TrapperView Class Reference

The view to graphically present the reads and their features. The user will mainly interact with this window. More...

#include <trapperview.h>

Collaboration diagram for TrapperView:

[legend]List of all members.

Public Slots
void	slotSwitchToMode (int i)
void	slotStartAlgo (int i)
void	slotScrollToMouse ()
void	slotScrollToPos ()
void	slotSetCenter ()
void	slotClearCenter ()
Signals
void	createView (QString)
void	message (const QString &)
Public Member Functions
	TrapperView (TrapperDoc *pDoc, QWidget *parent, const char *name, QString _viewMode=QString("everything"))
	~TrapperView ()
TrapperDoc *	getDocument () const
void	update (TrapperView *pSender)
void	print (QPrinter *pPrinter)
QString	mode ()
void	zoomIn ()
void	zoomInX ()
void	zoomInY ()
void	zoomOut ()
void	zoomOutX ()
void	zoomOutY ()
void	selectAll ()
void	selectBetween ()
void	findRead ()
void	enlarge ()
void	shrink ()
void	setDragMode (bool status)
void	copy ()
void	paste ()
void	cut ()
void	undo ()
TR_DNA	mousePressedRow ()
TR_DNA	mousePressedCol ()
void	sendMsg (const QString &msg)
Protected Types
typedef std::set< db_recno_t >	RecnoMap
Protected Member Functions
void	contentsDragEnterEvent (QDragEnterEvent *event)
void	contentsDropEvent (QDropEvent *event)
void	contentsMouseMoveEvent (QMouseEvent *e)
void	contentsMouseReleaseEvent (QMouseEvent *e)
void	contentsContextMenuEvent (QContextMenuEvent *e)
void	contentsMousePressEvent (QMouseEvent *e)
void	contentsDragMoveEvent (QDragMoveEvent *)
virtual void	closeEvent (QCloseEvent *)
void	doZoom ()
void	scrollTo (TR_PIX x, TR_PIX y)
void	drawContents (QPainter *p, TR_PIX cx, TR_PIX cy, TR_PIX cw, TR_PIX ch)
void	drawContents_helper (QPainter *p, QPainter *bitmapPainter, int cx, int cy, int cw, int ch, int dx, int dy)
	paint a rectangle of the window
void	paintFeatures (QPainter *p, QPainter *bitmapPainter, db_recno_t readRecno, TR_PIX x_pix, TR_PIX y_pix, TR_DNA x_dna_relative, TR_DNA dna_len, double width, TR_PIX height, bool selected, int center_relative, bool overlap, TR_DNA bg, TR_DNA eg)
	paint border line around the read rectangle. Then divide the rectangle into layers and paint features of the read into these layers.
void	paintGrid (QPainter *p, TR_PIX cx, TR_PIX cy, TR_PIX cw, TR_PIX ch)
	paint some extra dots in the background of the window. These will move along when the user scrolls. Nice to have some visual feedback of movement when there are no reads in the window
void	convertToPixelCoordinates (TR_PIX &x_pix, TR_PIX &y_pix, TR_DNA x_dna, TR_DNA y_dna)
void	convertToDnaCoordinates (TR_DNA &x_dna, TR_DNA &y_dna, const TR_PIX cx, const TR_PIX cy)
TR_PIX	dnaCoordToPixel_X (TR_DNA cx)
TR_PIX	dnaCoordToPixel_Y (TR_DNA cy)
TR_DNA	pixelCoordToDna_X (TR_PIX x_dna)
TR_DNA	pixelCoordToDna_Y (TR_PIX y_dna)
std::set< db_recno_t > &	getSelectedReads ()
void	select (db_recno_t recno, bool status)
bool	isSelected (db_recno_t recno)
void	clearSelected ()
std::vector< std::list< std::string > >	getInfo (const QPoint &pos)
void	runAlgo (const std::string &AlgoType, std::set< db_recno_t > &recnoList, AlgoParam *param=0)
void	writeSelected (QDataStream &data_stream)
void	readSelected (QDataStream &data_stream)
void	moveData (TR_PIX dx, TR_PIX dy)
void	fitContentsizeToData ()
void	clearLastMove ()
Protected Attributes
TR_PIX	basewidth
TR_PIX	spaceBetweenRows
TR_PIX	rowheight
TR_DNA	globalRows
TR_DNA	globalBases
TR_DNA	center_point
TrapperDoc *	doc
QLabel *	lab
double	magnifyX
u_int16_t	magnifyY
int	zoomfactor
ViewModes *	viewModes
QPopupMenu *	switchViewMenu
QPopupMenu *	algoMenu
QPopupMenu *	infoMenu
std::set< db_recno_t >	selectedReads
std::map< std::string, int >	zoom_cutoff
ReadsInRect *	readsInRect
bool	dragging
bool	allow_dragging
bool	moving
bool	last_click_selected_read
bool	last_click_changed_selection
db_recno_t	last_selected_recno
QPoint	curr_mouse_pos
TR_PIX	y_delta
TR_PIX	y_delta_previous
TR_DNA	last_move_x
TR_DNA	last_move_y
Private Member Functions
void	drawRubber (QPainter *p)
Private Attributes
QPixmap	dragPixmap
QBitmap	dragBitmap
QPainter	p3
QPoint	mousePressedPoint
QPoint	dragWindowPoint
QRect *	rubber_band
QPoint	RubberStart
QPoint	RubberEnd
bool	RubberOn
QPoint	oldMovePoint
bool	moveOn
Friends
class	TrapperDoc

