From 465e7bb79247630f7625022e96524a8ac1703b22 Mon Sep 17 00:00:00 2001
From: stefan <stefan@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Mon, 7 Jun 2010 08:32:47 +0000
Subject: [PATCH] New SequenceViewer, added new DisplayMode "Conservation 2"
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2346 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/gui/src/CMakeLists.txt | 2 +-
.../gui/src/sequence/alignment_view_object.cc | 80 ++++++++++++++-----
.../gui/src/sequence/alignment_view_object.hh | 10 ++-
3 files changed, 66 insertions(+), 26 deletions(-)
diff --git a/modules/gui/src/CMakeLists.txt b/modules/gui/src/CMakeLists.txt
index f8aeaaf00..744b59c57 100644
--- a/modules/gui/src/CMakeLists.txt
+++ b/modules/gui/src/CMakeLists.txt
@@ -480,7 +480,7 @@ module(NAME gui SOURCES ${OST_GUI_MOCS} ${OST_GUI_SOURCES}
${OST_GUI_INPUT_HEADERS}
${OST_GUI_DATA_VIEWER_HEADERS}
${OST_GUI_HEADERS}
- DEPENDS_ON gfx io mol_alg
+ DEPENDS_ON gfx io mol_alg seq_alg
LINK ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${BOOST_PYTHON_LIBRARIES} ${SPNAV_LIBRARIES})
include_directories(${PYTHON_INCLUDE_PATH})
qt4_add_resources(OST_QT_RESOURCE dngr.qrc)
diff --git a/modules/gui/src/sequence/alignment_view_object.cc b/modules/gui/src/sequence/alignment_view_object.cc
index c7be971ea..dc7197641 100644
--- a/modules/gui/src/sequence/alignment_view_object.cc
+++ b/modules/gui/src/sequence/alignment_view_object.cc
@@ -28,6 +28,7 @@
#include <ost/mol/view_op.hh>
#include <ost/seq/aligned_region.hh>
+#include <ost/seq/alg/conservation.hh>
#include "sequence_row.hh"
#include "secstr_row.hh"
@@ -83,10 +84,11 @@ QColor GetForeGroundColor(QColor background){
}
-
QMap<QString,int> AlignmentViewObject::group_map_ = GetGroupMap();
-const QString AlignmentViewObject::conservation_mode = "Highlight conservation";
+
+const QString AlignmentViewObject::conservation_mode_1 = "Highlight conservation 1";
+const QString AlignmentViewObject::conservation_mode_2 = "Highlight conservation 2";
AlignmentViewObject::AlignmentViewObject(const seq::AlignmentHandle& alignment, QObject* parent): SequenceViewObject(parent), alignment_(alignment)
{
@@ -95,6 +97,18 @@ AlignmentViewObject::AlignmentViewObject(const seq::AlignmentHandle& alignment,
this->AddSequence(seq_handle, seq_handle.GetName().c_str());
}
+ std::vector<Real> values = seq::alg::Conservation(alignment,false);
+
+ gradient_.SetColorAt(0,gfx::Color(0,0,1));
+ gradient_.SetColorAt(0.5,gfx::Color(1,1,1));
+ gradient_.SetColorAt(1,gfx::Color(1,0,0));
+ //Calculate Conservation Mode 1
+ for(unsigned int i=0; i<values.size(); i++){
+ gfx::Color color = gradient_.GetColorAt(values[i]);
+ conservation_1_[i] = QColor(color.Red()*255,color.Green()*255,color.Blue()*255);
+ }
+
+ //Calculate Conservation Mode 2
for(int j=0; j<alignment.GetLength(); j++){
int group = 0;
QString element = "";
@@ -120,49 +134,71 @@ AlignmentViewObject::AlignmentViewObject(const seq::AlignmentHandle& alignment,
}
if(element.size()==1){
- conservation_[j] = QColor(175,175,175);
+ conservation_2_[j] = QColor(175,175,175);
}
else if(group > 0){
- conservation_[j] = QColor(200,200,200);
+ conservation_2_[j] = QColor(200,200,200);
}
else{
- conservation_[j] = Qt::transparent;
+ conservation_2_[j] = Qt::transparent;
