diff --git a/modules/gui/pymod/CMakeLists.txt b/modules/gui/pymod/CMakeLists.txt
index c3fc64a17961c93349763793d7b1376b5791089e..03d7150c87557ff9a43ed0af4f98fe4aa98b0a01 100644
--- a/modules/gui/pymod/CMakeLists.txt
+++ b/modules/gui/pymod/CMakeLists.txt
@@ -8,7 +8,6 @@ set(OST_GUI_PYMOD_SOURCES
export_gosty.cc
export_remote_site_loader.cc
export_scene_win.cc
- export_sequence_viewer.cc
export_sequence_viewerV2.cc
export_perspective.cc
export_sip_handler.cc
diff --git a/modules/gui/pymod/export_gosty.cc b/modules/gui/pymod/export_gosty.cc
index 9cd97b7fdabdc80c208a521c47e50b136d5babb1..1a2216e2a09651cec0d3ed0947e925b5f675f0e6 100644
--- a/modules/gui/pymod/export_gosty.cc
+++ b/modules/gui/pymod/export_gosty.cc
@@ -92,10 +92,6 @@ void export_Gosty()
return_value_policy<reference_existing_object>())
.add_property("scene_win", make_function(&GostyApp::GetSceneWin,
return_value_policy<reference_existing_object>()))
- .def("GetSequenceViewer", &GostyApp::GetSequenceViewer,
- return_value_policy<reference_existing_object>())
- .add_property("seq_viewer", make_function(&GostyApp::GetSequenceViewer,
- return_value_policy<reference_existing_object>()))
.def("GetSequenceViewerV2", &GostyApp::GetSequenceViewerV2,
return_value_policy<reference_existing_object>())
.add_property("seq_viewer_v2", make_function(&GostyApp::GetSequenceViewerV2,
diff --git a/modules/gui/pymod/export_sequence_viewer.cc b/modules/gui/pymod/export_sequence_viewer.cc
deleted file mode 100644
index e6127166c5cb2c23903b9d407ad7437959c0addb..0000000000000000000000000000000000000000
--- a/modules/gui/pymod/export_sequence_viewer.cc
+++ /dev/null
@@ -1,39 +0,0 @@
-//------------------------------------------------------------------------------
-// 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
-//------------------------------------------------------------------------------
-#include <boost/python.hpp>
-
-#include <ost/gui/sequence_viewer/sequence_viewer.hh>
-
-#include "sip_handler.hh"
-
-using namespace boost::python;
-using namespace ost;
-using namespace ost::gui;
-
-
-void export_SequenceViewer()
-{
- class_<SequenceViewer, boost::noncopyable >("SequenceViewer", no_init)
- .def("Show", &SequenceViewer::show)
- .def("Hide", &SequenceViewer::hide)
- .def("GetQObject",&get_py_qobject<SequenceViewer>)
- .add_property("qobject", &get_py_qobject<SequenceViewer>)
- ;
-}
-
diff --git a/modules/gui/pymod/wrap_gui.cc b/modules/gui/pymod/wrap_gui.cc
index 149c7885f69b5b5fb4df54bb63f18104696aae57..542356c51e61d82d4d2cb28a1fc8dec414e7ee0b 100644
--- a/modules/gui/pymod/wrap_gui.cc
+++ b/modules/gui/pymod/wrap_gui.cc
@@ -32,7 +32,6 @@ void export_GLWin();
void export_Gosty();
void export_PyShell();
void export_SceneWin();
-void export_SequenceViewer();
void export_SequenceViewerV2();
void export_PanelBar();
void export_Perspective();
@@ -116,7 +115,6 @@ BOOST_PYTHON_MODULE(_gui)
export_Perspective();
export_SceneWin();
export_SceneSelection();
- export_SequenceViewer();
export_SequenceViewerV2();
export_RemoteSiteLoader();
export_FileLoader();
diff --git a/modules/gui/src/CMakeLists.txt b/modules/gui/src/CMakeLists.txt
index 744b59c57f4c95b260f2373cc4f15bde95f2d043..d972cbd0a7b1c2299f738d53af996da8a529b26b 100644
--- a/modules/gui/src/CMakeLists.txt
+++ b/modules/gui/src/CMakeLists.txt
@@ -12,13 +12,6 @@ side_bar.hh
splitter_panel_bar.hh
tabbed_panel_bar.hh
)
-set(OST_GUI_SEQUENCE_VIEWER_HEADERS
-sequence_item.hh
-sequence_viewer_base.hh
-sequence_viewer.hh
-sequence_scene.hh
-sequence_search_bar.hh
-)
set(OST_GUI_SEQUENCE_VIEW_HEADERS
align_properties_painter.hh
@@ -211,11 +204,6 @@ scene_menu.cc
widget.cc
widget_pool.cc
remote_site_loader.cc
-sequence_viewer/sequence_item.cc
-sequence_viewer/sequence_viewer_base.cc
-sequence_viewer/sequence_viewer.cc
-sequence_viewer/sequence_scene.cc
-sequence_viewer/sequence_search_bar.cc
sequence/align_properties_painter.cc
sequence/base_row.cc
sequence/background_painter.cc
@@ -346,11 +334,6 @@ scene_selection.hh
widget.hh
widget_geom_handler.hh
widget_pool.hh
-sequence_viewer/sequence_item.hh
-sequence_viewer/sequence_viewer_base.hh
-sequence_viewer/sequence_viewer.hh
-sequence_viewer/sequence_scene.hh
-sequence_viewer/sequence_search_bar.hh
sequence/align_properties_painter.hh
sequence/background_painter.hh
sequence/base_row.hh
diff --git a/modules/gui/src/gosty_app.cc b/modules/gui/src/gosty_app.cc
index 15f30c171f571daaddf5a0ce401c913bccd4beca..324aee547c90d6c59c7e4c35b5a2c8f499d1f97a 100644
--- a/modules/gui/src/gosty_app.cc
+++ b/modules/gui/src/gosty_app.cc
@@ -46,7 +46,7 @@ GostyApp* GostyApp::app_=NULL;
GostyApp::GostyApp():
py_shell_(NULL), w_py_shell_(NULL), gl_win_(NULL), w_gl_win_(NULL),
- scene_win_(NULL), w_scene_win_(NULL), seq_viewer_(NULL), seq_viewer_v2_(NULL), tool_options_win_(NULL),
+ scene_win_(NULL), w_scene_win_(NULL), seq_viewer_v2_(NULL), tool_options_win_(NULL),
w_tool_options_(NULL), main_(new GostyMainWindow),
perspective_(NULL), external_widgets_(QMap<QString,WidgetGeomHandler *>())
{
@@ -95,15 +95,6 @@ SceneWin* GostyApp::GetSceneWin()
return scene_win_;
}
-SequenceViewer* GostyApp::GetSequenceViewer()
-{
- if (seq_viewer_==NULL) {
- seq_viewer_=new SequenceViewer;
- seq_viewer_->SetDestroyOnClose(false);
- }
- return seq_viewer_;
-}
-
SequenceViewerV2* GostyApp::GetSequenceViewerV2()
{
if (seq_viewer_v2_==NULL) {
diff --git a/modules/gui/src/gosty_app.hh b/modules/gui/src/gosty_app.hh
index 46381ff1662237a5b60525407d7936eb05bd3eb4..e3f3a1f08bbf873f9364553a3bafd7188afb5173 100644
--- a/modules/gui/src/gosty_app.hh
+++ b/modules/gui/src/gosty_app.hh
@@ -30,7 +30,6 @@
#include <ost/config.hh>
#include <ost/gui/module_config.hh>
#include <ost/gui/scene_win/scene_win.hh>
-#include <ost/gui/sequence_viewer/sequence_viewer.hh>
#include <ost/gui/sequence/sequence_viewer.hh>
#include <ost/gui/main.hh>
#include <ost/gui/widget_geom_handler.hh>
@@ -92,7 +91,6 @@ public:
///
/// The sequence viewer is initialized when this method is first called. All
/// subsequent calls will return the same SequenceViewer instance.
