New SequenceViewer, added classes for secstr rows and normal sequence rows

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2176 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/gui/src/CMakeLists.txt

@@ -21,13 +21,15 @@ sequence_search_bar.hh
 )
 
 set(OST_GUI_SEQUENCE_VIEW_HEADERS
-painter.hh
 base_row.hh
+painter.hh
+secstr_row.hh
 seq_secstr_painter.hh
 seq_selection_painter.hh
 seq_text_painter.hh
 sequence_delegate.hh
 sequence_model.hh
+sequence_row.hh
 sequence_table_view.hh
 sequence_viewer.hh
 view_object.hh
@@ -207,11 +209,13 @@ sequence_viewer/sequence_viewer.cc
 sequence_viewer/sequence_scene.cc
 sequence_viewer/sequence_search_bar.cc
 sequence/base_row.cc
+sequence/secstr_row.cc
 sequence/seq_secstr_painter.cc
 sequence/seq_selection_painter.cc
 sequence/seq_text_painter.cc
 sequence/sequence_delegate.cc
 sequence/sequence_model.cc
+sequence/sequence_row.cc
 sequence/sequence_table_view.cc
 sequence/sequence_viewer.cc
 sequence/view_object.cc
@@ -331,13 +335,15 @@ sequence_viewer/sequence_viewer_base.hh
 sequence_viewer/sequence_viewer.hh
 sequence_viewer/sequence_scene.hh
 sequence_viewer/sequence_search_bar.hh
-sequence/painter.hh
 sequence/base_row.hh
+sequence/painter.hh
+sequence/secstr_row.hh
 sequence/seq_secstr_painter.hh
 sequence/seq_selection_painter.hh
 sequence/seq_text_painter.hh
 sequence/sequence_delegate.hh
 sequence/sequence_model.hh
+sequence/sequence_row.hh
 sequence/sequence_table_view.hh
 sequence/sequence_viewer.hh
 sequence/view_object.hh

modules/gui/src/sequence/base_row.cc

@@ -29,7 +29,24 @@
 namespace ost { namespace gui {
 
 BaseRow::BaseRow(QObject *parent) : QObject(parent)
-{ }
+{ this->SetFont(font_); }
+
+BaseRow::BaseRow(QFont font, QObject *parent) : QObject(parent)
+{
+  this->SetFont(font);
+}
+
+int BaseRow::GetColumnCount() const
+{
+  return -1;
+}
+
+void BaseRow::Init()
+{
+  QFontMetrics metrics = QFontMetrics(font_);
+  default_font_size_=QSize(metrics.boundingRect('W').width(),metrics.boundingRect('|').height());
+  default_cell_size_ = QSize(metrics.boundingRect('W').width()+2,metrics.boundingRect('|').height()*2);
+}
 
 void BaseRow::InsertPainter(Painter* painter, int pos)
 {
@@ -67,6 +84,29 @@ bool BaseRow::IsPainterPosValid(int pos)
   return false;
 }
 
+const QFont& BaseRow::GetFont() const
+{
+  return font_;
+}
+
+void BaseRow::SetFont(const QFont& font)
+{
+  font_ = font;
+  QFontMetrics metrics = QFontMetrics(font_);
+  default_font_size_=QSize(metrics.boundingRect('W').width(),metrics.boundingRect('|').height());
+  default_cell_size_ = QSize(metrics.boundingRect('W').width()+2,metrics.boundingRect('|').height()*2);
+}
+
+const QSize& BaseRow::GetFontSize() const
+{
+  return default_font_size_;
+}
+
+const QSize& BaseRow::GetCellSize() const
+{
+  return default_cell_size_;
+}
+
 const PainterList& BaseRow::GetPainters() const
 {
   return painter_;

modules/gui/src/sequence/base_row.hh

@@ -16,8 +16,8 @@
 // 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_ROW
-#define OST_SEQUENCE_VIEWER_ROW
+#ifndef OST_SEQUENCE_VIEWER_BASE_ROW
+#define OST_SEQUENCE_VIEWER_BASE_ROW
 