}
}
- this->AddDisplayMode(conservation_mode);
+ this->AddDisplayMode(conservation_mode_1);
+ this->AddDisplayMode(conservation_mode_2);
}
QVariant AlignmentViewObject::GetData(int row, int column, int role)
{
- if(column > 0 && this->GetCurrentDisplayMode() == conservation_mode){
- if(role == Qt::UserRole+3 ){
- if(column -1 < conservation_.size()){
- return QVariant(conservation_[column-1]);
+ if(column > 0){
+ if(this->GetCurrentDisplayMode() == conservation_mode_1){
+ if(role == Qt::UserRole+3 ){
+ if(column -1 < conservation_1_.size()){
+ return QVariant(conservation_1_[column-1]);
+ }
+ return QVariant(Qt::transparent);
}
+
+ if(role == Qt::ForegroundRole){
+ if(column -1 < conservation_1_.size()){
+ if(conservation_1_[column-1].red()>128){
+ return QVariant(Qt::black);
+ }
+ else{
+ return QVariant(Qt::white);
+ }
+ }
return QVariant(Qt::transparent);
+ }
}
-
- if(role == Qt::ForegroundRole){
- if(column -1 < conservation_.size()){
- return QVariant(Qt::black);
+ else if(this->GetCurrentDisplayMode() == conservation_mode_2){
+ if(role == Qt::UserRole+3 ){
+ if(column -1 < conservation_2_.size()){
+ return QVariant(conservation_2_[column-1]);
+ }
+ return QVariant(Qt::transparent);
+ }
+ if(role == Qt::ForegroundRole){
+ if(column -1 < conservation_2_.size()){
+ return QVariant(Qt::black);
}
return QVariant(Qt::transparent);
+ }
}
-
}
-
return BaseViewObject::GetData(row,column,role);
}
void AlignmentViewObject::SetDisplayMode(const QString& mode)
{
- if(this->display_modes_.contains(mode) && mode == conservation_mode){
- for(int i=0 ; i<this->GetRowCount(); i++){
- BaseRow* row = this->GetRow(i);
- row->RemovePainter(seq_secondary_structure_painter);
- row->RemovePainter(align_properties_painter);
- row->InsertPainter(conservation_painter,1);
+ if(this->display_modes_.contains(mode)){
+ if(mode == conservation_mode_1 || mode == conservation_mode_2){
+ for(int i=0 ; i<this->GetRowCount(); i++){
+ BaseRow* row = this->GetRow(i);
+ row->RemovePainter(seq_secondary_structure_painter);
+ row->RemovePainter(align_properties_painter);
+ row->InsertPainter(conservation_painter,1);
+ }
}
}
SequenceViewObject::SetDisplayMode(mode);
diff --git a/modules/gui/src/sequence/alignment_view_object.hh b/modules/gui/src/sequence/alignment_view_object.hh
index 242e1efea..b8fee2800 100644
--- a/modules/gui/src/sequence/alignment_view_object.hh
+++ b/modules/gui/src/sequence/alignment_view_object.hh
@@ -25,6 +25,8 @@
#include <ost/seq/alignment_handle.hh>
+#include <ost/gfx/gradient.hh>
+
#include "sequence_view_object.hh"
namespace ost { namespace gui {
@@ -37,18 +39,20 @@ public:
AlignmentViewObject(const seq::AlignmentHandle& alignment, QObject* parent = 0);
QVariant GetData(int row, int column, int role);
-
const seq::AlignmentHandle& GetAlignment();
void SetDisplayMode(const QString& mode);
private:
+ gfx::Gradient gradient_;
seq::AlignmentHandle alignment_;
- QMap<int, QColor> conservation_;
+ QMap<int, QColor> conservation_1_;
+ QMap<int, QColor> conservation_2_;
static QMap<QString,int> group_map_;
- static const QString conservation_mode;
+ static const QString conservation_mode_1;
+ static const QString conservation_mode_2;
};
--
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