,125 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library 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 Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+/*
+ Author: Marco Biasini
+ */
+
+#include "sequence_search_bar.hh"
+
+#include <QHBoxLayout>
+#include <QLineEdit>
+#include <QPainter>
+#include <QPaintEvent>
+#include <QLabel>
+#include <QKeyEvent>
+
+namespace ost { namespace gui {
+
+SeqSearchBar::SeqSearchBar(QWidget* parent):
+ QWidget(parent)
+{
+ subject_=new QLineEdit(this);
+ search_all_=new QCheckBox("search in all sequences", this);
+ search_in_=new QComboBox(this);
+ QHBoxLayout* l= new QHBoxLayout(this);
+ l->addSpacing(2);
+ l->addWidget(subject_, 0);
+ l->setStretch(0,1);
+ l->addWidget(search_all_, 0);
+ QLabel* label=new QLabel("search in:", this);
+ l->addSpacing(10);
+ l->addWidget(label, 0);
+ l->addWidget(search_in_, 0);
+ //subject_->setMaximumWidth(200);
+ setLayout(l);
+ l->setSizeConstraint(QLayout::SetMaximumSize);
+ l->setMargin(1);
+ search_all_->setCheckState(Qt::Checked);
+ search_in_->setEnabled(false);
+#if defined(__APPLE__)
+ subject_->setAttribute(Qt::WA_MacSmallSize, true);
+ search_all_->setAttribute(Qt::WA_MacSmallSize, true);
+ search_in_->setAttribute(Qt::WA_MacSmallSize, true);
+ label->setAttribute(Qt::WA_MacSmallSize, true);
+#endif
+ connect(subject_, SIGNAL(textChanged(const QString&)), this,
+ SLOT(OnSubjectChanged(const QString&)));
+ connect(search_all_, SIGNAL(stateChanged(int)), this,
+ SLOT(OnSearchAllChanged(int)));
+ connect(search_in_, SIGNAL(currentIndexChanged(int)), this,
+ SLOT(OnSearchInChanged(int)));
+}
+
+void SeqSearchBar::UpdateItems(const QStringList& sequences)
+{
+ search_in_->clear();
+
+ for(int i=0;i< sequences.size(); i++){
+ search_in_->addItem(sequences[i]);
+ }
+
+ if (sequences.empty()) {
+ search_all_->setCheckState(Qt::Checked);
+ search_in_->setEnabled(false);
+ }
+ subject_->setFocus(Qt::ActiveWindowFocusReason);
+ subject_->selectAll();
+}
+void SeqSearchBar::OnSearchAllChanged(int state)
+{
+ if (state==Qt::Unchecked) {
+ search_in_->setEnabled(true);
+ } else {
+ search_in_->setEnabled(false);
+ }
+ emit Changed(subject_->text(), search_all_->checkState()==Qt::Checked,
+ search_in_->currentText());
+}
+
+void SeqSearchBar::OnSearchInChanged(int index)
+{
+ emit Changed(subject_->text(), search_all_->checkState()==Qt::Checked,
+ search_in_->currentText());
+}
+
+void SeqSearchBar::OnSubjectChanged(const QString& str)
+{
+ emit Changed(str, search_all_->checkState()==Qt::Checked,
+ search_in_->currentText());
+}
+
+void SeqSearchBar::paintEvent(QPaintEvent* paint_event)
+{
+ QPainter p(this);
+ p.setBrush(QBrush(QColor(Qt::blue).lighter(300)));
+ p.setPen(QPen(QColor(Qt::blue).lighter(200)));
+ p.drawRect(rect());
+ paint_event->accept();
+}
+
+void SeqSearchBar::keyPressEvent(QKeyEvent* key_event)
+{
+ if (key_event->key()==Qt::Key_Escape) {
+ this->hide();
+ key_event->accept();
+ }
+ QWidget::keyPressEvent(key_event);
+}
+
+}}
diff --git a/modules/gui/src/sequence/sequence_search_bar.hh b/modules/gui/src/sequence/sequence_search_bar.hh
new file mode 100644
index 0000000000000000000000000000000000000000..865a42be22c30a828ba24285319f8f6d5bb592cc
--- /dev/null
+++ b/modules/gui/src/sequence/sequence_search_bar.hh
