New SequenceViewer, support for seq::AlignmentHandle

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2297 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/gui/pymod/export_sequence_viewerV2.cc

@@ -32,6 +32,8 @@ void export_SequenceViewerV2()
   class_<SequenceViewerV2, boost::noncopyable >("SequenceViewerV2",init<>())
     .def("Show", &SequenceViewerV2::show)
     .def("Hide", &SequenceViewerV2::hide)
+    .def("AddAlignment", &SequenceViewerV2::AddAlignment)
+    .def("RemoveAlignment", &SequenceViewerV2::RemoveAlignment)
     .def("GetQObject",&get_py_qobject<SequenceViewerV2>)
     .add_property("qobject", &get_py_qobject<SequenceViewerV2>)
   ;

modules/gui/src/CMakeLists.txt

@@ -36,6 +36,7 @@ sequence_table_view.hh
 sequence_viewer.hh
 tick_painter.hh
 title_row.hh
+alignment_view_object.hh
 base_view_object.hh
 sequence_view_object.hh
 )
@@ -227,6 +228,7 @@ sequence/sequence_table_view.cc
 sequence/sequence_viewer.cc
 sequence/tick_painter.cc
 sequence/title_row.cc
+sequence/alignment_view_object.cc
 sequence/base_view_object.cc
 sequence/sequence_view_object.cc
 gosty_app.cc
@@ -360,6 +362,7 @@ sequence/sequence_table_view.hh
 sequence/sequence_viewer.hh
 sequence/tick_painter.hh
 sequence/title_row.hh
+sequence/alignment_view_object.hh
 sequence/base_view_object.hh
 sequence/sequence_view_object.hh
 plot_viewer/plot_axis_base.hh

modules/gui/src/sequence/alignment_view_object.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 "sequence_row.hh"
+#include "secstr_row.hh"
+
+#include "painter.hh"
+#include "background_painter.hh"
+#include "seq_secstr_painter.hh"
+#include "seq_selection_painter.hh"
+#include "seq_text_painter.hh"
+
+#include "alignment_view_object.hh"
+
+namespace ost { namespace gui {
+
+AlignmentViewObject::AlignmentViewObject(const seq::AlignmentHandle& alignment, QObject* parent): SequenceViewObject(parent)
+{
+  for(int i=0; i<alignment.GetCount();i++){
+    seq::SequenceHandle seq_handle = alignment.GetSequence(i).Copy();
+    this->AddSequence(seq_handle, seq_handle.GetName().c_str());
+  }
+}
+
+}}

modules/gui/src/sequence/alignment_view_object.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_ALIGNMENT_VIEW_OBJECT
+#define OST_SEQUENCE_VIEWER_ALIGNMENT_VIEW_OBJECT
+
+/*
+  Author: Stefan Scheuber
+ */
+
+#include <ost/seq/alignment_handle.hh>
+
+#include "sequence_view_object.hh"
+
+namespace ost { namespace gui {
+
+class AlignmentViewObject : public SequenceViewObject
+{
+  Q_OBJECT
+
+public:
+  AlignmentViewObject(const seq::AlignmentHandle& alignment, QObject* parent = 0);
+};
+
+
+}}
+
+#endif

modules/gui/src/sequence/sequence_model.cc

@@ -26,6 +26,7 @@
 
 #include <QtGui>
 
+#include "alignment_view_object.hh"
 #include "sequence_view_object.hh"
 
 #include "title_row.hh"
@@ -78,6 +79,19 @@ void SequenceModel::InsertChain(QString& name, mol::ChainView& view){
   this->endInsertRows();
 }
 
+void SequenceModel::InsertAlignment(const seq::AlignmentHandle& alignment){
+  int cols = this->columnCount();
+  int new_cols = alignment.GetLength();
+  this->beginInsertRows(QModelIndex(),this->rowCount(),this->rowCount()+alignment.GetCount()-1);
+  objects_.append(new AlignmentViewObject(alignment, this));
+  if(new_cols > cols){
+    this->max_columns = new_cols;
+    this->beginInsertColumns(QModelIndex(), cols, new_cols);
+    this->endInsertColumns();
+  }
+  this->endInsertRows();
+}
+
 void SequenceModel::InsertSequences(const QList<QString>& names, seq::SequenceList& list){
   this->beginInsertRows(this->index(this->rowCount(),0),this->rowCount(),this->rowCount()+list.GetCount());
   objects_.append(new SequenceViewObject(list, names, this));
@@ -116,6 +130,10 @@ void SequenceModel::RemoveGfxEntity(gfx::EntityP& entity){
   }
 }
 