---

Detailed Description

The view to graphically present the reads and their features. The user will mainly interact with this window.

Functionality given to the user: Scrolling, zooming, drag and drop of the reads to move them around, selecting reads and start algorithms.

This software is designed to have totally decoupled view and data classes. The view is stateless ( it does not store any data ) and will for every update newly read in all data needed to paint up the view. In other words, the view does not cash anything.

This has some nice implications: Data algorithm classes will work directly with the data classes and will not be aware of any views. Any number of views can be opened up and they will be independent and will not be aware of each other.

For it to be possible to take this design approach the data classes must respond quickly to queries because any delay here will make the views appear sluggish. Scrolling will here be the toughest test for the speed of the data class queries. Because by scrolling, new data should be painted very fast to the view. The user would not like big delays here.

To make the data class queries very fast, the data is stored in the embedded database Berkeley Db.

About how the reads and features get shown in TrapperView: TrapperView is inherited from QScrollView. QScrollView gives us the scroll bars and also gives convertion methods between the coordinate system of the actual window ( the viewport ) and the coordinate system of the content window ( the big window the user has to scroll to see all of it ). QScrollView gives us the possibility to place out "static" widgets on the content window, and QScrollView would then handle the scrolling automatically. But we would like a totally stateless view so we take another approach. We reimplement the virtual method drawContents() that is called everytime some part of the window should be painted, e.g. when the user has dragged the scrollbars. The method drawContents() takes as arguments the "content" pixel coordinates of a rectangle to be painted. Some background pixels are painted to enhance the "movement feeling" when scrolling. Then drawContents_helper() is called ( which is also is reused when painting reads in a drag & drop ). In drawContents_helper() we first convert to DNA coordinates, i.e. the x-axis unit is a nucleotid-base and the y-axis unit is a row. We then use the class ReadsInRect that can tell us which reads are visible in our painting rectangle. Now paintFeatures() is called for each read. In paintFeatures(), features for the read are painted in different layers inside the read rectangle.

Definition at line 115 of file trapperview.h.

---

Member Typedef Documentation

typedef std::set<db_recno_t> TrapperView::RecnoMap [protected]

Definition at line 280 of file trapperview.h.

