diff --git a/modules/gui/src/CMakeLists.txt b/modules/gui/src/CMakeLists.txt
index b8443780cb107591dabc42a9673dd059a39bedd7..f646e95be392341a479c836cbfbe806a7fa2f5bd 100644
--- a/modules/gui/src/CMakeLists.txt
+++ b/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
diff --git a/modules/gui/src/sequence/base_row.cc b/modules/gui/src/sequence/base_row.cc
index 823b4f86ba239ab11b9606c3b8497b38bd93ad72..dab716f65d8d4b186068ef78f8c9df4b22603ff1 100644
--- a/modules/gui/src/sequence/base_row.cc
+++ b/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_;
diff --git a/modules/gui/src/sequence/base_row.hh b/modules/gui/src/sequence/base_row.hh
index 9ed545fe00820dc5a84aa084198bd844bc34191b..5d749c5d29015744dbfc2936bab2f226edfe0908 100644
--- a/modules/gui/src/sequence/base_row.hh
+++ b/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;
diff --git a/modules/gui/src/sequence/secstr_row.cc b/modules/gui/src/sequence/secstr_row.cc
new file mode 100644
index 0000000000000000000000000000000000000000..680533df1612adc21b41cc784b4d4b9297a24758
--- /dev/null
+++ b/modules/gui/src/sequence/secstr_row.cc
@@ -0,0 +1,132 @@
+//------------------------------------------------------------------------------
+// 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);
+ }
+}
+
+}}
diff --git a/modules/gui/src/sequence/secstr_row.hh b/modules/gui/src/sequence/secstr_row.hh
new file mode 100644
index 0000000000000000000000000000000000000000..4e3286a77ce15390c8cc47c7c4308731924abd4d
--- /dev/null
+++ b/modules/gui/src/sequence/secstr_row.hh
@@ -0,0 +1,60 @@
+//------------------------------------------------------------------------------
+// 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
diff --git a/modules/gui/src/sequence/sequence_row.cc b/modules/gui/src/sequence/sequence_row.cc
new file mode 100644
index 0000000000000000000000000000000000000000..6be93018c3572bce633f614f1d7bc42de53f087b
--- /dev/null
+++ b/modules/gui/src/sequence/sequence_row.cc
@@ -0,0 +1,149 @@
+//------------------------------------------------------------------------------
+// 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);
+ }
+ }
+}
+
+}}
diff --git a/modules/gui/src/sequence/sequence_row.hh b/modules/gui/src/sequence/sequence_row.hh
new file mode 100644
index 0000000000000000000000000000000000000000..07c1c1a6e1cec30f56e369200d5aaf69877e67ae
--- /dev/null
+++ b/modules/gui/src/sequence/sequence_row.hh
@@ -0,0 +1,67 @@
+//------------------------------------------------------------------------------
+// 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