+void SequenceModel::RemoveAlignment(const seq::AlignmentHandle& alignment){
+
+}
+
 int SequenceModel::GetColumnCount() const{
   int cols = 0;
   for(int i = 0; i<objects_.size();i++){

modules/gui/src/sequence/sequence_model.hh

@@ -29,6 +29,7 @@
 #include <ost/mol/chain_view.hh>
 
 #include <ost/seq/sequence_list.hh>
+#include <ost/seq/alignment_handle.hh>
 
 #include <ost/gfx/entity.hh>
 
@@ -44,11 +45,13 @@ class SequenceModel : public QAbstractTableModel
 public:
   SequenceModel(QObject *parent = 0);
 
+  void InsertAlignment(const seq::AlignmentHandle& alignment);
   void InsertGfxEntity(gfx::EntityP& entity);
   void InsertChain(QString& name, mol::ChainView& view);
   void InsertSequence(QString& name, seq::SequenceHandle& seq);
   void InsertSequences(const QList<QString>& names, seq::SequenceList& list);
 
+  void RemoveAlignment(const seq::AlignmentHandle& alignment);
   void RemoveGfxEntity(gfx::EntityP& entity);
 
   QModelIndexList GetModelIndexes(gfx::EntityP& entity, const mol::EntityView& view);

modules/gui/src/sequence/sequence_view_object.cc

@@ -74,6 +74,9 @@ SequenceViewObject::SequenceViewObject(gfx::EntityP& entity, QObject* parent): B
   }
 }
 
+SequenceViewObject::SequenceViewObject(QObject* parent): BaseViewObject(parent), entity_(gfx::EntityP())
+{ }
+
 void SequenceViewObject::AddSequence(seq::SequenceHandle& sequence, const QString& name)
 {
   SequenceRow* new_row = new SequenceRow(name, sequence, this);

modules/gui/src/sequence/sequence_view_object.hh

@@ -43,6 +43,7 @@ public:
   SequenceViewObject(seq::SequenceHandle& sequence, const QString& name, QObject* parent = 0);
   SequenceViewObject(mol::ChainView& chain, const QString& name, QObject* parent = 0);
   SequenceViewObject(gfx::EntityP& entity, QObject* parent = 0);
+  SequenceViewObject(QObject* parent = 0);
 
   void AddSequence(seq::SequenceHandle& sequence, const QString& name=QString());
   void AddChain(mol::ChainView& chain, const QString& name=QString());

modules/gui/src/sequence/sequence_viewer.cc

@@ -128,6 +128,18 @@ void SequenceViewerV2::NodeRemoved(const gfx::GfxNodeP& node)
   }
 }
 
+void SequenceViewerV2::AddAlignment(const seq::AlignmentHandle& alignment)
+{
+  if(alignment.GetCount()>0 && alignment.GetLength()>0){
+    model_->InsertAlignment(alignment);
+  }
+}
+
+void SequenceViewerV2::RemoveAlignment(const seq::AlignmentHandle& alignment)
+{
+  model_->RemoveAlignment(alignment);
+}
+
 void SequenceViewerV2::UpdateSearchBar()
 {
   QStringList sequence_names_;

modules/gui/src/sequence/sequence_viewer.hh

@@ -25,6 +25,8 @@
 
 #include <QWidget>
 
+#include <ost/seq/alignment_handle.hh>
+
 #include <ost/gfx/scene.hh>
 #include <ost/gfx/gfx_object.hh>
 
@@ -49,6 +51,9 @@ public:
   virtual void NodeRemoved(const gfx::GfxNodeP& node);
   virtual void SelectionChanged(const gfx::GfxObjP& o, const mol::EntityView& view);
 
+  virtual void AddAlignment(const seq::AlignmentHandle& alignment);
+  virtual void RemoveAlignment(const seq::AlignmentHandle& alignment);
+
   virtual bool Restore(const QString&){return true;};
   virtual bool Save(const QString&){return true;};