---

Constructor & Destructor Documentation

TrapperView::TrapperView (  TrapperDoc *  pDoc, QWidget *  parent, const char *  name, QString  _viewMode = QString("everything") )

Constructor for the view Parameters: pDoc  your document instance that the view represents. Create a document before calling the constructor or connect an already existing document to a new MDI child widget. Definition at line 71 of file trapperview.cpp. References allow_dragging, basewidth, center_point, doc, dragging, fitContentsizeToData(), globalBases, globalRows, last_click_changed_selection, last_click_selected_read, GeneralMaker::listRegistered(), magnifyX, magnifyY, moving, rowheight, rubber_band, spaceBetweenRows, viewModes, zoom_cutoff, and zoomfactor. : QScrollView(parent, name,/** wflags**/ WResizeNoErase|WStaticContents|WDestructiveClose/*|WNoAutoErase*/), doc( pDoc ) { // cerr << "in TrapperView::TrapperView" << endl; // cerr<<"doc: "<<doc<<endl; viewport()->setAcceptDrops( true ); setDragAutoScroll( true ); allow_dragging = true; dragging = false; moving = false; rubber_band = 0; last_click_selected_read = false; last_click_changed_selection = false; if ( _viewMode.isNull() ) { _viewMode = "closeup"; } viewModes = new ViewModes( _viewMode, doc ); //Ugly business here... list<string> type_list = GeneralMaker::listRegistered(); for( list<string>::iterator it = type_list.begin(); it != type_list.end(); ++it ) { zoom_cutoff[ *it ] = 0; } zoom_cutoff["DnaStrData"] = 4; zoom_cutoff["QualityData"] = 4; zoom_cutoff["ChromatData"] = 8; // globalRows = 1000; // globalBases = 50000; globalRows = 50; globalBases = 2000; // rowheight = 20; // basewidth = 10; rowheight = 5; basewidth = 1; magnifyX = magnifyY = 1; zoomfactor = 2; spaceBetweenRows = 0; center_point = 0; fitContentsizeToData(); viewport()->setPaletteBackgroundColor(white); viewport()->setBackgroundMode( Qt::FixedColor ); setCaption( "yes" ); viewport()->setMouseTracking(TRUE); }

TrapperView::~TrapperView (   )

Destructor for the main view Definition at line 126 of file trapperview.cpp. References viewModes. { if ( viewModes ) { delete viewModes; viewModes = NULL; } }

---

Member Function Documentation

void TrapperView::clearLastMove (   )  [protected]

Definition at line 566 of file trapperview.cpp. References last_move_x, and last_move_y. Referenced by clearSelected(), readSelected(), select(), and slotStartAlgo(). { last_move_x = last_move_y = 0; }

void TrapperView::clearSelected (   )  [protected]

Definition at line 1139 of file trapperview.cpp. References clearLastMove(), and selectedReads. Referenced by contentsMousePressEvent(), contentsMouseReleaseEvent(), cut(), findRead(), readSelected(), selectAll(), and selectBetween(). { selectedReads.clear(); clearLastMove(); }

void TrapperView::closeEvent (  QCloseEvent *   )  [protected, virtual]

Definition at line 190 of file trapperview.cpp. { // LEAVE THIS EMPTY: THE EVENT FILTER IN THE TrapperApp CLASS TAKES CARE FOR CLOSING // QWidget closeEvent must be prevented. }

void TrapperView::contentsContextMenuEvent (  QContextMenuEvent *  e  )  [protected]

