From ba26165951a034fec35c81719544d5bef562af05 Mon Sep 17 00:00:00 2001
From: stefan <stefan@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Mon, 3 May 2010 10:53:10 +0000
Subject: [PATCH] New sequence viewer, added secondary structure rendering
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2163 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/gui/src/CMakeLists.txt | 3 +
.../gui/src/sequence/seq_secstr_painter.cc | 99 +++++++++++++++++++
.../gui/src/sequence/seq_secstr_painter.hh | 43 ++++++++
modules/gui/src/sequence/seq_text_painter.cc | 4 +-
modules/gui/src/sequence/sequence_model.cc | 12 +++
modules/gui/src/sequence/sequence_model.hh | 3 +
modules/gui/src/sequence/sequence_viewer.cc | 16 +--
modules/gui/src/sequence/view_object.cc | 76 +++++++++++---
modules/gui/src/sequence/view_object.hh | 30 +++++-
9 files changed, 257 insertions(+), 29 deletions(-)
create mode 100644 modules/gui/src/sequence/seq_secstr_painter.cc
create mode 100644 modules/gui/src/sequence/seq_secstr_painter.hh
diff --git a/modules/gui/src/CMakeLists.txt b/modules/gui/src/CMakeLists.txt
index 01ed36015..4bba75bb2 100644
--- a/modules/gui/src/CMakeLists.txt
+++ b/modules/gui/src/CMakeLists.txt
@@ -23,6 +23,7 @@ sequence_search_bar.hh
set(OST_GUI_SEQUENCE_VIEW_HEADERS
painter.hh
row.hh
+seq_secstr_painter.hh
seq_selection_painter.hh
seq_text_painter.hh
sequence_delegate.hh
@@ -206,6 +207,7 @@ sequence_viewer/sequence_viewer.cc
sequence_viewer/sequence_scene.cc
sequence_viewer/sequence_search_bar.cc
sequence/row.cc
+sequence/seq_secstr_painter.cc
sequence/seq_selection_painter.cc
sequence/seq_text_painter.cc
sequence/sequence_delegate.cc
@@ -331,6 +333,7 @@ sequence_viewer/sequence_scene.hh
sequence_viewer/sequence_search_bar.hh
sequence/painter.hh
sequence/row.hh
+sequence/seq_secstr_painter.hh
sequence/seq_selection_painter.hh
sequence/seq_text_painter.hh
sequence/sequence_delegate.hh
diff --git a/modules/gui/src/sequence/seq_secstr_painter.cc b/modules/gui/src/sequence/seq_secstr_painter.cc
new file mode 100644
index 000000000..095841b25
--- /dev/null
+++ b/modules/gui/src/sequence/seq_secstr_painter.cc
@@ -0,0 +1,99 @@
+//------------------------------------------------------------------------------
+// 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 "seq_secstr_painter.hh"
+#include "view_object.hh"
+
+namespace ost { namespace gui {
+
+SeqSecStrPainter::SeqSecStrPainter(QObject* parent)
+ : Painter(parent)
+{}
+
+void SeqSecStrPainter::Paint(QPainter* painter, const QStyleOptionViewItem& option, const QModelIndex& index){
+ QVariant var = index.data(Qt::UserRole);
+ painter->save();
+ painter->setPen(QPen(Qt::lightGray));
+ ListEntry entry = index.data(Qt::UserRole).value<ListEntry>();
+ if(entry.secstr.size()>0){
+ QSize size = index.data(Qt::UserRole+1).toSize();
+ QVarLengthArray<mol::SecStructure>& sec_str = entry.secstr;
+ int column = index.column()-1;
+ if(column < sec_str.size()){
+ mol::SecStructure sec_element = sec_str[column];
+
+ int std_diff = (size.height()/2);
+ int diff = size.height()/1.25;
+ int center = option.rect.top()+(option.rect.height()/2);
+
+ if (sec_element.IsCoil()) {
+ int pos = center - std_diff;
+ painter->drawLine(option.rect.left(),pos,option.rect.right(),pos);
+ pos = center + std_diff;
+ painter->drawLine(option.rect.left(),pos,option.rect.right(),pos);
+ //stack.push_back(QPointF(s.first*advance_, -.6*height_));
+ //stack.push_back(QPointF((s.last+1)*advance_, -.6*height_));
+ } else if (sec_element.IsHelical()) {
+ int pos = center - diff;
+ painter->drawLine(option.rect.left(),pos,option.rect.right(),pos);
+ pos = center + diff;
+ painter->drawLine(option.rect.left(),pos,option.rect.right(),pos);
+ if(column - 1 > 0 && !sec_str[column-1].IsHelical()){
