diff --git a/modules/conop/src/model_check.hh b/modules/conop/src/model_check.hh
index 25bdfb88b85e92094e28c717bcf3840d78d64ce2..9053c239109f3ad1e5f378c3140181cf14aba31f 100644
--- a/modules/conop/src/model_check.hh
+++ b/modules/conop/src/model_check.hh
@@ -8,9 +8,9 @@ namespace ost { namespace conop {
class DLLEXPORT_OST_CONOP Checker {
public:
- Checker(CompoundLibPtr lib, const mol::EntityHandle& ent,
- DiagEngine& diags): lib_(lib), ent_(ent), diags_(diags),
- checked_unk_res_(false)
+ Checker(CompoundLibPtr lib, const mol::EntityHandle& ent,
+ DiagEngine& diags): lib_(lib), ent_(ent), diags_(diags),
+ checked_unk_res_(false)
{}
void CheckForUnknownAtoms();
void CheckForCompleteness(bool require_hydrogens=false);
@@ -20,10 +20,10 @@ public:
const std::vector<Diag*>& GetDiags() const { return diags_.GetDiags(); }
private:
- CompoundLibPtr lib_;
- mol::EntityHandle ent_;
- DiagEngine& diags_;
- bool checked_unk_res_;
+ CompoundLibPtr lib_;
+ mol::EntityHandle ent_;
+ DiagEngine& diags_;
+ bool checked_unk_res_;
};
}} /* ost::conop */
diff --git a/modules/gui/src/sequence_viewer/sequence_model.cc b/modules/gui/src/sequence_viewer/sequence_model.cc
index 0a98033c703cef68d0cd0c49fee8b8dd85f065c2..d64020ad925ca9307ca3fafd423f7de027d4684c 100644
--- a/modules/gui/src/sequence_viewer/sequence_model.cc
+++ b/modules/gui/src/sequence_viewer/sequence_model.cc
@@ -50,7 +50,8 @@ SequenceModel::SequenceModel(QObject *parent)
this->endInsertRows();
}
-void SequenceModel::InsertSequence(QString& name, seq::SequenceHandle& seq){
+void SequenceModel::InsertSequence(QString& name, seq::SequenceHandle& seq)
+{
int cols = this->columnCount();
int new_cols = seq.GetLength();
this->beginInsertRows(QModelIndex(),this->rowCount(),this->rowCount());
@@ -63,7 +64,7 @@ void SequenceModel::InsertSequence(QString& name, seq::SequenceHandle& seq){
this->endInsertRows();
}
-void SequenceModel::InsertChain(QString& name, mol::ChainView& view){
+void SequenceModel::InsertChain(QString& name, mol::ChainView& view) {
int cols = this->columnCount();
int new_cols = view.GetResidueCount();
this->beginInsertRows(QModelIndex(),this->rowCount(),this->rowCount());
@@ -89,8 +90,10 @@ void SequenceModel::InsertAlignment(const seq::AlignmentHandle& alignment){
this->endInsertRows();
}
-void SequenceModel::InsertSequences(const QList<QString>& names, seq::SequenceList& list){
- this->beginInsertRows(this->index(this->rowCount(),0),this->rowCount(),this->rowCount()+list.GetCount());
+void SequenceModel::InsertSequences(const QList<QString>& names,
+ seq::SequenceList& list){
+ this->beginInsertRows(this->index(this->rowCount(),0),
+ this->rowCount(),this->rowCount()+list.GetCount());
objects_.append(new SequenceViewObject(list, names, this));
this->endInsertRows();
}
@@ -143,7 +146,7 @@ void SequenceModel::RemoveAlignment(const seq::AlignmentHandle& alignment){
}
}
-int SequenceModel::GetColumnCount() const{
+int SequenceModel::GetColumnCount() const {
int cols = 0;
for(int i = 0; i<objects_.size();i++){
int ob_cols = objects_[i]->GetMaxColumnCount();
@@ -154,7 +157,8 @@ int SequenceModel::GetColumnCount() const{
return cols;
}
-SequenceViewObject* SequenceModel::GetItem(const gfx::EntityP& entity){
+SequenceViewObject* SequenceModel::GetItem(const gfx::EntityP& entity)
+{
if(entity != NULL){
for (int i = 0 ; i< objects_.size(); i++){