 /*
   Author: Stefan Scheuber
@@ -37,15 +37,24 @@ class BaseRow : public QObject
 
 public:
   BaseRow(QObject *parent = 0);
+  BaseRow(QFont font, QObject *parent = 0);
+
+  void Init();
+
+  virtual int GetColumnCount() const;
 
   void InsertPainter(Painter* painter, int pos = -1);
   void RemovePainter(Painter* painter);
-
   Painter* GetPainter(int pos);
   int GetPainterCount();
-
   const PainterList& GetPainters() const;
 
+  const QFont& GetFont() const;
+  void SetFont(const QFont& font);
+  const QSize& GetFontSize() const;
+
+  virtual const QSize& GetCellSize() const;
+
   virtual QVariant GetData(int column, int role) const;
   virtual bool SetData(int column, const QVariant& value, int role);
   virtual Qt::ItemFlags Flags(int column) const;
@@ -54,6 +63,9 @@ public:
 private:
   bool IsPainterPosValid(int pos);
   PainterList painter_;
+  QFont font_;
+  QSize default_font_size_;
+  QSize default_cell_size_;
 };
 
 typedef QList<BaseRow*> BaseRowList;

modules/gui/src/sequence/secstr_row.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: Stefan Scheuber
+ */
+
+
+#include <QtGui>
+
+#include <ost/mol/mol.hh>
+#include <ost/mol/view_op.hh>
+
+#include <ost/gfx/entity.hh>
+
+#include "secstr_row.hh"
+
+namespace ost { namespace gui {
+
+SecStrRow::SecStrRow(const QString& name, mol::ChainView& chain, ViewObject* parent) : SequenceRow(name,parent)
+{ this->SetChain(chain); }
+
+void SecStrRow::SetSequence(seq::SequenceHandle& sequence)
+{
+  //Do nothing
+}
+
+void SecStrRow::SetChain(mol::ChainView& chain)
+{
+  String seq_str;
+  seq_str.reserve(chain.GetResidueCount());
+  for (mol::ResidueViewList::const_iterator r=chain.GetResidueList().begin(),
+       e2=chain.GetResidueList().end(); r!=e2; ++r) {
+    mol::ResidueView res=*r;
+    seq_str.append(1, res.GetOneLetterCode());
+  }
+  if (!seq_str.empty()) {
+    seq::SequenceHandle sequence=seq::CreateSequence(this->GetName().toStdString(), seq_str);
+    mol::EntityView v_one_chain=chain.GetEntity().GetHandle().CreateEmptyView();
+    v_one_chain.AddChain(chain, mol::ViewAddFlag::INCLUDE_ALL);
+    sequence.AttachView(v_one_chain);
+
+    mol::alg::SecStructureSegments sec = mol::alg::ExtractSecStructureSegments(chain);
+    secstr_ = QVarLengthArray<mol::SecStructure>(chain.GetResidueCount());
+    for (mol::alg::SecStructureSegments::iterator i=sec.begin(),
+         e=sec.end(); i!=e; ++i) {
+      mol::alg::SecStructureSegment s=*i;
+      for(int i = s.first; i <= s.last ;i++){
+        secstr_[i] = s.ss_type;
+      }
+    }
+    this->chain_ = chain;
+    this->SetSequence(sequence);
+  }
+}
+
+QVariant SecStrRow::GetData(int column, int role) const
+{
+  if(column > 0 && column < this->GetSequence().GetLength()){
+    if (role==Qt::UserRole){
+      QVariant variant;
+      variant.setValue(secstr_);
+      return variant;
+    }
+    if (role==Qt::UserRole+1){
+      return QVariant(this->GetFontSize());
+    }
+  }
+  return SequenceRow::GetData(column, role);
+}
+
+void SecStrRow::DoubleClicked(int column)
+{
+  if(column>0){
+    column-=1;
+    if(this->secstr_.size()>0 && column < this->secstr_.size()){
+      mol::SecStructure& src_str = this->secstr_[column];
+      QVarLengthArray<bool> src_type(3);
+      src_type[0] = src_str.IsHelical();
+      src_type[1] = src_str.IsExtended();
+      src_type[2] = src_str.IsCoil();
+      int i = column;
+      QSet<int> cols_to_add;
+      mol::SecStructure& col_str = this->secstr_[i];
+      while(i >= 0 && (col_str = this->secstr_[i])){
+        if(src_type[0] == col_str.IsHelical()
+            && src_type[1] == col_str.IsExtended()
+            && src_type[2] == col_str.IsCoil()){
+        cols_to_add.insert(i+1);
+        --i;
+        }
+        else{break;}
+      }
+      i = column + 1;
+      if(i < this->secstr_.size()){
+        while(i < this->secstr_.size() && (col_str = this->secstr_[i])){
+          if(src_type[0] == col_str.IsHelical()
+              && src_type[1] == col_str.IsExtended()
+              && src_type[2] == col_str.IsCoil()){
+          cols_to_add.insert(i+1);
+          ++i;
+          }
+          else{
+            break;
+          }
+        }
+      }
+      this->SetSelection(cols_to_add, QSet<int>());
+    }
+  }
+  else{
+    SequenceRow::DoubleClicked(column);
+  }
+}
+
+}}