- SequenceViewer* GetSequenceViewer();
SequenceViewerV2* GetSequenceViewerV2();
/// \brief get tool options window
@@ -156,7 +154,6 @@ private:
SceneWin* scene_win_;
QWidget* w_scene_win_;
- SequenceViewer* seq_viewer_;
SequenceViewerV2* seq_viewer_v2_;
ToolOptionsWin* tool_options_win_;
diff --git a/modules/gui/src/main.cc b/modules/gui/src/main.cc
index 9836c6e9057805a340c8559ee51183e08232581d..9abeac746c3a53ed5d99ea631814997db97e2ced 100644
--- a/modules/gui/src/main.cc
+++ b/modules/gui/src/main.cc
@@ -43,7 +43,6 @@
#include "gl_win.hh"
//#include "entity_explorer/entity_explorer.hh"
#include "mdi_sub_window.hh"
-#include "sequence_viewer/sequence_viewer.hh"
#include "tools/tool_options_win.hh"
#include "plot_viewer/plot_viewer_proxy.hh"
#include "plot_viewer/plot_viewer.hh"
diff --git a/modules/gui/src/sequence/sequence_table_view.cc b/modules/gui/src/sequence/sequence_table_view.cc
index 52f9083c5dd986d0fb15b432dfaf31ccdadd3a82..807c130da835bf75bcb219073a9ea704d7faf5e3 100644
--- a/modules/gui/src/sequence/sequence_table_view.cc
+++ b/modules/gui/src/sequence/sequence_table_view.cc
@@ -67,7 +67,6 @@ SequenceTableView::SequenceTableView(QAbstractItemModel * model)
delegate_ = new SequenceDelegate(qobject_cast<SequenceModel*>(this->model()),this);
#if !(defined(__APPLE__) && (QT_VERSION>=0x040600))
- std::cout << "INIT STATIC" << QT_VERSION << std::endl;
this->InitStaticRow();
this->InitStaticColumn();
this->InitStaticField();
diff --git a/modules/gui/src/sequence_viewer/sequence_item.cc b/modules/gui/src/sequence_viewer/sequence_item.cc
deleted file mode 100644
index 6200f6c15f6ea86c4ee5f970255cb10be60b1f96..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_item.cc
+++ /dev/null
@@ -1,494 +0,0 @@
-//------------------------------------------------------------------------------
-// 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: Marco Biasini
- */
-
-#include <ost/mol/mol.hh>
-#include <boost/bind.hpp>
-
-#include "sequence_item.hh"
-#include "sequence_scene.hh"
-
-#include <QPainter>
-#include <QGraphicsSceneMouseEvent>
-#include <QGraphicsSceneContextMenuEvent>
-#include <QGraphicsItem>
-#include <QDebug>
-
-namespace ost { namespace gui {
-
-using boost::bind;
-
-Knob::Knob(const QString& text, const QColor& color,
- SequenceItem* parent):
- QGraphicsItem(parent)
-{
-
-}
-
-void Knob::paint(QPainter* painter, const QStyleOptionGraphicsItem*,
- QWidget* widget)
-{
- painter->setBrush(QBrush(color_));
- painter->setPen(QPen(color_.darker()));
- painter->drawEllipse(this->boundingRect());
- if (this->isUnderMouse()) {
- painter->setPen(QPen(color_.darker()));
- } else {
- painter->setPen(QPen(Qt::white));
- }
- painter->drawText(this->boundingRect(), Qt::AlignCenter, text_);
-}
-
-QRectF Knob::boundingRect() const
-{
- return QRectF(0.0, 0.0, 15.0, 15.0);
-}
-
-
-SequenceHeader::SequenceHeader(SequenceItem* parent):
- QGraphicsItem(parent)
-{
- font_=QFont("Courier", 12);
- font_.setKerning(false);
- font_.setFixedPitch(true);
-}
-
-
-void SequenceHeader::paint(QPainter* painter, const QStyleOptionGraphicsItem*,
- QWidget* widget)
-{
- SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
- painter->setFont(font_);
- QFontMetrics m(font_);
- QString name(si->GetSequence().GetName().c_str());
- QRectF br=this->boundingRect();
- name=m.elidedText(name, Qt::ElideMiddle, br.width());
- painter->drawText(br, Qt::AlignTop, name);
-}
-
-QRectF SequenceHeader::boundingRect() const
-{
- QFontMetrics metrics(font_);
- SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
- QString name(si->GetSequence().GetName().c_str());
- QRectF rect(0, -2,name.size()*si->GetCharWidth()*1.1,
- si->GetCharHeight()+2);
- SequenceScene* s=dynamic_cast<SequenceScene*>(this->scene());
- rect.setWidth(std::min(qreal(s->GetHeaderWidth()), rect.width()));
- return rect;
-}
-
-SequenceBody::SequenceBody(SequenceItem* parent):
- QGraphicsItem(parent)
-{
-
-}
-
-
-void SequenceBody::paint(QPainter* painter, const QStyleOptionGraphicsItem*,
- QWidget* widget)
-{
- SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
- seq::SequenceHandle seq=si->GetSequence();
- if (!seq.IsValid()) {
- return;
- }
- QString qstr(seq.GetString().c_str());
- QColor sel_color(Qt::yellow);
- if (si->IsSecStructureVisible()) {
- sel_color.setAlpha(50);
- painter->setBrush(QBrush(sel_color));
- painter->setPen(QPen(QColor(Qt::yellow).darker()));
- painter->drawPath(si->GetSecStructPaths());
- }
- painter->setFont(si->GetFont());
- painter->setPen(QPen(Qt::black));
- QString tt("X");
- QRectF br=this->boundingRect();
- for (int i=0; i<qstr.size(); ++i) {
- tt[0]=qstr[i];
- QRectF rect(br.left()+i*si->GetCharWidth(), br.top(),
- br.width(), br.height());
- painter->drawText(rect, Qt::AlignLeft|Qt::AlignVCenter, tt);
- }
-
- sel_color=QColor(Qt::green).lighter();
- painter->setPen(QPen(Qt::green));
- sel_color.setAlpha(100);
- painter->setBrush(QBrush(sel_color));
- QRectF text_bounds=painter->boundingRect(boundingRect(),
- Qt::AlignLeft|Qt::AlignVCenter,
- qstr);
- const SequenceItem::Selection& sel=si->GetSelection();
- for (size_t i=0; i<sel.size(); ++i) {
- painter->drawRect(QRectF(sel[i].Loc*si->GetCharWidth(), 0,
- sel[i].Length*si->GetCharWidth(),
- si->GetCharHeight()));
- }
-}
-
-QRectF SequenceBody::boundingRect() const
-{
- SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
- seq::SequenceHandle seq=si->GetSequence();
- if (!seq.IsValid()) {
- return QRectF();
- }
- return QRectF(0, -2, seq.GetLength()*si->GetCharWidth(),
- si->GetCharHeight()+2);
-}
-
-
-SequenceItem::SequenceItem(const seq::SequenceHandle& seq,
- QGraphicsItem* parent):
- QGraphicsItem(parent), seq_(seq), show_sec_struct_(true)
-{
- header_=new SequenceHeader(this);
- body_=new SequenceBody(this);
- body_->translate(120.0, 0.0);
- font_=QFont("Courier", 12);
- font_.setKerning(false);
- font_.setFixedPitch(true);
- QFontMetrics metrics(font_);
- advance_=metrics.boundingRect('W').width();
- height_=metrics.boundingRect('|').height();
- ascent_=metrics.ascent();
- this->setAcceptedMouseButtons(Qt::LeftButton);
- this->ExtractSecStructSegments();
- selection_change_=false;
-}
-
-SequenceHeader* SequenceItem::GetHeader()
-{
- return header_;
-}
-
-SequenceBody* SequenceItem::GetBody()
-{
- return body_;
-}
-
-const seq::SequenceHandle& SequenceItem::GetSequence() const
-{
- return seq_;
-}
-
-QRectF SequenceItem::GetCharBounds(int pos) const
-{
- QPointF a(pos*advance_, 0);
- return QRectF(this->mapToScene(a), QSizeF(advance_, height_));
-}
-
-float SequenceItem::GetCharWidth() const
-{
- return advance_;
-}
-
-float SequenceItem::GetCharHeight() const
-{
- return height_;
-}
-
-void SequenceItem::paint(QPainter* painter, const QStyleOptionGraphicsItem*,
- QWidget* widget)
-{
-}
-
-QRectF SequenceItem::boundingRect() const
-{
- QRectF child_r(this->childrenBoundingRect());
- if (show_sec_struct_) {
- return QRectF(child_r.topLeft(),
- QSize(child_r.width(), child_r.height()*2.5));
- } else {
- return QRectF(child_r.topLeft(),
- QSize(child_r.width(), child_r.height()));
- }
-}
-
-void SequenceItem::ExtractSecStructSegments()
-{
- if (!seq_.HasAttachedView()) {
- return;
- }
- mol::ChainView chain=seq_.GetAttachedView().GetChainList()[0];
- sec_=mol::alg::ExtractSecStructureSegments(chain);
- this->SecStructSegmentsToPaths();
-}
-
-void SequenceHeader::contextMenuEvent(QGraphicsSceneContextMenuEvent* event)
-{
- //...