Definition at line 907 of file trapperview.cpp. References algoMenu, AlgoMaker::algosRegistered(), getInfo(), infoMenu, TrapperConf::instance(), last_click_changed_selection, last_click_selected_read, moving, slotClearCenter(), slotScrollToMouse(), slotScrollToPos(), slotSetCenter(), slotStartAlgo(), slotSwitchToMode(), switchViewMenu, and TrapperConf::viewModeNames(). { if ( last_click_changed_selection ) { updateContents(); } moving = false; last_click_selected_read = false; last_click_changed_selection = false; QPopupMenu* contextMenu = new QPopupMenu( this ); Q_CHECK_PTR( contextMenu ); QLabel *caption = new QLabel( "<font color=darkblue><u><b>" "Context Menu</b></u></font>", this ); caption->setAlignment( Qt::AlignCenter ); contextMenu->insertItem( caption ); //Algo stuff algoMenu = new QPopupMenu( this ); Q_CHECK_PTR( algoMenu ); list<string> algos = AlgoMaker::algosRegistered(); list<string>::iterator stIt; for (stIt = algos.begin() ; stIt != algos.end(); ++stIt ) { algoMenu->insertItem ( stIt->c_str() ); } connect( algoMenu, SIGNAL( activated( int ) ), this, SLOT( slotStartAlgo( int ) ) ); contextMenu->insertItem( "&Operations", algoMenu ); //Info stuff infoMenu = new QPopupMenu(this); vector<list<string> > infos = getInfo( e->pos() ); QPtrList<QPopupMenu> infolist; infolist.setAutoDelete( true ); for( size_t i = 0; i < infos.size(); i++ ) { stIt = infos[i].begin(); if ( stIt == infos[i].end() ) continue; infolist.append(new QPopupMenu(this)); ++stIt; for ( ; stIt != infos[i].end(); ++stIt ) { // infoMenu->insertItem ( stIt->c_str() ); infolist.last()->insertItem ( stIt->c_str() ); } infoMenu->insertItem(infos[i].begin()->c_str(), infolist.last()); } //No connecting here, 'cause only info... contextMenu->insertItem( "&Info", infoMenu ); //Viewmode stuff switchViewMenu = new QPopupMenu( this ); Q_CHECK_PTR( switchViewMenu ); TrapperConf * conf = TrapperConf::instance(); QStringList names = conf->viewModeNames(); QStringList::Iterator it = names.begin(); for ( ; it != names.end(); ++it ) { switchViewMenu->insertItem ( *it ); } connect( switchViewMenu, SIGNAL( activated( int ) ), this, SLOT( slotSwitchToMode( int ) ) ); contextMenu->insertItem( "&Switch to viewmode", switchViewMenu ); contextMenu->insertSeparator(); contextMenu->insertItem("Set chromat center", this, SLOT(slotSetCenter())); contextMenu->insertItem("Clear chromat center", this, SLOT(slotClearCenter())); contextMenu->insertSeparator(); contextMenu->insertItem("Scroll Here", this, SLOT(slotScrollToMouse()) ); contextMenu->insertItem("Scroll to pos", this, SLOT(slotScrollToPos()) ); contextMenu->exec( QCursor::pos() ); delete contextMenu; delete switchViewMenu;//Previous memory leak?? delete algoMenu; delete infoMenu; }

void TrapperView::contentsDragEnterEvent (  QDragEnterEvent *  event  )  [protected]

Definition at line 1448 of file trapperview.cpp. { // cerr << "in TrapperView::dragEnterEvent" << endl; event->accept( TRUE ); }

void TrapperView::contentsDragMoveEvent (  QDragMoveEvent *   )  [protected]

Definition at line 1456 of file trapperview.cpp. { // e->setPoint( QPoint( mousePressedPoint.x(), e->pos().y() ) ); // cerr << "in TrapperView::dragMoveEvent" << endl; // cerr<<"x(): "<<e->pos().x()<<endl; // cerr<<"y(): "<<e->pos().y()<<endl; }

void TrapperView::contentsDropEvent (  QDropEvent *  event  )  [protected]

Definition at line 1467 of file trapperview.cpp. References convertToDnaCoordinates(), getDocument(), mousePressedPoint, moveData(), readSelected(), and TR_DNA. { // cerr << "in TrapperView::dropEvent" << endl; QPoint deltaMovement = event->pos() - mousePressedPoint; TR_DNA x_dna_movDelta; TR_DNA y_dna_movDelta; convertToDnaCoordinates( x_dna_movDelta, y_dna_movDelta, deltaMovement.x(), deltaMovement.y() ); // cerr << "dropped happened with delta x=" << x_dna_movDelta << " y=" << y_dna_movDelta << endl; TrapperView* w = dynamic_cast<TrapperView*>( event->source() ); if ( !w) { //Drop from another app... return; } assert(w); if ( w->getDocument() == this->getDocument() ) { moveData( deltaMovement.x(), deltaMovement.y() ); } else { QByteArray ar( event->encodedData("min_mime_type") ); QDataStream data_stream(ar, IO_ReadOnly); readSelected(data_stream); updateContents(); } }

void TrapperView::contentsMouseMoveEvent (  QMouseEvent *  e  )  [protected]