modules/gui/src/sequence/secstr_row.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_SECSTR_ROW
+#define OST_SEQUENCE_VIEWER_SECSTR_ROW
+
+/*
+  Author: Stefan Scheuber
+ */
+
+#include <QObject>
+#include <QVarLengthArray>
+
+#include <ost/mol/chain_view.hh>
+#include <ost/mol/alg/sec_structure_segments.hh>
+
+#include "sequence_row.hh"
+
+namespace ost { namespace gui {
+
+class SecStrRow : public SequenceRow
+{
+  Q_OBJECT
+
+public:
+  SecStrRow(const QString& name, mol::ChainView& chain, ViewObject* parent);
+
+  virtual QVariant GetData(int column, int role) const;
+  virtual void DoubleClicked(int column);
+
+  void SetSequence(seq::SequenceHandle& sequence);
+  void SetChain(mol::ChainView& chain);
+
+private:
+  mol::ChainView chain_;
+  QVarLengthArray<mol::SecStructure> secstr_;
+};
+
+typedef QList<BaseRow*> BaseRowList;
+
+}}
+
+Q_DECLARE_METATYPE(QVarLengthArray<ost::mol::SecStructure>)
+
+#endif

modules/gui/src/sequence/sequence_row.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: Stefan Scheuber
+ */
+
+
+#include <QtGui>
+
+#include <ost/mol/mol.hh>
+#include <ost/mol/view_op.hh>
+
+#include <ost/gfx/entity.hh>
+
+#include "view_object.hh"
+#include "sequence_row.hh"
+
+namespace ost { namespace gui {
+
+SequenceRow::SequenceRow(const QString& name, seq::SequenceHandle& sequence, ViewObject* parent) : BaseRow(QFont("Courier",11),parent), name_(name), sequence_(sequence)
+{ }
+
+SequenceRow::SequenceRow(const QString& name, ViewObject* parent) : BaseRow(QFont("Courier",11),parent), name_(name)
+{ }
+
+int SequenceRow::GetColumnCount() const
+{
+  return sequence_.GetLength()+1;
+}
+
+void SequenceRow::SetName(const QString& name)
+{
+  this->name_ = name;
+}
+
+const QString& SequenceRow::GetName()
+{
+  return this->name_;
+}
+
+void SequenceRow::SetSequence(seq::SequenceHandle& sequence)
+{
+  this->sequence_ = sequence;
+}
+
+const seq::SequenceHandle& SequenceRow::GetSequence() const
+{
+  return this->sequence_;
+}
+
+QVariant SequenceRow::GetData(int column, int role) const
+{
+  if(column<0 || column > sequence_.GetLength())return QVariant();
+
+  if(column == 0) {
+    if (role == Qt::DisplayRole){
+      return QVariant(this->name_);
+    }
+  }
+  else if(column > 0) {
+    if (role==Qt::DisplayRole) {
+      return QVariant(QString(this->sequence_.GetOneLetterCode(column - 1)));
+    }
+    if (role==Qt::FontRole){
+      return QVariant(this->GetFont());
+    }
+    if (role==Qt::SizeHintRole){
+      return QVariant(this->GetCellSize());
+    }
+  }
+  return QVariant();
+}
+
+Qt::ItemFlags SequenceRow::Flags(int column) const
+{
+  if(column<0 || column > this->GetColumnCount())return Qt::NoItemFlags;
+
+  if(column==0){
+    return Qt::ItemIsSelectable|Qt::ItemIsEnabled;
+  }
+  else if(column>0){