-}
-void SequenceBody::mousePressEvent(QGraphicsSceneMouseEvent* event)
-{
- SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
- event->accept();
- last_index_=-1;
- good_ole_click_=true;
- merge_select_=event->modifiers() & Qt::ShiftModifier;
- si->BeginSelectionChange();
-}
-
-void SequenceBody::mouseDoubleClickEvent(QGraphicsSceneMouseEvent* event)
-{
- SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
- int index=std::max(0, int(event->pos().x()/si->GetCharWidth()));
- // find the secondary structure element -- if any that we are in
- mol::alg::SecStructureSegments::iterator i=si->GetSecStructSegments().begin(),
- e=si->GetSecStructSegments().end();
- for (;i!=e; ++i) {
- if (i->first<=index && i->last>=index) {
- si->Select(i->first, i->last+1, !merge_select_);
- break;
- }
- }
- good_ole_click_=false;
-}
-void SequenceHeader::mousePressEvent(QGraphicsSceneMouseEvent* event)
-{
- event->accept();
-}
-
-void SequenceHeader::mouseReleaseEvent(QGraphicsSceneMouseEvent* event)
-{
- SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
- if (si->IsEverythingSelected()) {
- si->ClearSelection();
- } else {
- si->SelectAll();
- }
-
-}
-
-void SequenceBody::mouseReleaseEvent(QGraphicsSceneMouseEvent* event)
-{
- SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
- if (good_ole_click_) {
- int index=std::max(0, int(event->pos().x()/si->GetCharWidth()));
- si->Select(index, index+1, !merge_select_);
- }
- si->EndSelectionChange();
-}
-
-void SequenceBody::mouseMoveEvent(QGraphicsSceneMouseEvent* event)
-{
- SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
- good_ole_click_=false;
- if (!si->GetSequence().IsValid()) {
- return;
- }
- float x=event->pos().x();
- int index=std::max(0, int(x/si->GetCharWidth()));
- if (last_index_!=-1 && last_index_!=index) {
- si->Select(last_index_, index, !merge_select_);
- } else {
- last_index_=index;
- }
-}
-
-void SequenceItem::StackToPath(std::vector<QPointF>& stack)
-{
- if (!stack.empty()) {
- sec_paths_.moveTo(QPointF(stack.front().x(), stack.front().y()+.5*ascent_));
- for (std::vector<QPointF>::iterator j=stack.begin()+1,
- e2=stack.end(); j!=e2; ++j) {
- sec_paths_.lineTo(QPointF(j->x(), j->y()+0.5*ascent_));
- }
- for (std::vector<QPointF>::reverse_iterator j=stack.rbegin(),
- e2=stack.rend(); j!=e2; ++j) {
- sec_paths_.lineTo(QPointF(j->x(), -j->y()+.5*ascent_));
- }
- sec_paths_.closeSubpath();
- stack.clear();
- }
-}
-
-void SequenceItem::SecStructSegmentsToPaths()
-{
- sec_paths_=QPainterPath();
-
- sec_paths_.setFillRule(Qt::WindingFill);
- std::vector<QPointF> stack;
- int last_end=-2;
- for (mol::alg::SecStructureSegments::iterator i=sec_.begin(),
- e=sec_.end(); i!=e; ++i) {
- mol::alg::SecStructureSegment s=*i;
- if (last_end!=s.first-1) {
- this->StackToPath(stack);
- }
- if (s.ss_type.IsCoil()) {
- stack.push_back(QPointF(s.first*advance_, -.6*height_));
- stack.push_back(QPointF((s.last+1)*advance_, -.6*height_));
- } else if (s.ss_type.IsHelical()) {
- stack.push_back(QPointF(s.first*advance_, -.6*height_));
- stack.push_back(QPointF(s.first*advance_, -.9*height_));
- stack.push_back(QPointF((s.last+1)*advance_, -.9*height_));
- stack.push_back(QPointF((s.last+1)*advance_, -.6*height_));
- } else if (s.ss_type.IsExtended()) {
- stack.push_back(QPointF(s.first*advance_, -.6*height_));
- stack.push_back(QPointF(s.first*advance_, -.9*height_));
- stack.push_back(QPointF((s.last-0.5)*advance_, -.9*height_));
- stack.push_back(QPointF((s.last-0.5)*advance_, -1.3*height_));
- stack.push_back(QPointF((s.last+1)*advance_, -.6*height_));
-
- }
- last_end=s.last;
- }
- this->StackToPath(stack);
-}
-
-void SequenceItem::Select(int i1, int i2, bool clear)
-{
- if (selection_change_>0) {
- selection_=ref_sel_;
- }
- int a1=std::min(i1, i2);
- int len=std::abs(i1-i2);
- Range sel_start(a1, len);
- Range* sel=&sel_start;
- bool modified=false;
- if (clear) {
- selection_.clear();
- selection_.push_back(*sel);
- } else {
- for (size_t i=0; i<selection_.size(); ++i) {
- if (sel->Loc>=selection_[i].Loc && sel->Loc<selection_[i].End()) {
- int old_end=selection_[i].End();
- if (sel->End()<=selection_[i].End()) {
- selection_[i].Length=int(sel->Loc-selection_[i].Loc);
- if (old_end-sel->End()>0) {
- selection_.push_back(Range(sel->End(), old_end-sel->End()));
- }
- } else {
- selection_[i].Length=int(sel->Loc-selection_[i].Loc);
- if (sel->End()-old_end>0) {
- selection_.push_back(Range(old_end, sel->End()-old_end));
- }
- }
- modified=true;
- break;
- } else if (sel->End()>selection_[i].Loc &&
- sel->End()<=selection_[i].End()) {
- int nn=selection_[i].Loc;
- selection_[i].Length-=sel->End()-selection_[i].Loc;
- selection_[i].Loc=sel->End();
- modified=true;
- selection_.push_back(Range(sel->Loc, nn-sel->Loc));
- break;
- } else if (sel->Loc<selection_[i].Loc &&
- sel->End()>selection_[i].End()) {
- selection_[i].Length=0;
- } else if (sel->Loc==selection_[i].End()) {
- selection_[i].Length+=sel->Length;
- sel->Length=0;
- sel=&selection_[i];
- modified=true;
- } else if (sel->End()==selection_[i].Loc) {
- selection_[i].Loc-=sel->Length;
- selection_[i].Length+=sel->Length;
- sel->Length=0;
- sel=&selection_[i];