if(SequenceViewObject* seq_view_object = qobject_cast<SequenceViewObject*>(objects_[i])){
@@ -167,7 +171,8 @@ SequenceViewObject* SequenceModel::GetItem(const gfx::EntityP& entity){
return NULL;
}
-AlignmentViewObject* SequenceModel::GetItem(const seq::AlignmentHandle& alignment){
+AlignmentViewObject* SequenceModel::GetItem(const seq::AlignmentHandle& alignment)
+{
for (int i = 0 ; i< objects_.size(); i++){
if(AlignmentViewObject* alignment_object = qobject_cast<AlignmentViewObject*>(objects_[i])){
if(alignment == alignment_object->GetAlignment()){
@@ -178,7 +183,8 @@ AlignmentViewObject* SequenceModel::GetItem(const seq::AlignmentHandle& alignmen
return NULL;
}
-const PainterList& SequenceModel::GetPainters(const QModelIndex& index) const{
+const PainterList& SequenceModel::GetPainters(const QModelIndex& index) const
+{
QPair<int, BaseViewObject*> pair = this->GetRowWithItem(index);
if(pair.second){
return pair.second->GetRow(pair.first)->GetPainters();
@@ -255,7 +261,8 @@ int SequenceModel::GetGlobalRow(BaseViewObject* obj, int row) const
return glob_row;
}
-QModelIndexList SequenceModel::GetModelIndexes(gfx::EntityP& entity, const mol::EntityView& view)
+QModelIndexList SequenceModel::GetModelIndexes(gfx::EntityP& entity,
+ const mol::EntityView& view)
{
QModelIndexList list;
if(BaseViewObject* object = this->GetItem(entity)){
@@ -275,7 +282,8 @@ QModelIndexList SequenceModel::GetModelIndexes(gfx::EntityP& entity, const mol::
return list;
}
-QModelIndexList SequenceModel::GetModelIndexes(const QString& subject, const QString& sequence_name)
+QModelIndexList SequenceModel::GetModelIndexes(const QString& subject,
+ const QString& sequence_name)
{
QModelIndexList list;
for (int i = 0; i<objects_.size(); i++){
@@ -295,7 +303,8 @@ QModelIndexList SequenceModel::GetModelIndexes(const QString& subject, const QSt
return list;
}
-void SequenceModel::SelectionChanged(const QItemSelection& sel, const QItemSelection& desel)
+void SequenceModel::SelectionChanged(const QItemSelection& sel,
+ const QItemSelection& desel)
{
QMap<int,QPair<QSet<int>,QSet<int> > > sel_map;
const QModelIndexList& sel_indexes = sel.indexes();
diff --git a/modules/gui/src/sequence_viewer/sequence_row.cc b/modules/gui/src/sequence_viewer/sequence_row.cc
index 30199dd6f7c69c0653064f0259f5870590a60adf..1d431cbae8bc0998d00e0e3281429aaf8bbaacbf 100644
--- a/modules/gui/src/sequence_viewer/sequence_row.cc
+++ b/modules/gui/src/sequence_viewer/sequence_row.cc
@@ -34,13 +34,18 @@
#include <QtGui>
namespace ost { namespace gui {
-SequenceRow::SequenceRow(const QString& name, seq::ConstSequenceHandle sequence, SequenceViewObject* parent) : BaseRow(QFont("Courier",11),parent), name_(name), name_font_(QFont("Courier",11)), sequence_(sequence)
+SequenceRow::SequenceRow(const QString& name, seq::ConstSequenceHandle sequence,
+ SequenceViewObject* parent) :
+ BaseRow(QFont("Courier",11),parent), name_(name),
+ name_font_(QFont("Courier",11)), sequence_(sequence)
{
name_font_.setBold(true);
name_font_.setItalic(true);
}
-SequenceRow::SequenceRow(const QString& name, SequenceViewObject* parent) : BaseRow(QFont("Courier",11),parent), name_(name), name_font_(QFont("Courier",11))
+SequenceRow::SequenceRow(const QString& name, SequenceViewObject* parent) :
+ BaseRow(QFont("Courier",11),parent), name_(name),
+ name_font_(QFont("Courier",11))
{