@@ -0,0 +1,59 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library 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 Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_SEQUENCE_VIEWER_SEQUENCE_SEARCH_BAR_HH
+#define OST_SEQUENCE_VIEWER_SEQUENCE_SEARCH_BAR_HH
+
+/*
+ Author: Marco Biasini
+ */
+#include <ost/gui/module_config.hh>
+#include <ost/seq/alignment_handle.hh>
+#include <QWidget>
+#include <QComboBox>
+#include <QCheckBox>
+#include <QSet>
+
+namespace ost { namespace gui {
+
+/// \brief search bar to search in multiple sequence alignment
+class DLLEXPORT_OST_GUI SeqSearchBar : public QWidget {
+ Q_OBJECT
+public:
+ SeqSearchBar(QWidget* parent=NULL);
+
+ void UpdateItems(const QStringList& sequences);
+signals:
+ void Changed(const QString&, bool, const QString&);
+public slots:
+ void OnSubjectChanged(const QString&);
+ void OnSearchInChanged(int);
+ void OnSearchAllChanged(int);
+protected:
+ virtual void paintEvent(QPaintEvent* paint_event);
+ virtual void keyPressEvent(QKeyEvent* key_event);
+private:
+ seq::AlignmentHandle ali_;
+ QLineEdit* subject_;
+ QCheckBox* search_all_;
+ QComboBox* search_in_;
+};
+
+}}
+
+#endif
diff --git a/modules/gui/src/sequence/sequence_table_view.cc b/modules/gui/src/sequence/sequence_table_view.cc
index 877c423eaaf8c23564f4303c85f18cab3e481444..4529101fed75e0805f086a646287e8e4a1ebecb2 100644
--- a/modules/gui/src/sequence/sequence_table_view.cc
+++ b/modules/gui/src/sequence/sequence_table_view.cc
@@ -95,8 +95,7 @@ void SequenceTableView::InitStaticColumn()
static_column_->setVerticalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
static_column_->show();
static_column_->setStyleSheet("QTableView { border: 0px;"
- "background-color: #FFFFFF;"
- "selection-background-color: #EEEEEE}"
+ "background-color: #FFFFFF}"
"QTableView::item{ border: none;"
"padding: 0px; border-width: 0px; margin: 0px;}");
static_column_->setShowGrid(false);
@@ -130,8 +129,7 @@ void SequenceTableView::InitStaticRow()
static_row_->setVerticalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
static_row_->show();
static_row_->setStyleSheet("QTableView { border: 0px;"
- "background-color: #FFFFFF;"
- "selection-background-color: #EEEEEE}"
+ "background-color: #FFFFFF}"
"QTableView::item{ border: none;"
"padding: 0px; border-width: 0px; margin: 0px;}");
static_row_->setShowGrid(false);
@@ -169,8 +167,7 @@ void SequenceTableView::InitStaticField(){
static_field_->setVerticalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
static_field_->show();
static_field_->setStyleSheet("QTableView { border: 0px;"
- "background-color: #FFFFFF;"
- "selection-background-color: #EEEEEE}"
+ "background-color: #FFFFFF}"
"QTableView::item{ border: none;"
"padding: 0px; border-width: 0px; margin: 0px;}");
static_field_->setShowGrid(false);
diff --git a/modules/gui/src/sequence/sequence_viewer.cc b/modules/gui/src/sequence/sequence_viewer.cc
index fd6a3cf2bcecfcb040758d1f80bb1b624f71b4c6..722c962d7bfb8fee5d1955b51d12bf300f7d59fe 100644
--- a/modules/gui/src/sequence/sequence_viewer.cc
+++ b/modules/gui/src/sequence/sequence_viewer.cc
@@ -22,10 +22,11 @@
*/
#include <boost/pointer_cast.hpp>
-#include <QVBoxLayout>
-#include <QPushButton>
-#include <QHeaderView>
#include <QAbstractItemView>
+#include <QHeaderView>