- modified=true;
- }
- }
- if (!modified) {
- selection_.push_back(Range(a1, len));
- }
- }
- Selection::iterator i=std::remove_if(selection_.begin(), selection_.end(),
- bind(&Range::Length, _1)==size_t(0));
- selection_.erase(i, selection_.end());
- if (!selection_change_) {
- emit this->SelectionChanged(this);
- } else {
- selection_change_=2;
- }
- update();
-}
-
-void SequenceItem::ClearSelection()
-{
- selection_.clear();
- if (selection_change_>0) {
- selection_change_=2;
- } else {
- emit this->SelectionChanged(this);
- update();
- }
-}
-
-void SequenceItem::SelectAll()
-{
- if (!seq_.IsValid()) {
- return;
- }
- selection_.clear();
- selection_.push_back(Range(0, seq_.GetLength()));
- if (selection_change_>0) {
- selection_change_=1;
- } else {
- emit this->SelectionChanged(this);
- update();
- }
-}
-
-void SequenceItem::BeginSelectionChange()
-{
- selection_change_=1;
- ref_sel_=selection_;
-}
-
-void SequenceItem::EndSelectionChange()
-{
- if (selection_change_==2) {
- emit this->SelectionChanged(this);
- }
- selection_change_=0;
-}
-
-bool SequenceItem::IsEverythingSelected() const
-{
- return selection_.size()==1 && selection_.front().Loc==0 &&
- selection_.front().End()>=static_cast<size_t>(seq_.GetLength());
-}
-
-const SequenceItem::Selection& SequenceItem::GetSelection() const
-{
- return selection_;
-}
-
-mol::alg::SecStructureSegments& SequenceItem::GetSecStructSegments()
-{
- return sec_;
-}
-
-void SequenceItem::SetShowSecStructure(bool show)
-{
- show_sec_struct_=show;
-}
-
-bool SequenceItem::IsSecStructureVisible() const
-{
- return show_sec_struct_;
-}
-
-}}
diff --git a/modules/gui/src/sequence_viewer/sequence_item.hh b/modules/gui/src/sequence_viewer/sequence_item.hh
deleted file mode 100644
index aeaa63d1a9af36e29a925aa5af3b5fc214b2c8be..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_item.hh
+++ /dev/null
@@ -1,153 +0,0 @@
-//------------------------------------------------------------------------------
-// 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_GUI_SEQUENCE_ITEM_HH
-#define OST_GUI_SEQUENCE_ITEM_HH
-
-#include <ost/gui/module_config.hh>
-#include <ost/mol/sec_structure.hh>
-#include <ost/mol/alg/sec_structure_segments.hh>
-
-#include <ost/seq/sequence_handle.hh>
-
-#include <QGraphicsItem>
-#include <QFont>
-
-namespace ost { namespace gui {
-
-class SequenceItem;
-class SequenceHeader;
-
-class DLLEXPORT_OST_GUI Knob : public QGraphicsItem {
-public:
- Knob(const QString& text, const QColor& color,
- SequenceItem* parent=NULL);
-
- virtual void paint(QPainter* painter, const QStyleOptionGraphicsItem* opts,
- QWidget* widget=NULL);
- virtual QRectF boundingRect() const;
-private:
- QString text_;
- QColor color_;
-};
-
-class DLLEXPORT_OST_GUI SequenceHeader : public QGraphicsItem {
-public:
- SequenceHeader(SequenceItem* parent=NULL);
-
- virtual void paint(QPainter* painter, const QStyleOptionGraphicsItem* opts,
- QWidget* widget=NULL);
- virtual QRectF boundingRect() const;
-protected:
- virtual void mousePressEvent(QGraphicsSceneMouseEvent* event);
- virtual void mouseReleaseEvent(QGraphicsSceneMouseEvent* event);
- virtual void contextMenuEvent(QGraphicsSceneContextMenuEvent* event);
-private:
- QFont font_;
-};
-
-class DLLEXPORT_OST_GUI SequenceBody : public QGraphicsItem {
-public:
- SequenceBody(SequenceItem* parent=NULL);
-
- virtual void paint(QPainter* painter, const QStyleOptionGraphicsItem* opts,
- QWidget* widget=NULL);
- virtual QRectF boundingRect() const;
-protected:
- virtual void mousePressEvent(QGraphicsSceneMouseEvent* event);
- virtual void mouseReleaseEvent(QGraphicsSceneMouseEvent* event);
- virtual void mouseMoveEvent(QGraphicsSceneMouseEvent* event);
-
- virtual void mouseDoubleClickEvent(QGraphicsSceneMouseEvent* event);
-private:
- QFont font_;
- bool merge_select_;
- bool good_ole_click_;
- int last_index_;
-};
-
-
-class DLLEXPORT_OST_GUI SequenceItem : public QObject, // required for signals
- public QGraphicsItem {
- Q_OBJECT
-public:
- typedef std::vector<Range> Selection;
-
- SequenceItem(const seq::SequenceHandle& seq, QGraphicsItem* parent=NULL);
-
- /// \brief get sequence
- const seq::SequenceHandle& GetSequence() const;
-
- virtual void paint(QPainter* painter, const QStyleOptionGraphicsItem* opts,
- QWidget* widget=NULL);
- virtual QRectF boundingRect() const;
-
- QRectF GetCharBounds(int pos) const;
-
- float GetCharWidth() const;
- float GetCharHeight() const;
-
- SequenceBody* GetBody();
- SequenceHeader* GetHeader();
- QPainterPath& GetSecStructPaths() { return sec_paths_; }
- QFont GetFont() { return font_; }
-
- const Selection& GetSelection() const;
- void Select(int i1, int i2, bool clear=true);
-
- void BeginSelectionChange();
- void EndSelectionChange();
-
- bool IsEverythingSelected() const;
- void ClearSelection();
- void SelectAll();
- void SetShowSecStructure(bool show=true);
- bool IsSecStructureVisible() const;
-
- mol::alg::SecStructureSegments& GetSecStructSegments();
-signals:
-
- /// \brief emitted whenever the selection changes
- ///
- /// When using BeginSelectionChange(), no signal is emitted until
- /// EndSelectionChange() is called.