name_font_.setBold(true);
name_font_.setItalic(true);
diff --git a/modules/gui/src/sequence_viewer/sequence_table_view.cc b/modules/gui/src/sequence_viewer/sequence_table_view.cc
index 90b4baa5bc4ef8ce742a006ab5b38227409e059a..68eb7d2d8766a8204987f7aae0e641e1980cd9f3 100644
--- a/modules/gui/src/sequence_viewer/sequence_table_view.cc
+++ b/modules/gui/src/sequence_viewer/sequence_table_view.cc
@@ -60,8 +60,10 @@ SequenceTableView::SequenceTableView(QAbstractItemModel * model)
this->setHorizontalScrollMode(ScrollPerPixel);
this->setVerticalScrollMode(ScrollPerPixel);
- connect(this->horizontalHeader(),SIGNAL(sectionResized(int,int,int)), this, SLOT(ResizeWidth(int,int,int)));
- connect(this->verticalHeader(),SIGNAL(sectionResized(int,int,int)), this, SLOT(ResizeHeight(int,int,int)));
+ connect(this->horizontalHeader(),SIGNAL(sectionResized(int,int,int)),
+ this, SLOT(ResizeWidth(int,int,int)));
+ connect(this->verticalHeader(),SIGNAL(sectionResized(int,int,int)),
+ this, SLOT(ResizeHeight(int,int,int)));
delegate_ = new SequenceDelegate(qobject_cast<SequenceModel*>(this->model()),this);
@@ -140,8 +142,10 @@ void SequenceTableView::InitStaticRow()
static_row_->setItemDelegate(delegate_);
- connect(static_row_->horizontalScrollBar(), SIGNAL(valueChanged(int)), this->horizontalScrollBar(), SLOT(setValue(int)));
- connect(horizontalScrollBar(), SIGNAL(valueChanged(int)), static_row_->horizontalScrollBar(), SLOT(setValue(int)));
+ connect(static_row_->horizontalScrollBar(), SIGNAL(valueChanged(int)),
+ this->horizontalScrollBar(), SLOT(setValue(int)));
+ connect(horizontalScrollBar(), SIGNAL(valueChanged(int)),
+ static_row_->horizontalScrollBar(), SLOT(setValue(int)));
this->updateStaticRow();
}
@@ -179,10 +183,14 @@ void SequenceTableView::InitStaticField(){
static_field_->setHorizontalScrollMode(ScrollPerPixel);
static_field_->setVerticalScrollMode(ScrollPerPixel);
- connect(static_field_->horizontalScrollBar(), SIGNAL(valueChanged(int)), this->horizontalScrollBar(), SLOT(setValue(int)));
- connect(horizontalScrollBar(), SIGNAL(valueChanged(int)), static_field_->horizontalScrollBar(), SLOT(setValue(int)));
- connect(static_field_->verticalScrollBar(), SIGNAL(valueChanged(int)), this->verticalScrollBar(), SLOT(setValue(int)));
- connect(verticalScrollBar(), SIGNAL(valueChanged(int)), static_field_->verticalScrollBar(), SLOT(setValue(int)));
+ connect(static_field_->horizontalScrollBar(), SIGNAL(valueChanged(int)),
+ this->horizontalScrollBar(), SLOT(setValue(int)));
+ connect(horizontalScrollBar(), SIGNAL(valueChanged(int)),
+ static_field_->horizontalScrollBar(), SLOT(setValue(int)));
+ connect(static_field_->verticalScrollBar(), SIGNAL(valueChanged(int)),
+ this->verticalScrollBar(), SLOT(setValue(int)));
+ connect(verticalScrollBar(), SIGNAL(valueChanged(int)),
+ static_field_->verticalScrollBar(), SLOT(setValue(int)));
this->updateStaticField();
}
@@ -222,7 +230,8 @@ void SequenceTableView::resizeEvent(QResizeEvent * event)
#endif
}
-QModelIndex SequenceTableView::moveCursor(CursorAction action, Qt::KeyboardModifiers modifiers)
+QModelIndex SequenceTableView::moveCursor(CursorAction action,
+ Qt::KeyboardModifiers modifiers)
{
QModelIndex current = QTableView::moveCursor(action, modifiers);
diff --git a/modules/gui/src/sequence_viewer/sequence_viewer.cc b/modules/gui/src/sequence_viewer/sequence_viewer.cc