+#include <QPushButton>
+#include <QShortcut>
+#include <QVBoxLayout>
#include <ost/mol/chain_view.hh>
#include <ost/mol/entity_view.hh>
@@ -75,6 +76,13 @@ SequenceViewerV2::SequenceViewerV2(QWidget* parent): Widget(NULL,parent)
layout->setMargin(0);
layout->setSpacing(0);
+ seq_search_bar_ = new SeqSearchBar(this);
+ seq_search_bar_->hide();
+ layout->addWidget(seq_search_bar_);
+ QShortcut* shortcut=new QShortcut(QKeySequence(tr("Ctrl+F")), this);
+ connect(shortcut, SIGNAL(activated()), this, SLOT(FindInSequence()));
+ connect(seq_search_bar_, SIGNAL(Changed(const QString&, bool, const QString&)), this, SLOT(OnSearchBarUpdate(const QString&, bool, const QString&)));
+
seq_table_view_ = new SequenceTableView(model_);
layout->addWidget(seq_table_view_);
this->setLayout(layout);
@@ -106,6 +114,7 @@ void SequenceViewerV2::NodeAdded(const gfx::GfxNodeP& n)
seq_table_view_->resizeColumnsToContents();
seq_table_view_->resizeRowsToContents();
}
+ this->UpdateSearchBar();
}
void SequenceViewerV2::NodeRemoved(const gfx::GfxNodeP& node)
@@ -115,6 +124,16 @@ void SequenceViewerV2::NodeRemoved(const gfx::GfxNodeP& node)
}
}
+void SequenceViewerV2::UpdateSearchBar()
+{
+ QStringList sequence_names_;
+ for(int i = 1; i< model_->rowCount(); i++){
+ QString name = model_->data(model_->index(i,0),Qt::DisplayRole).toString();
+ sequence_names_.append(name);
+ }
+ seq_search_bar_->UpdateItems(sequence_names_);
+}
+
void SequenceViewerV2::SelectionModelChanged(const QItemSelection& sel, const QItemSelection& desel)
{
gfx::Scene::Instance().DetachObserver(this);
@@ -126,21 +145,10 @@ void SequenceViewerV2::SelectionChanged(const gfx::GfxObjP& o,
const mol::EntityView& view)
{
disconnect(seq_table_view_->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(SelectionModelChanged(const QItemSelection&, const QItemSelection&)));
- QItemSelectionModel* model = seq_table_view_->selectionModel();
gfx::EntityP entity=boost::dynamic_pointer_cast<gfx::Entity>(o);
if(entity){
const QModelIndexList& list = model_->GetModelIndexes(entity, view);
- QSet<int> rows_visited;
- for(int i = 0; i<list.size(); i++){
- int row =list[i].row();
- if(!rows_visited.contains(row)){
- model->select(list[i],QItemSelectionModel::Rows|QItemSelectionModel::Deselect);
- rows_visited.insert(row);
- }
- }
- for(int i = 0; i<list.size(); i++){
- model->select(list[i],QItemSelectionModel::Select);
- }
+ this->SelectList(list);
}
connect(seq_table_view_->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(SelectionModelChanged(const QItemSelection&, const QItemSelection&)));
}
@@ -172,6 +180,46 @@ void SequenceViewerV2::MouseWheelEvent(QWheelEvent* event)
event->accept();
}
+void SequenceViewerV2::FindInSequence()
+{
+ if(seq_search_bar_->isHidden()){
+ seq_search_bar_->show();
+ }
+ else{
+ seq_search_bar_->hide();
+ }
+}
+
+void SequenceViewerV2::OnSearchBarUpdate(const QString& subject,
+ bool search_in_all, const QString& name)
+{
+ seq_table_view_->selectionModel()->clear();
+ if(search_in_all){
+ const QModelIndexList& list = model_->GetModelIndexes(subject);
+ this->SelectList(list);
+ }
+ else{
+ const QModelIndexList& list = model_->GetModelIndexes(subject,name);
+ this->SelectList(list);
+ }
+}
+
+void SequenceViewerV2::SelectList(const QModelIndexList& list)
+{