- void SelectionChanged(SequenceItem* item);
-private:
- void ExtractSecStructSegments();
- void SecStructSegmentsToPaths();
- void StackToPath(std::vector<QPointF>& stack);
-
- QPainterPath sec_paths_;
- mol::alg::SecStructureSegments sec_;
- SequenceHeader* header_;
- SequenceBody* body_;
- seq::SequenceHandle seq_;
- QFont font_;
- Selection selection_;
- Selection ref_sel_;
- float advance_;
- float height_;
- float ascent_;
- int selection_change_;
- bool show_sec_struct_;
-};
-
-typedef std::vector<SequenceItem*> SequenceItemList;
-}}
-
-#endif
diff --git a/modules/gui/src/sequence_viewer/sequence_scene.cc b/modules/gui/src/sequence_viewer/sequence_scene.cc
deleted file mode 100644
index 4b77a71e3e61d610ecfa973a87ae242be634d3d2..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_scene.cc
+++ /dev/null
@@ -1,134 +0,0 @@
-//------------------------------------------------------------------------------
-// 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
-//------------------------------------------------------------------------------
-#include "sequence_scene.hh"
-#include <boost/bind.hpp>
-#include <QPainter>
-
-namespace ost { namespace gui {
-
-using boost::bind;
-
-void SequenceScene::drawBackground(QPainter* painter, const QRectF& rect)
-{
- if (sequences_.empty()) {
- return;
- }
- QBrush stripe_brushes[]={
- QBrush(QColor(Qt::white)),
- QBrush(QColor(245, 245, 245))
- };
- float width=sequences_[0]->GetCharWidth()*5;
- QRectF stripe(QPointF(((int(rect.left()/width)-1)-1)*width+header_width_,
- rect.top()),
- QSizeF(width, rect.height()));
- int n=round(rect.width()/width)+2;
- int start=std::max(0, int(floor(rect.left()/width)))-1;
- for (int i=0; i<n; ++i, stripe.translate(width, 0.0)) {
- painter->fillRect(stripe, stripe_brushes[(i+start+2) % 2]);
- }
- painter->setPen(QPen(Qt::gray));
- const static int STEP_SIZE=10;
- float s=sequences_[0]->GetCharWidth()*STEP_SIZE;
- int n_rulers=round(rect.width()/s);
- int first=std::max(0, int(floor(rect.left()/s)));
- painter->fillRect(QRectF(QPointF(0.0, rect.top()),
- QSizeF(header_width_, rect.height())),
- QBrush(Qt::white));
- for (int i=first;i<first+n_rulers+2; ++i) {
- painter->drawText(QRectF(QPointF(i*s-50+header_width_,
- rect.top()), QSizeF(100, 30)),
- Qt::AlignCenter, QString::number(i*STEP_SIZE));
- painter->drawLine(QPointF(i*s+header_width_, rect.top()+30),
- QPointF(i*s+header_width_, rect.top()+30+rect.height()));
- }
-
-}
-
-void SequenceScene::SetContextMenu(QMenu* menu)
-{
- context_menu_=menu;
-}
-
-QMenu* SequenceScene::GetContextMenu()
-{
- return context_menu_;
-}
-
-SequenceScene::SequenceScene(QObject* parent):
- QGraphicsScene(parent), header_width_(120.0)
-{
- connect(this, SIGNAL(sceneRectChanged(const QRectF&)), this,
- SLOT(OnSceneRectChange(const QRectF&)));
- context_menu_=NULL;
-}
-
-void SequenceScene::RepackSequences()
-{
- if (sequences_.empty()) {
- return;
- }
- sequences_.front()->setPos(0.0, 50.0);
- for (std::vector<SequenceItem*>::iterator i=sequences_.begin()+1,
- e=sequences_.end(); i!=e; ++i) {
- (*i)->setPos(0.0, (*(i-1))->pos().y()+
- (*(i-1))->boundingRect().height());
- }
-}
-
-void SequenceScene::AddSequence(SequenceItem* seq)
-{
- this->addItem(seq);
- if (!sequences_.empty()) {
- seq->setPos(0.0, sequences_.back()->pos().y()+
- sequences_.back()->boundingRect().height());
- } else {
- seq->setPos(0.0, 50.0);
- }
- sequences_.push_back(seq);
- update();
-}
-
-void SequenceScene::RemoveSequence(SequenceItem* seq)
-{
- this->removeItem(seq);
- std::vector<SequenceItem*>::iterator f=std::find(sequences_.begin(),
- sequences_.end(), seq);
- if(f != sequences_.end())
- {
- sequences_.erase(f);
- }
- RepackSequences();
-}
-
-void SequenceScene::SetHeaderWidth(float width)
-{
- header_width_=width;
- update();
-}
-
-float SequenceScene:: GetHeaderWidth() const
-{
- return header_width_;
-}
-
-void SequenceScene::OnSceneRectChange(const QRectF& rect)
-{
-}
-
-}}
diff --git a/modules/gui/src/sequence_viewer/sequence_scene.hh b/modules/gui/src/sequence_viewer/sequence_scene.hh
deleted file mode 100644
index 2547d9fbdf27527b2870617058affc08c9e76b2e..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_scene.hh
+++ /dev/null
@@ -1,67 +0,0 @@
-//------------------------------------------------------------------------------
-// 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_GUI_SEQUENCE_SCENE_HH
-#define OST_GUI_SEQUENCE_SCENE_HH
-
-#include <ost/gui/module_config.hh>
-#include <ost/gui/sequence_viewer/sequence_item.hh>
-
-#include <QGraphicsScene>
-
-namespace ost { namespace gui {
-
-
-class SequenceScene : public QGraphicsScene {
- Q_OBJECT
-public:
- typedef std::vector<Range> Selection;
-
- SequenceScene(QObject* parent=NULL);
-
- void SetContextMenu(QMenu* menu);
-
- QMenu* GetContextMenu();
- std::vector<SequenceItem*>& GetSequences() { return sequences_; }
- const Selection& GetSelection() const;
-
- /// \brief get length of longest sequence (including gaps) in the alignment
- void GetMaxSequenceLength();
-
-
- void SetHeaderWidth(float width);
- float GetHeaderWidth() const;
- void AddSequence(SequenceItem* seq);
- void RemoveSequence(SequenceItem* seq);
- void RepackSequences();
-public slots:
- void OnSceneRectChange(const QRectF& rect);
-protected:
- virtual void drawBackground(QPainter* painter, const QRectF& rect);
-private:
- void UpdateAlignment();
- Selection selection_;
- Selection ref_sel_;
- std::vector<SequenceItem*> sequences_;
- QMenu* context_menu_;
- float header_width_;
-};
-
-}}
-
-#endif
diff --git a/modules/gui/src/sequence_viewer/sequence_search_bar.cc b/modules/gui/src/sequence_viewer/sequence_search_bar.cc
deleted file mode 100644
index 808d45904e21293e5360e7bd5e3e8e25de82c132..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_search_bar.cc
+++ /dev/null
@@ -1,127 +0,0 @@
-//------------------------------------------------------------------------------
-// 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: Marco Biasini
- */
-
-#include "sequence_search_bar.hh"
-#include "sequence_item.hh"
-
-#include <QHBoxLayout>
-#include <QLineEdit>
-#include <QPainter>
-#include <QPaintEvent>
-#include <QLabel>
-#include <QKeyEvent>
-
-namespace ost { namespace gui {
-
-SequenceSearchBar::SequenceSearchBar(QWidget* parent):
- QWidget(parent)
-{
- subject_=new QLineEdit(this);
- search_all_=new QCheckBox("search in all sequences", this);
- search_in_=new QComboBox(this);
- QHBoxLayout* l= new QHBoxLayout(this);
- l->addSpacing(2);
- l->addWidget(subject_, 0);
- l->addWidget(search_all_, 0);
- QLabel* label=new QLabel("search in:", this);
- l->addSpacing(10);
- l->addWidget(label, 0);
- l->addWidget(search_in_, 0);
- l->addStretch(1);
- subject_->setMaximumWidth(200);
- setLayout(l);
- l->setSizeConstraint(QLayout::SetMaximumSize);
- l->setMargin(1);
- search_all_->setCheckState(Qt::Checked);