+ painter->drawLine(option.rect.left(),center+std_diff,option.rect.left(),center+diff);
+ painter->drawLine(option.rect.left(),center-std_diff,option.rect.left(),center-diff);
+ }
+ if(column + 1 < sec_str.size() && !sec_str[column+1].IsHelical()){
+ painter->drawLine(option.rect.right(),center+std_diff,option.rect.right(),center+diff);
+ painter->drawLine(option.rect.right(),center-std_diff,option.rect.right(),center-diff);
+ }
+ } else if (sec_element.IsExtended()) {
+ int pos = center - diff;
+ if(column - 1 > 0 && !sec_str[column-1].IsExtended()){
+ painter->drawLine(option.rect.left(),center+std_diff,option.rect.left(),center+diff);
+ painter->drawLine(option.rect.left(),center-std_diff,option.rect.left(),center-diff);
+ }
+ if(column + 1 < sec_str.size() && !sec_str[column+1].IsExtended()){
+ int max_diff = size.height();
+ painter->drawLine(option.rect.left(),center+diff,option.rect.left(),center+max_diff);
+ painter->drawLine(option.rect.left(),center-diff,option.rect.left(),center-max_diff);
+ painter->drawLine(option.rect.left(),center+max_diff,option.rect.right(),center+std_diff);
+ painter->drawLine(option.rect.left(),center-max_diff,option.rect.right(),center-std_diff);
+ }
+ else{
+ painter->drawLine(option.rect.left(),pos,option.rect.right(),pos);
+ pos = center + diff;
+ painter->drawLine(option.rect.left(),pos,option.rect.right(),pos);
+ }
+ }
+ if(!(column+1 < sec_str.size())){
+ painter->drawLine(option.rect.right(),center+std_diff,option.rect.right(),center-std_diff);
+ }
+ }
+ }
+ painter->restore();
+}
+
+}}
diff --git a/modules/gui/src/sequence/seq_secstr_painter.hh b/modules/gui/src/sequence/seq_secstr_painter.hh
new file mode 100644
index 000000000..7255a5f3e
--- /dev/null
+++ b/modules/gui/src/sequence/seq_secstr_painter.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_SEQ_SECSTR_PAINTER
+#define OST_SEQUENCE_VIEWER_SEQ_SECSTR_PAINTER
+
+/*
+ Author: Stefan Scheuber
+ */
+
+#include <QObject>
+
+#include "painter.hh"
+
+namespace ost { namespace gui {
+
+class SeqSecStrPainter : public Painter
+{
+ Q_OBJECT
+public:
+ SeqSecStrPainter(QObject* parent = 0);
+ void Paint(QPainter *painter, const QStyleOptionViewItem &option,
+ const QModelIndex &index);
+};
+
+}}
+
+#endif
diff --git a/modules/gui/src/sequence/seq_text_painter.cc b/modules/gui/src/sequence/seq_text_painter.cc
index 9ac48a688..30c1e1623 100644
--- a/modules/gui/src/sequence/seq_text_painter.cc
+++ b/modules/gui/src/sequence/seq_text_painter.cc
@@ -38,8 +38,8 @@ void SeqTextPainter::Paint(QPainter* painter, const QStyleOptionViewItem& option
QVariant value = index.data(Qt::DisplayRole);
if (value.isValid()){
QString text = value.toString();
- painter->setFont(QFont("Courier",10));
- painter->drawText(option.rect, Qt::AlignLeft|Qt::AlignVCenter, text);
+ painter->setFont(index.data(Qt::FontRole).value<QFont>());
+ painter->drawText(option.rect, Qt::AlignCenter, text);
}
painter->restore();
}
diff --git a/modules/gui/src/sequence/sequence_model.cc b/modules/gui/src/sequence/sequence_model.cc
index 06199fbf4..f52ddfd60 100644
--- a/modules/gui/src/sequence/sequence_model.cc
+++ b/modules/gui/src/sequence/sequence_model.cc
@@ -45,6 +45,18 @@ void SequenceModel::InsertSequence(QString& name, seq::SequenceHandle& seq){
this->endInsertRows();
}
+void SequenceModel::InsertChain(QString& name, mol::ChainView& view){
+ int cols = this->columnCount();
+ int new_cols = view.GetResidueCount();
+ this->beginInsertRows(QModelIndex(),this->rowCount(),this->rowCount());
+ objects_.append(new ViewObject(view, name, this));
+ if(new_cols > cols){
+ this->beginInsertColumns(QModelIndex(), cols, new_cols);
+ this->endInsertColumns();
+ }
+ this->endInsertRows();
+}
+