+ QItemSelectionModel* model = seq_table_view_->selectionModel();
+ QSet<int> rows_visited;
+ for(int i = 0; i<list.size(); i++){
+ int row =list[i].row();
+ if(!rows_visited.contains(row)){
+ model->select(list[i],QItemSelectionModel::Rows|QItemSelectionModel::Deselect);
+ rows_visited.insert(row);
+ }
+ }
+ for(int i = 0; i<list.size(); i++){
+ model->select(list[i],QItemSelectionModel::Select);
+ }
+}
+
SequenceViewerV2::~SequenceViewerV2(){
gfx::Scene::Instance().DetachObserver(this);
}
diff --git a/modules/gui/src/sequence/sequence_viewer.hh b/modules/gui/src/sequence/sequence_viewer.hh
index 3940c68fad19cfed610c9911242cb74cfccbcd98..112bb1c4b5ab92b591873c3b66140324d56d00ba 100644
--- a/modules/gui/src/sequence/sequence_viewer.hh
+++ b/modules/gui/src/sequence/sequence_viewer.hh
@@ -32,6 +32,7 @@
#include <ost/gui/module_config.hh>
+#include "sequence_search_bar.hh"
#include "sequence_model.hh"
#include "sequence_table_view.hh"
@@ -51,7 +52,18 @@ public:
virtual bool Restore(const QString&){return true;};
virtual bool Save(const QString&){return true;};
+public slots:
+/// \internal
+void OnSearchBarUpdate(const QString&, bool, const QString&);
+
+private slots:
+/// \brief show sequence search bar
+void FindInSequence();
+
private:
+ void UpdateSearchBar();
+ void SelectList(const QModelIndexList& list);
+ SeqSearchBar* seq_search_bar_;
SequenceModel* model_;
SequenceTableView* seq_table_view_;
diff --git a/modules/gui/src/sequence/view_object.cc b/modules/gui/src/sequence/view_object.cc
index 01d80818a08b725cdd655dec051f1b9f5b204aff..88dfede657186f09ebef54ba712c8d1c10ca5396 100644
--- a/modules/gui/src/sequence/view_object.cc
+++ b/modules/gui/src/sequence/view_object.cc
@@ -229,6 +229,35 @@ QMap<int, QList<int> > ViewObject::GetIndexesForView(const mol::EntityView& view
}
}
+QMap<int, QList<int> > ViewObject::GetIndexesForSubject(const QString& subject, const QString& sequence_name)
+{
+ if(subject.size()==0){
+ return QMap<int, QList<int> >();
+ }
+ QMap<int, QList<int> > selected_indexes;
+ String subject_str = subject.toStdString();
+ for(int i=0; i< rows_.size(); i++){
+ if(SequenceRow* secstr_row = qobject_cast<SequenceRow*>(rows_[i])){
+ if(sequence_name.size()==0 || sequence_name==secstr_row->GetName()){
+ seq::SequenceHandle seq = secstr_row->GetSequence();
+ String seq_str=seq.GetString();
+ size_t pos=0;
+ size_t first=String::npos;
+ while ((pos=seq_str.find(subject_str, pos))!=String::npos) {
+ if (first==String::npos) {
+ first=pos;
+ }
+ for(int j=0; j < subject.size(); j++){
+ selected_indexes[i].append(pos+j+1);
+ }
+ pos+=subject.length();
+ }
+ }
+ }
+ }
+ return selected_indexes;
+}
+
Qt::ItemFlags ViewObject::Flags(int row, int column) const
{
if(row<0 || row >= rows_.size())return Qt::NoItemFlags;
diff --git a/modules/gui/src/sequence/view_object.hh b/modules/gui/src/sequence/view_object.hh
index a6d99bc74c2a84d3c91f2d273c9855136e1ce502..4e88d9eb6e919b7d222b5ecc075522022417f64c 100644
--- a/modules/gui/src/sequence/view_object.hh
+++ b/modules/gui/src/sequence/view_object.hh
@@ -78,6 +78,7 @@ public:
void ZoomOut();
QMap<int, QList<int> > GetIndexesForView(const mol::EntityView& view);
+ QMap<int, QList<int> > GetIndexesForSubject(const QString& subject, const QString& sequence_name=QString());
private:
QList<BaseRow*> rows_;