From 9fcb2f6dfc60526f2b2d00679431f8814ef10ba5 Mon Sep 17 00:00:00 2001
From: stefan <stefan@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Fri, 28 May 2010 15:09:35 +0000
Subject: [PATCH] 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 | 2 +
modules/gui/src/CMakeLists.txt | 3 ++
.../gui/src/sequence/alignment_view_object.cc | 51 +++++++++++++++++++
.../gui/src/sequence/alignment_view_object.hh | 43 ++++++++++++++++
modules/gui/src/sequence/sequence_model.cc | 18 +++++++
modules/gui/src/sequence/sequence_model.hh | 3 ++
.../gui/src/sequence/sequence_view_object.cc | 3 ++
.../gui/src/sequence/sequence_view_object.hh | 1 +
modules/gui/src/sequence/sequence_viewer.cc | 12 +++++
modules/gui/src/sequence/sequence_viewer.hh | 5 ++
10 files changed, 141 insertions(+)
create mode 100644 modules/gui/src/sequence/alignment_view_object.cc
create mode 100644 modules/gui/src/sequence/alignment_view_object.hh
diff --git a/modules/gui/pymod/export_sequence_viewerV2.cc b/modules/gui/pymod/export_sequence_viewerV2.cc
index cd010952f..0a744dccc 100644
--- a/modules/gui/pymod/export_sequence_viewerV2.cc
+++ b/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>)
;
diff --git a/modules/gui/src/CMakeLists.txt b/modules/gui/src/CMakeLists.txt
index b4ca43ed3..36b468e63 100644
--- a/modules/gui/src/CMakeLists.txt
+++ b/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
diff --git a/modules/gui/src/sequence/alignment_view_object.cc b/modules/gui/src/sequence/alignment_view_object.cc
new file mode 100644
index 000000000..bee250f9f
--- /dev/null
+++ b/modules/gui/src/sequence/alignment_view_object.cc
@@ -0,0 +1,51 @@
+//------------------------------------------------------------------------------
+// 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());
+ }
+}
+
+}}
diff --git a/modules/gui/src/sequence/alignment_view_object.hh b/modules/gui/src/sequence/alignment_view_object.hh
new file mode 100644
index 000000000..a75159c22
--- /dev/null
+++ b/modules/gui/src/sequence/alignment_view_object.hh
@@ -0,0 +1,43 @@
+//------------------------------------------------------------------------------
+// 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
diff --git a/modules/gui/src/sequence/sequence_model.cc b/modules/gui/src/sequence/sequence_model.cc
index dc26ce348..e054a9046 100644
--- a/modules/gui/src/sequence/sequence_model.cc
+++ b/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++){
diff --git a/modules/gui/src/sequence/sequence_model.hh b/modules/gui/src/sequence/sequence_model.hh
index 98cbe3aa4..218dbb4c9 100644
--- a/modules/gui/src/sequence/sequence_model.hh
+++ b/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);
diff --git a/modules/gui/src/sequence/sequence_view_object.cc b/modules/gui/src/sequence/sequence_view_object.cc
index d3e53093a..b5a44c067 100644
--- a/modules/gui/src/sequence/sequence_view_object.cc
+++ b/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);
diff --git a/modules/gui/src/sequence/sequence_view_object.hh b/modules/gui/src/sequence/sequence_view_object.hh
index 9d85f85b8..9c443095f 100644
--- a/modules/gui/src/sequence/sequence_view_object.hh
+++ b/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());
diff --git a/modules/gui/src/sequence/sequence_viewer.cc b/modules/gui/src/sequence/sequence_viewer.cc
index d00a1b07b..c73f0a51a 100644
--- a/modules/gui/src/sequence/sequence_viewer.cc
+++ b/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_;
diff --git a/modules/gui/src/sequence/sequence_viewer.hh b/modules/gui/src/sequence/sequence_viewer.hh
index b04d242dc..b4134f1fe 100644
--- a/modules/gui/src/sequence/sequence_viewer.hh
+++ b/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;};
--
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