- search_in_->setEnabled(false);
-#if defined(__APPLE__)
- subject_->setAttribute(Qt::WA_MacSmallSize, true);
- search_all_->setAttribute(Qt::WA_MacSmallSize, true);
- search_in_->setAttribute(Qt::WA_MacSmallSize, true);
- label->setAttribute(Qt::WA_MacSmallSize, true);
-#endif
- connect(subject_, SIGNAL(textChanged(const QString&)), this,
- SLOT(OnSubjectChanged(const QString&)));
- connect(search_all_, SIGNAL(stateChanged(int)), this,
- SLOT(OnSearchAllChanged(int)));
- connect(search_in_, SIGNAL(currentIndexChanged(int)), this,
- SLOT(OnSearchInChanged(int)));
-}
-
-void SequenceSearchBar::Show(const std::vector<SequenceItem*>& sequences)
-{
- search_in_->clear();
-
- for (size_t i=0;i<sequences.size(); ++i) {
- QString name(sequences[i]->GetSequence().GetName().c_str());
- search_in_->addItem(name);
- }
- if (sequences.empty()) {
- search_all_->setCheckState(Qt::Checked);
- search_in_->setEnabled(false);
- }
- this->show();
- subject_->setFocus(Qt::ActiveWindowFocusReason);
- subject_->selectAll();
-}
-void SequenceSearchBar::OnSearchAllChanged(int state)
-{
- if (state==Qt::Unchecked) {
- search_in_->setEnabled(true);
- } else {
- search_in_->setEnabled(false);
- }
- emit Changed(subject_->text(), search_all_->checkState()==Qt::Checked,
- search_in_->currentIndex());
-}
-
-void SequenceSearchBar::OnSearchInChanged(int index)
-{
- emit Changed(subject_->text(), search_all_->checkState()==Qt::Checked,
- search_in_->currentIndex());
-}
-
-void SequenceSearchBar::OnSubjectChanged(const QString& str)
-{
- emit Changed(str, search_all_->checkState()==Qt::Checked,
- search_in_->currentIndex());
-}
-
-void SequenceSearchBar::paintEvent(QPaintEvent* paint_event)
-{
- QPainter p(this);
- p.setBrush(QBrush(QColor(Qt::blue).lighter(300)));
- p.setPen(QPen(QColor(Qt::blue).lighter(200)));
- p.drawRect(rect());
- paint_event->accept();
-}
-
-void SequenceSearchBar::keyPressEvent(QKeyEvent* key_event)
-{
- if (key_event->key()==Qt::Key_Escape) {
- this->hide();
- key_event->accept();
- }
- QWidget::keyPressEvent(key_event);
-}
-
-}}
diff --git a/modules/gui/src/sequence_viewer/sequence_search_bar.hh b/modules/gui/src/sequence_viewer/sequence_search_bar.hh
deleted file mode 100644
index fae7280dc6d119f47063e29645a5baaa882c95fe..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_search_bar.hh
+++ /dev/null
@@ -1,60 +0,0 @@
-//------------------------------------------------------------------------------
-// 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_SEARCH_BAR_HH
-#define OST_SEQUENCE_SEARCH_BAR_HH
-
-/*
- Author: Marco Biasini
- */
-#include <ost/gui/module_config.hh>
-#include <ost/seq/alignment_handle.hh>
-#include <QWidget>
-#include <QComboBox>
-#include <QCheckBox>
-
-namespace ost { namespace gui {
-
-class SequenceItem;
-
-/// \brief search bar to search in multiple sequence alignment
-class DLLEXPORT_OST_GUI SequenceSearchBar : public QWidget {
- Q_OBJECT
-public:
- SequenceSearchBar(QWidget* parent=NULL);
-
- void Show(const std::vector<SequenceItem*>& sequences);
-signals:
- void Changed(const QString&, bool, int);
-public slots:
- void OnSubjectChanged(const QString&);
- void OnSearchInChanged(int);
- void OnSearchAllChanged(int);
-protected:
- virtual void paintEvent(QPaintEvent* paint_event);
- virtual void keyPressEvent(QKeyEvent* key_event);
-private:
- seq::AlignmentHandle ali_;
- QLineEdit* subject_;
- QCheckBox* search_all_;
- QComboBox* search_in_;
-};
-
-}}
-
-#endif
diff --git a/modules/gui/src/sequence_viewer/sequence_viewer.cc b/modules/gui/src/sequence_viewer/sequence_viewer.cc
deleted file mode 100644
index 05d5d03cf1c64f68a374105eee97fe1bafb3b979..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_viewer.cc
+++ /dev/null
@@ -1,242 +0,0 @@
-//------------------------------------------------------------------------------
-// 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
-//------------------------------------------------------------------------------
-#include <QMenu>
-
-#include <ost/dyn_cast.hh>
-#include <ost/mol/view_op.hh>
-
-#include <ost/gfx/entity.hh>
-#include <ost/gfx/scene.hh>
-#include <ost/gfx/gfx_node_visitor.hh>
-#include <ost/gfx/gfx_node.hh>
-#include <ost/gfx/gfx_object.hh>
-
-#include <ost/gui/widget_registry.hh>
-#include <ost/gui/gosty_app.hh>
-
-#include "sequence_viewer.hh"
-
-
-namespace ost { namespace gui {
-
-struct GetNodesVisitor: public gfx::GfxNodeVisitor {
- GetNodesVisitor(): nodes_() {}
- virtual void VisitObject(gfx::GfxObj* o, const Stack& st) {
- nodes_.push_back(o->shared_from_this());
- }
- gfx::NodePtrList nodes_;
- gfx::NodePtrList GetNodes(){return nodes_;}
-};
-
-class SequenceViewerFactory: public WidgetFactory {
-public:
- SequenceViewerFactory() :
- WidgetFactory("ost::gui::SequenceViewer", "Sequence Viewer") {
- }
-
- virtual Widget* Create(QWidget* parent) {
- return GostyApp::Instance()->GetSequenceViewer();
- }
-};
-
-OST_REGISTER_WIDGET(SequenceViewer, SequenceViewerFactory);
-
-SequenceViewer::SequenceViewer(QWidget* parent):
- SequenceViewerBase(parent), we_are_changing_the_selection_(false)
-{
- gfx::Scene::Instance().AttachObserver(this);
- this->SetDisplayStyle(SequenceViewer::LOOSE);
-
- gfx::GfxNodeP root_node = gfx::Scene::Instance().GetRootNode();
- GetNodesVisitor gnv;
- gfx::Scene::Instance().Apply(gnv);
- gfx::NodePtrList list = gnv.GetNodes();
- for(unsigned int i=0; i<list.size();i++){
- this->NodeAdded(list[i]);
- }
-}
-
-SequenceViewer::~SequenceViewer()
-{
- gfx::Scene::Instance().DetachObserver(this);
-}
-
-void SequenceViewer::NodeAdded(const gfx::GfxNodeP& n)
-{
- if (gfx::EntityP o=dyn_cast<gfx::Entity>(n)) {
- // extract all chains
- mol::EntityView v=o->GetView();
- 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;
- }
- String name=o->GetName();
- if (chain.GetName()!="" && chain.GetName()!=" ") {
- name+=" ("+chain.GetName()+")";
- }
- seq::SequenceHandle seq=seq::CreateSequence(name, seq_str);
- mol::EntityView v_one_chain=v.GetHandle().CreateEmptyView();
- v_one_chain.AddChain(chain, mol::ViewAddFlag::INCLUDE_ALL);
- seq.AttachView(v_one_chain);
- SequenceItem* item=new SequenceItem(seq);
- connect(item, SIGNAL(SelectionChanged(SequenceItem*)),
- this, SLOT(ItemSelectionChanged(SequenceItem*)));
- this->AddSequence(item);
- obj_map_.insert(std::make_pair(item, o));
- }
- }
-}
-
-void SequenceViewer::ItemSelectionChanged(SequenceItem* item)
-{
- if (we_are_changing_the_selection_==true) {
- return;
- }
- we_are_changing_the_selection_=true;
- // map sequence item back to graphical object
- if (gfx::GfxObjP p=this->GfxObjForSeqItem(item)) {
- gfx::EntityP ec=dyn_cast<gfx::Entity>(p);
- seq::SequenceHandle seq=item->GetSequence();
- mol::EntityView att_v=seq.GetAttachedView();
- if (!att_v) {
- we_are_changing_the_selection_=false;
- return;
- }
- const SequenceItem::Selection& sel=item->GetSelection();
- // reset selection of "our" chain