void SequenceModel::InsertSequences(QString& name, seq::SequenceList& list){
this->beginInsertRows(this->index(this->rowCount(),0),this->rowCount(),this->rowCount()+list.GetCount());
objects_.append(new ViewObject(list, name, this));
diff --git a/modules/gui/src/sequence/sequence_model.hh b/modules/gui/src/sequence/sequence_model.hh
index 234cebc7b..2b7bc481b 100644
--- a/modules/gui/src/sequence/sequence_model.hh
+++ b/modules/gui/src/sequence/sequence_model.hh
@@ -25,6 +25,8 @@
#include <QAbstractTableModel>
+#include <ost/mol/chain_view.hh>
+
#include <ost/seq/sequence_list.hh>
#include "sequence_model.hh"
@@ -39,6 +41,7 @@ class SequenceModel : public QAbstractTableModel
public:
SequenceModel(QObject *parent = 0);
+ void InsertChain(QString& name, mol::ChainView& view);
void InsertSequence(QString& name, seq::SequenceHandle& seq);
void InsertSequences(QString& name, seq::SequenceList& list);
diff --git a/modules/gui/src/sequence/sequence_viewer.cc b/modules/gui/src/sequence/sequence_viewer.cc
index 4fa20eac3..25fbcfee1 100644
--- a/modules/gui/src/sequence/sequence_viewer.cc
+++ b/modules/gui/src/sequence/sequence_viewer.cc
@@ -67,25 +67,11 @@ void SequenceViewerV2::NodeAdded(const gfx::GfxNodeP& n)
for (mol::ChainViewList::const_iterator c=v.GetChainList().begin(),
e1=v.GetChainList().end(); c!=e1; ++c) {
mol::ChainView chain=*c;
- 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()) {
- continue;
- }
QString name = QString(o->GetName().c_str());
if (chain.GetName()!="" && chain.GetName()!=" ") {
name= name + " ("+chain.GetName().c_str()+")";
}
- seq::SequenceHandle sequence=seq::CreateSequence(name.toStdString(), seq_str);
- mol::EntityView v_one_chain=v.GetHandle().CreateEmptyView();
- v_one_chain.AddChain(chain, mol::ViewAddFlag::INCLUDE_ALL);
- sequence.AttachView(v_one_chain);
- model_->InsertSequence(name,sequence);
+ model_->InsertChain(name,chain);
}
seq_table_view_->resizeColumnsToContents();
seq_table_view_->resizeRowsToContents();
diff --git a/modules/gui/src/sequence/view_object.cc b/modules/gui/src/sequence/view_object.cc
index 43d6601e0..ce504fd8f 100644
--- a/modules/gui/src/sequence/view_object.cc
+++ b/modules/gui/src/sequence/view_object.cc
@@ -24,9 +24,12 @@
#include <QtGui>
+#include <ost/mol/mol.hh>
+
#include "painter.hh"
-#include "seq_text_painter.hh"
+#include "seq_secstr_painter.hh"
#include "seq_selection_painter.hh"
+#include "seq_text_painter.hh"
#include "view_object.hh"
@@ -47,19 +50,25 @@ ViewObject::ViewObject(seq::SequenceHandle& sequence, const QString& name, QObje
this->Init();
}
+ViewObject::ViewObject(mol::ChainView& chain, const QString& name, QObject *parent): QObject(parent), name_(name)
+{
+ this->AddChain(chain);
+ this->Init();
+}
+
void ViewObject::Init()
{
font_ = QFont("Courier",10);
QFontMetrics metrics = QFontMetrics(font_);
- default_size_ = QSize(metrics.width(QString("_"))+2,metrics.height()+2);
+ default_size_=QSize(metrics.boundingRect('W').width(),metrics.boundingRect('|').height());
+ default_cell_size_ = QSize(metrics.boundingRect('W').width()+2,metrics.boundingRect('|').height()+2);
}
void ViewObject::InsertRow(int pos, Row* row)
{
if(pos >= 0 && pos <= rows_.size()){
- seq::SequenceHandle sequence = seq::SequenceHandle();
- QPair<Row*, seq::SequenceHandle> pair(row,sequence);
- rows_.insert(pos,pair);
+ ListEntry entry(row);
+ rows_.insert(pos,entry);
}
}
@@ -67,7 +76,7 @@ void ViewObject::RemoveRow(Row* row)
{
QList<int> rows_to_delete;
for (int i = 0; i < rows_.size(); ++i){
- if(rows_[i].first == row){
+ if(rows_[i].row == row){
rows_to_delete.append(i);
}
}
@@ -79,7 +88,7 @@ void ViewObject::RemoveRow(Row* row)
Row* ViewObject::GetRow(int pos)
{
if(pos >= 0 && pos < rows_.size()){
- return rows_[pos].first;
+ return rows_[pos].row;