+    return Qt::ItemIsSelectable|Qt::ItemIsEnabled;
+  }
+  return BaseRow::Flags(column);
+}
+
+void SequenceRow::DoubleClicked(int column)
+{
+  QSet<int> all;
+  int seq_length = this->sequence_.GetLength();
+  for(int i = 0; i < seq_length; i++){
+    all.insert(i+1);
+  }
+  this->SetSelection(all,QSet<int>());
+}
+
+void SequenceRow::SetSelection(const QSet<int>& added, const QSet<int>& removed)
+{
+  ViewObject* view_object = qobject_cast<ViewObject*>(this->parent());
+  if(view_object){
+    if(gfx::EntityP entity = view_object->GetGfxObject()){
+      mol::EntityView sel = entity->GetSelection();
+      mol::EntityView view = this->sequence_.GetAttachedView().GetHandle().CreateEmptyView();
+
+      QSetIterator<int> i(removed);
+      while (i.hasNext()){
+        int column = i.next()-1;
+        if(column >= 0 && column < this->sequence_.GetLength()){
+          if (mol::ResidueView rv = this->sequence_.GetResidue(this->sequence_.GetResidueIndex(column))) {
+            view.AddResidue(rv, mol::ViewAddFlag::INCLUDE_ATOMS);
+          }
+        }
+      }
+      sel = mol::Difference(sel,view);
+      view = this->sequence_.GetAttachedView().GetHandle().CreateEmptyView();
+      i = QSetIterator<int>(added);
+      while (i.hasNext()){
+        int column = i.next()-1;
+        if(column >= 0 && column < this->sequence_.GetLength()){
+          if (mol::ResidueView rv=this->sequence_.GetResidue(this->sequence_.GetResidueIndex(column))) {
+            view.AddResidue(rv, mol::ViewAddFlag::INCLUDE_ATOMS);
+          }
+        }
+      }
+      sel = mol::Union(sel,view);
+      sel.AddAllInclusiveBonds();
+      entity->SetSelection(sel);
+    }
+  }
+}
+
+}}

modules/gui/src/sequence/sequence_row.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_ROW
+#define OST_SEQUENCE_VIEWER_SEQUENCE_ROW
+
+/*
+  Author: Stefan Scheuber
+ */
+
+#include <QObject>
+
+#include <ost/seq/sequence_handle.hh>
+
+#include "base_row.hh"
+
+namespace ost { namespace gui {
+
+class ViewObject;
+
+class SequenceRow : public BaseRow
+{
+  Q_OBJECT
+
+public:
+  SequenceRow(const QString& name, seq::SequenceHandle& sequence, ViewObject* parent);
+  SequenceRow(const QString& name, ViewObject* parent);
+
+  virtual int GetColumnCount() const;
+
+  virtual QVariant GetData(int column, int role) const;
+  virtual Qt::ItemFlags Flags(int column) const;
+  virtual void DoubleClicked(int column);
+
+  void SetName(const QString& name);
+  const QString& GetName();
+
+  virtual void SetSequence(seq::SequenceHandle& sequence);
+  const seq::SequenceHandle& GetSequence() const;
+
+  void SetSelection(const QSet<int>& added, const QSet<int>& removed);
+
+private:
+  QString name_;
+  seq::SequenceHandle sequence_;
+};
+
+typedef QList<BaseRow*> BaseRowList;
+
+}}
+
+#endif