- mol::EntityView sel_v=ec->GetSelection();
- if (mol::ChainView c=sel_v.FindChain(att_v.GetChainList().front().GetHandle())) {
- sel_v.RemoveChain(c);
- }
- if (sel.empty()) {
- try {
- ec->SetSelection(sel_v);
- } catch(...) {
- }
- we_are_changing_the_selection_=false;
- return;
- }
- for (SequenceItem::Selection::const_iterator j=sel.begin(),
- e=sel.end(); j!=e; ++j) {
- for (size_t k=j->Loc; k<j->End(); ++k) {
- if (int(k)>seq.GetLength() || seq.GetOneLetterCode(k)=='-') {
- continue;
- }
- if (mol::ResidueView rv=seq.GetResidue(k)) {
- sel_v.AddResidue(rv, mol::ViewAddFlag::INCLUDE_ATOMS);
- }
- }
- }
- sel_v.AddAllInclusiveBonds();
- try {
- ec->SetSelection(sel_v);
- } catch(...) {
- }
-
- }
- we_are_changing_the_selection_=false;
-}
-
-void SequenceViewer::NodeRemoved(const gfx::GfxNodeP& node)
-{
- if (gfx::EntityP o=dyn_cast<gfx::Entity>(node)) {
- SequenceItemList seq_items=this->SeqItemsForGfxObj(o);
- for (SequenceItemList::iterator i=seq_items.begin(),
- e=seq_items.end(); i!=e; ++i) {
- SequenceItem* seq_item=*i;
- this->RemoveSequence(seq_item);
- delete seq_item;
- }
- }
-}
-
-void SequenceViewer::SelectionChanged(const gfx::GfxObjP& o,
- const mol::EntityView& view)
-{
- if (we_are_changing_the_selection_) {
- return;
- }
- we_are_changing_the_selection_=true;
- gfx::EntityP ec=dyn_cast<gfx::Entity>(o);
-
-
- std::vector<bool> selected_cols;
- selected_cols.resize(this->GetLongestSequenceLength(), false);
-
- // get affected sequence items
- SequenceItemList seq_items=this->SeqItemsForGfxObj(o);
-
- for (SequenceItemList::iterator i=seq_items.begin(),
- e=seq_items.end(); i!=e; ++i) {
- SequenceItem* seq_item=*i;
-
- if(view.GetChainCount()==0){
- this->SelectColumns(seq_item, selected_cols);
- }
- else
- {
- seq::SequenceHandle seq=seq_item->GetSequence();
- mol::ChainView dst_chain=(seq.GetAttachedView().GetChainList())[0];
- if (mol::ChainView src_chain=view.FindChain(dst_chain.GetName())) {
- // for each residue in the selection deduce index in sequence
- for (mol::ResidueViewList::const_iterator j=src_chain.GetResidueList().begin(),
- e2=src_chain.GetResidueList().end(); j!=e2; ++j) {
- mol::ResidueView dst_res=dst_chain.FindResidue(j->GetHandle());
- assert(dst_res.IsValid());
- int p=seq.GetPos(dst_res.GetIndex());
- assert(p>=0 && p<=seq.GetLength());
- selected_cols[p]=true;
- }
- this->SelectColumns(seq_item, selected_cols);
- std::fill(selected_cols.begin(), selected_cols.end(), false);
- }
- }
- }
- we_are_changing_the_selection_=false;
-}
-
-SequenceItemList SequenceViewer::SeqItemsForGfxObj(const gfx::GfxObjP& obj)
-{
- SequenceItemList seq_items;
- gfx::EntityP ec=dyn_cast<gfx::Entity>(obj);
- std::map<SequenceItem*, gfx::EntityP>::iterator i,e;
- for (i=obj_map_.begin(), e=obj_map_.end(); i!=e; ++i) {
- if (i->second==ec) {
- seq_items.push_back(i->first);
- }
- }
- return seq_items;
-}
-
-gfx::GfxObjP SequenceViewer::GfxObjForSeqItem(SequenceItem* item)
-{
- std::map<SequenceItem*, gfx::EntityP>::iterator i=obj_map_.find(item);
- return (i!=obj_map_.end()) ? i->second : gfx::EntityP();
-}
-
-}}
diff --git a/modules/gui/src/sequence_viewer/sequence_viewer.hh b/modules/gui/src/sequence_viewer/sequence_viewer.hh
deleted file mode 100644
index 0b5811dc1fb17fd7905501845b01a77d592d75c8..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_viewer.hh
+++ /dev/null
@@ -1,60 +0,0 @@
-//------------------------------------------------------------------------------
-// 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_HH
-#define OST_SEQUENCE_VIEWER_HH
-
-/*
- Author: Marco Biasini
- */
-
-#include <map>
-
-#include <ost/gfx/scene_observer.hh>
-#include <ost/gui/sequence_viewer/sequence_viewer_base.hh>
-#include <ost/gfx/entity.hh>
-
-namespace ost { namespace gui {
-
-class SequenceItem;
-
-/// \brief sequence view
-class DLLEXPORT_OST_GUI SequenceViewer : public SequenceViewerBase,
- public gfx::SceneObserver {
- Q_OBJECT
-public:
- SequenceViewer(QWidget* parent=NULL);
- ~SequenceViewer();
-
- virtual void NodeAdded(const gfx::GfxNodeP& node);
-
- virtual void NodeRemoved(const gfx::GfxNodeP& node);
-
- virtual void SelectionChanged(const gfx::GfxObjP& obj, const mol::EntityView& sel);
-public slots:
- void ItemSelectionChanged(SequenceItem* item);
-private:
- SequenceItemList SeqItemsForGfxObj(const gfx::GfxObjP& obj);
- gfx::GfxObjP GfxObjForSeqItem(SequenceItem* seq_item);
- std::map<SequenceItem*, gfx::EntityP> obj_map_;
- bool we_are_changing_the_selection_;
-};
-
-}}
-
-#endif
diff --git a/modules/gui/src/sequence_viewer/sequence_viewer_base.cc b/modules/gui/src/sequence_viewer/sequence_viewer_base.cc
deleted file mode 100644
index 61cae9aac9015f3c3db6a27741a12c7f84da109a..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_viewer_base.cc
+++ /dev/null
@@ -1,237 +0,0 @@
-//------------------------------------------------------------------------------
-// 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
-//------------------------------------------------------------------------------
-#include "sequence_viewer_base.hh"
-#include "sequence_search_bar.hh"
-#include <QShortcut>
-#include <QVBoxLayout>
-#include <QPainter>
-
-namespace ost { namespace gui {
-
-SequenceViewerBase::SequenceViewerBase(QWidget* parent):
- Widget(NULL, parent), style_(DENSE), sel_mode_(ROW),
- scene_(new SequenceScene(this)), search_bar_(new SequenceSearchBar(this)),
- view_(new QGraphicsView(NULL, this))
-{
- QVBoxLayout* l=new QVBoxLayout;
- this->setLayout(l);
- l->setMargin(0);
- l->setSpacing(0);
- view_->setScene(scene_);
- l->addWidget(search_bar_, 0);
- l->addWidget(view_, 1);
- view_->setScene(scene_);
- view_->setRenderHints(QPainter::Antialiasing|QPainter::TextAntialiasing);
- view_->setViewportUpdateMode(QGraphicsView::FullViewportUpdate);
- QShortcut* shortcut=new QShortcut(QKeySequence(tr("Ctrl+F")), this);
- connect(shortcut, SIGNAL(activated()), this, SLOT(FindInSequence()));
- connect(search_bar_, SIGNAL(Changed(const QString&, bool, int)), this,
- SLOT(OnSearchBarUpdate(const QString&, bool, int)));
- search_bar_->hide();
- view_->setAlignment(Qt::AlignLeft|Qt::AlignTop);
-}
-
-namespace {
-
-size_t update_select_state(seq::SequenceHandle seq, const String& subject,
- std::vector<bool>& sel_state)
-{
- size_t pos=0;
- size_t first=String::npos;
- String seq_str=seq.GetString();
- while ((pos=seq_str.find(subject, pos))!=String::npos) {
- if (first==String::npos) {
- first=pos;
- }
- std::fill_n(sel_state.begin()+pos, subject.length(), true);
- pos+=subject.length();
- }
- return first;
-}
-
-
-void set_sel(std::vector<bool>& selected, SequenceItem* item)
-{
- std::vector<bool>::iterator c=selected.begin();
- item->ClearSelection();
- while (c!=selected.end()) {
- std::vector<bool>::iterator e=c;
- while ((*(++e))==*c && e!=selected.end()) {}
- if (*c) {
- // this is really ugly!