}
return NULL;
}
@@ -97,7 +106,44 @@ void ViewObject::AddSequence(seq::SequenceHandle& sequence)
p = new SeqTextPainter(this);
new_row->InsertPainter(p);
QPair<Row*, seq::SequenceHandle> pair(new_row,sequence);
- rows_.append(pair);
+ //rows_.append(pair);
+}
+
+void ViewObject::AddChain(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);
+
+ Row* new_row = new Row(this);
+ Painter* p = new SeqSelectionPainter(this);
+ new_row->InsertPainter(p);
+ p = new SeqSecStrPainter(this);
+ new_row->InsertPainter(p);
+ p = new SeqTextPainter(this);
+ new_row->InsertPainter(p);
+ QPair<Row*, seq::SequenceHandle> pair(new_row,sequence);
+ mol::alg::SecStructureSegments sec = mol::alg::ExtractSecStructureSegments(chain);
+ QVarLengthArray<mol::SecStructure> sec_str(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++){
+ sec_str[i] = s.ss_type;
+ }
+ }
+ ListEntry entry(new_row, sequence, sec_str);
+ rows_.append(entry);
+ }
}
QVariant ViewObject::GetData(int row, int column, int role)
@@ -113,12 +159,20 @@ QVariant ViewObject::GetData(int row, int column, int role)
}
else if(column > 0) {
if (role==Qt::DisplayRole) {
- return QVariant(QString(rows_[row].second.GetOneLetterCode(column - 1)));
+ return QVariant(QString(rows_[row].seq.GetOneLetterCode(column - 1)));
}
if (role==Qt::FontRole){
return QVariant(font_);
}
if (role==Qt::SizeHintRole){
+ return QVariant(default_cell_size_);
+ }
+ if (role==Qt::UserRole){
+ QVariant variant;
+ variant.setValue(rows_[row]);
+ return variant;
+ }
+ if (role==Qt::UserRole+1){
return QVariant(default_size_);
}
}
@@ -129,9 +183,9 @@ int ViewObject::GetMaxColumnCount() const
{
int columns = 0;
for(int i = 0; i < rows_.size(); i++){
- int col_length = rows_[i].second.GetLength();
+ int col_length = rows_[i].seq.GetLength();
if(columns < col_length){
- columns = rows_[i].second.GetLength() + 1;
+ columns = rows_[i].seq.GetLength() + 1;
}
}
return columns;
diff --git a/modules/gui/src/sequence/view_object.hh b/modules/gui/src/sequence/view_object.hh
index d8ae32802..795d996cd 100644
--- a/modules/gui/src/sequence/view_object.hh
+++ b/modules/gui/src/sequence/view_object.hh
@@ -26,9 +26,13 @@
#include <QObject>
#include <QPair>
#include <QList>
+#include <QVarLengthArray>
#include <QFont>
#include <QSize>
+#include <ost/mol/alg/sec_structure_segments.hh>
+#include <ost/mol/entity_handle.hh>
+
#include <ost/seq/sequence_list.hh>
#include "row.hh"
@@ -36,13 +40,33 @@
namespace ost { namespace gui {
+struct ListEntry {
+ Row* row;
+ seq::SequenceHandle seq;
+ QVarLengthArray<mol::SecStructure> secstr;
+ ListEntry(): row(NULL)
+ {}
+ ListEntry(Row* r): row(r)
+ {}
+ ListEntry(Row* r,
+ seq::SequenceHandle& sequence): row(r), seq(sequence)
+ {}
+ ListEntry(Row* r,
+ seq::SequenceHandle& sequence,
+ QVarLengthArray<mol::SecStructure>& sec): row(r), seq(sequence), secstr(sec)
+ {}
+};
+
+
class ViewObject : public QObject
{
Q_OBJECT
+
public:
ViewObject(seq::SequenceList& sequences, const QString& name, QObject* parent = 0);
ViewObject(seq::SequenceHandle& sequence, const QString& name, QObject* parent = 0);
+ ViewObject(mol::ChainView& chain, const QString& name, QObject* parent = 0);
void InsertRow(int pos, Row* row);
void RemoveRow(Row* row);
@@ -55,6 +79,7 @@ public:
int GetMaxColumnCount() const;
void AddSequence(seq::SequenceHandle& sequence);
+ void AddChain(mol::ChainView& chain);
QVariant GetData(int row, int column, int role);
@@ -66,12 +91,15 @@ public:
private:
void Init();
QString name_;
- QList<QPair<Row*, seq::SequenceHandle> > rows_;
+ QList<ListEntry> rows_;
QFont font_;
QSize default_size_;
+ QSize default_cell_size_;
};
}}
+Q_DECLARE_METATYPE(ost::gui::ListEntry)
+
#endif
--
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