index a34e917b6c20e86e2ba752c08d3b5e2ced3a2c29..29314805cad9465325bad4281f8e670a3e8bb2ad 100644
--- a/modules/gui/src/sequence_viewer/sequence_viewer.cc
+++ b/modules/gui/src/sequence_viewer/sequence_viewer.cc
@@ -132,7 +132,8 @@ void SequenceViewer::InitSearchBar()
seq_search_bar_ = new SeqSearchBar(this);
seq_search_bar_->hide();
layout()->addWidget(seq_search_bar_);
- connect(seq_search_bar_, SIGNAL(Changed(const QString&, bool, const QString&)), this, SLOT(OnSearchBarUpdate(const QString&, bool, const QString&)));
+ connect(seq_search_bar_, SIGNAL(Changed(const QString&, bool, const QString&)),
+ this, SLOT(OnSearchBarUpdate(const QString&, bool, const QString&)));
}
void SequenceViewer::InitView()
diff --git a/modules/gui/src/sequence_viewer/tick_painter.cc b/modules/gui/src/sequence_viewer/tick_painter.cc
index eee4143d692c2e38ebc1a925543307fc3ec59dff..4c1558a5a5c02469670cddeaf8c31e77aa67d2ba 100644
--- a/modules/gui/src/sequence_viewer/tick_painter.cc
+++ b/modules/gui/src/sequence_viewer/tick_painter.cc
@@ -32,7 +32,8 @@ TickPainter::TickPainter(QObject* parent)
: Painter(parent), pen_(QPen(Qt::darkGray))
{}
-void TickPainter::Paint(QPainter* painter, const QStyleOptionViewItem& option, const QModelIndex& index){
+void TickPainter::Paint(QPainter* painter, const QStyleOptionViewItem& option,
+ const QModelIndex& index){
painter->save();
painter->setPen(pen_);
QVariant value = index.data(Qt::DisplayRole);
diff --git a/modules/gui/src/sequence_viewer/title_row.cc b/modules/gui/src/sequence_viewer/title_row.cc
index ba7aaf280a761b9a91c39f9d26dbf02013171974..d4dd16fa5757f5ea4f43e1d5a971f1802c4381e4 100644
--- a/modules/gui/src/sequence_viewer/title_row.cc
+++ b/modules/gui/src/sequence_viewer/title_row.cc
@@ -41,29 +41,30 @@ QVariant TitleRow::GetData(int column, int role) const
if(column<0){
return QVariant();
}
- else if(role==Qt::DisplayRole && column%10==9){
- return QVariant(QString::number(column+1));
- }
- else if(role==Qt::DisplayRole && column%10==0){
- return QVariant(QString::number(column));
- }
- else if (role==Qt::FontRole){
- if(column < 999){
- return QVariant(font_);
- }
- else{
+ switch (role) {
+ case Qt::DisplayRole:
+ if (column % 10 == 9) {
+ return QVariant(QString::number(column+1));
+ }
+ if (column % 10 == 0) {
+ return QVariant(QString::number(column));
+ }
+ return QVariant();
+ case Qt::FontRole:
+ if(column < 999){
+ return QVariant(font_);
+ }
return QVariant(small_font_);
- }
- }
- else if (role==Qt::TextAlignmentRole){
- return QVariant(Qt::AlignHCenter|Qt::AlignBottom);
- }
- else if (role==Qt::SizeHintRole){
+ case Qt::TextAlignmentRole:
+ return QVariant(Qt::AlignHCenter|Qt::AlignBottom);
+ case Qt::SizeHintRole: {
QSize size = this->GetCellSize();
size.setHeight(10);
return QVariant(size);
+ }
+ default:
+ return BaseRow::GetData(column, role);
}
- return BaseRow::GetData(column, role);
}
Qt::ItemFlags TitleRow::Flags(int column) const
@@ -79,7 +80,8 @@ void TitleRow::DoubleClicked(int column)
if(this->parent()){
if(SequenceModel* model = qobject_cast<SequenceModel*>(this->parent()->parent())){
int rows = model->rowCount()-1;
- QItemSelection add = QItemSelection(model->index(1,column),model->index(rows,column));
+ QItemSelection add = QItemSelection(model->index(1,column),
+ model->index(rows,column));
model->SelectionChanged(add,QItemSelection());
}
}