- item->BeginSelectionChange();
- item->Select(c-selected.begin(), e-selected.begin(), false);
- }
- c=e;
- }
- item->EndSelectionChange();
-}
-
-}
-
-void SequenceViewerBase::FindInSequence()
-{
- if (scene_->GetSequences().empty()) {
- return;
- }
- search_bar_->Show(scene_->GetSequences());
-}
-
-int SequenceViewerBase::GetLongestSequenceLength() const
-{
- std::vector<SequenceItem*>::iterator i=scene_->GetSequences().begin(),
- e=scene_->GetSequences().end();
- int longest=0;
- for (; i!=e; ++i) {
- longest=std::max(longest, (*i)->GetSequence().GetLength());
- }
- return longest;
-}
-
-void SequenceViewerBase::SelectColumns(std::vector<bool>& selected_cols)
-{
- std::vector<SequenceItem*>::iterator i=scene_->GetSequences().begin(),
- e=scene_->GetSequences().end();
- for (; i!=e; ++i) {
- set_sel(selected_cols, *i);
- }
-}
-
-void SequenceViewerBase::SelectColumns(SequenceItem* seq_item,
- std::vector<bool>& selected_cols)
-{
- set_sel(selected_cols, seq_item);
-}
-
-void SequenceViewerBase::ClearSelection()
-{
- std::vector<SequenceItem*>::iterator i=scene_->GetSequences().begin(),
- e=scene_->GetSequences().end();
- for (; i!=e; ++i) {
- (*i)->ClearSelection();
- }
-}
-
-void SequenceViewerBase::OnSearchBarUpdate(const QString& subject,
- bool search_in_all, int seq_id)
-{
- String std_subj=subject.toStdString();
- this->ClearSelection();
- if (scene_->GetSequences().empty() || (seq_id==-1 && !search_in_all)) {
- return;
- }
- if (subject.size()==0) {
- return;
- }
-
- std::vector<bool> selected;
- selected.resize(GetLongestSequenceLength(), false);
- /// \todo implement selection for SelMode==COLUMN
- std::pair<int, size_t> first(0, String::npos);
- if (search_in_all) {
- for (size_t i=0; i<scene_->GetSequences().size(); ++i) {
- (scene_->GetSequences())[i]->ClearSelection();
- seq::SequenceHandle s=(scene_->GetSequences())[i]->GetSequence();
- size_t pos=update_select_state(s, std_subj, selected);
- if (pos!=String::npos && first.second==String::npos) {
- first.second=pos;
- first.first=i;
- }
- if (sel_mode_==ROW) {
- set_sel(selected, (scene_->GetSequences())[i]);
- std::fill_n(selected.begin(), selected.size(), false);
- }
- }
- } else {
- first.first=seq_id;
- SequenceItem* s=(scene_->GetSequences())[seq_id];
- size_t pos=update_select_state(s->GetSequence(), std_subj, selected);
- if (pos!=String::npos) {
- first.second=pos;
- }
- if (sel_mode_==ROW) {
- set_sel(selected, s);
- }
- }
- if (sel_mode_==COLUMN) {
- this->SelectColumns(selected);
- }
- if (first.second!=String::npos) {
- QRectF r=(scene_->GetSequences()[first.first]->GetCharBounds(first.second));
-
- view_->ensureVisible(r);
- }
- scene_->update();
-}
-
-void SequenceViewerBase::SetDisplayStyle(Style style)
-{
- style_=style;
- for (std::vector<SequenceItem*>::iterator i=scene_->GetSequences().begin(),
- e=scene_->GetSequences().end(); i!=e; ++i) {
- (*i)->SetShowSecStructure(style_==LOOSE);
- }
- scene_->RepackSequences();
-}
-
-void SequenceViewerBase::SetSelMode(SelMode mode)
-{
- sel_mode_=mode;
-}
-
-SequenceViewerBase::SelMode SequenceViewerBase::GetSelMode() const
-{
- return sel_mode_;
-}
-
-SequenceViewerBase::Style SequenceViewerBase::GetDisplayStyle() const
-{
- return style_;
-}
-
-void SequenceViewerBase::AddSequence(SequenceItem* seq)
-{
- seq->SetShowSecStructure(style_==LOOSE);
- scene_->AddSequence(seq);
- QRectF rect=scene_->itemsBoundingRect();
- view_->setSceneRect(QRectF(0, 0, +rect.left()+rect.width(),
- rect.height()+rect.top()));
-}
-
-void SequenceViewerBase::RemoveSequence(SequenceItem* seq)
-{
- scene_->RemoveSequence(seq);
-}
-
-void SequenceViewerBase::Clear()
-{
-
-}
-
-bool SequenceViewerBase::Restore(const QString& prefix)
-{
- return true;
-}
-
-bool SequenceViewerBase::Save(const QString& prefix)
-{
- return true;
-}
-
-}}
diff --git a/modules/gui/src/sequence_viewer/sequence_viewer_base.hh b/modules/gui/src/sequence_viewer/sequence_viewer_base.hh
deleted file mode 100644
index 6bc183765c54a9f3b3b4f20f33eb0a0cd20a6e73..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_viewer_base.hh
+++ /dev/null
@@ -1,99 +0,0 @@
-//------------------------------------------------------------------------------
-// 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_GUI_SEQUENCE_VIEWER_BASE_HH
-#define OST_GUI_SEQUENCE_VIEWER_BASE_HH
-/*
- Author: Marco Biasini
- */
-
-#include <ost/gui/sequence_viewer/sequence_item.hh>
-#include <ost/gui/sequence_viewer/sequence_scene.hh>
-
-#include <ost/gui/widget.hh>
-
-#include <QGraphicsView>
-
-namespace ost { namespace gui {
-
-class SequenceSearchBar;
-
-/// \brief base class for sequence viewers
-///
-/// subclassed by AlignmentViewer and SequenceViewer
-class DLLEXPORT_OST_GUI SequenceViewerBase : public Widget {
- Q_OBJECT
-public:
- typedef enum {
- DENSE,
- LOOSE,
- } Style;
-
- typedef enum {
- COLUMN,
- ROW
- } SelMode;
-public:
- SequenceViewerBase(QWidget* parent=NULL);
- void SetDisplayStyle(Style style);
-
- void SetSelMode(SelMode mode);
-
- SelMode GetSelMode() const;
- Style GetDisplayStyle() const;
-
- /// \brief add sequence
- ///
- /// issue: should we copy the sequence object to avoid weird side-effects?
- void AddSequence(SequenceItem* seq);
-
- /// \brief remove sequence
- void RemoveSequence(SequenceItem* seq);
-
- /// \brief select columns in all sequences
- void SelectColumns(std::vector<bool>& selected_cols);
-
- /// \brief select columns in sequence
- void SelectColumns(SequenceItem* seq, std::vector<bool>& selected_cols);
- /// \brief get length of longest sequence including gaps
- int GetLongestSequenceLength() const;
- /// \brief remove all sequences
- void Clear();
-
- virtual bool Restore(const QString& prefix);
- virtual bool Save(const QString& prefix);
-public slots:
- /// \brief clear selection
- void ClearSelection();
-
- /// \internal
- void OnSearchBarUpdate(const QString&, bool, int);
-
- /// \brief show sequence search bar
- void FindInSequence();
-
-private:
- Style style_;
- SelMode sel_mode_;
- SequenceScene* scene_;
- SequenceSearchBar* search_bar_;
- QGraphicsView* view_;
-};
-
-}}
-#endif
diff --git a/scripts/init.py b/scripts/init.py
index 020a660797852353077ff6c36a8f10834c1dd05a..424ae43981cb059c86a629547b66c4111cf927e2 100644
--- a/scripts/init.py
+++ b/scripts/init.py
@@ -35,7 +35,6 @@ def _InitPanels(app):
panels.AddWidgetToPool('ost.gui.PythonShell', 1)
panels.AddWidgetToPool('ost.gui.RemoteLoader', -1)
panels.AddWidgetToPool('ost.gui.SceneWin', 1)
- panels.AddWidgetToPool('ost.gui.SequenceViewer', 1)
panels.AddWidgetToPool('ost.gui.SequenceViewerV2', 1)
if not panels.Restore("ui/perspective/panels"):
panels.AddWidget(gui.PanelPosition.LEFT_PANEL, app.scene_win)
@@ -43,7 +42,7 @@ def _InitPanels(app):
'ost.gui.FileBrowser', False)
panels.AddWidgetByName(gui.PanelPosition.LEFT_PANEL,
'ost.gui.RemoteLoader', False)
- panels.AddWidget(gui.PanelPosition.BOTTOM_PANEL, app.seq_viewer)
+ panels.AddWidget(gui.PanelPosition.BOTTOM_PANEL, app.seq_viewer_v2)
panels.AddWidget(gui.PanelPosition.BOTTOM_PANEL, app.py_shell)
def _InitFrontEnd():