New SequenceViewer, added searchbar (Ctrl+F)

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2237 5a81b35b-ba03-0410-adc8-b2c5c5119f08

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

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;

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;
 
 

modules/gui/src/sequence/sequence_search_bar.cc

+//------------------------------------------------------------------------------
+// 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);
+}
+
+}}

modules/gui/src/sequence/sequence_search_bar.hh

+//------------------------------------------------------------------------------
+// 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

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);

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);
 }

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_;
 

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;

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_;