Definition at line 720 of file trapperview.cpp. References allow_dragging, curr_mouse_pos, dragging, dragPixmap, dragWindowPoint, drawContents_helper(), drawRubber(), last_click_selected_read, mousePressedPoint, moving, pixelCoordToDna_X(), pixelCoordToDna_Y(), rubber_band, RubberEnd, RubberOn, sendMsg(), writeSelected(), y_delta, and y_delta_previous. { QString msg = "Row: " + QString().setNum(pixelCoordToDna_Y(e->y())) + ", col: " + QString().setNum(pixelCoordToDna_X(e->x())); sendMsg( msg ); bool nobutton = Qt::NoButton & e->state(); if ( nobutton ) { moving = false; return; } if ( allow_dragging && dragging ) { // if ( dragging ) { // cerr<<"Dragging..."<<endl; ReadDrag *d = new ReadDrag( dragPixmap, dragWindowPoint, this ); // QCString ar("hej"); QByteArray ar; QDataStream data_stream(ar, IO_WriteOnly); writeSelected(data_stream); d->setEncodedData(ar); d->dragCopy(); // do NOT delete d. dragging = FALSE; moving = false; last_click_selected_read = false; // cerr<<"Stopped dragging"<<endl; } else if ( last_click_selected_read ) { // else if ( !selectedReads.empty() ) { //"Normal" moving moving = true; curr_mouse_pos = e->pos();//Don't really need this?? // y_delta = pixelCoordToDna_Y( (curr_mouse_pos - mousePressedPoint).y() ); y_delta = (curr_mouse_pos - mousePressedPoint).y(); if ( pixelCoordToDna_Y( y_delta) == pixelCoordToDna_Y( y_delta_previous ) ) { // moving = false; return; } y_delta_previous = y_delta; //MOVINGTEST QPainter p(viewport()); drawContents_helper(&p, 0,0,0,0,0,0,0); return; //END MOVINGTEST updateContents(); } else if ( rubber_band != 0 ) { //RUBBERTEST QPainter p(viewport()); p.setPen(QColor(255,255,255)); p.setRasterOp(NotROP); if(RubberOn) drawRubber(&p); RubberEnd= contentsToViewport(e->pos()); drawRubber(&p); RubberOn=TRUE; return; //END RUBBERTEST curr_mouse_pos = e->pos(); QRect oldband = rubber_band->normalize(); rubber_band->setSize( QSize( curr_mouse_pos.x() - mousePressedPoint.x(), curr_mouse_pos.y() - mousePressedPoint.y() ) ); // updateContents(); QPoint margin( 1, 1 ); QRect norm = rubber_band->normalize(); updateContents( QRect( norm.topLeft() - margin, norm.bottomRight() + margin ).unite( QRect(oldband.topLeft() - margin, oldband.bottomRight() + margin ) ) ); } }

void TrapperView::contentsMousePressEvent (  QMouseEvent *  e  )  [protected]

Definition at line 572 of file trapperview.cpp. References clearSelected(), convertToDnaCoordinates(), doc, dragBitmap, dragging, dragPixmap, dragWindowPoint, drawContents_helper(), ReadsInRect::first(), GeneralData::getRecno(), isSelected(), last_click_changed_selection, last_click_selected_read, last_selected_recno, mousePressedPoint, moveOn, moving, p3, pixelCoordToDna_X(), pixelCoordToDna_Y(), readsInRect, rubber_band, RubberEnd, RubberOn, RubberStart, select(), selectedReads, sendMsg(), ReadsInRect::setWindowCoord(), TR_DNA, y_delta, and y_delta_previous. { QString msg = "Row: " + QString().setNum(pixelCoordToDna_Y(e->y())) + ", col: " + QString().setNum(pixelCoordToDna_X(e->x())); sendMsg( msg ); y_delta = 0; y_delta_previous = 0; bool ctrlclick = Qt::ControlButton & e->state(); bool leftbutton = Qt::LeftButton & e->stateAfter(); // if ( ctrlclick ) // cerr<<"ctrlclick!!!!!!!!!!!!!! "<<endl; mousePressedPoint.setX( e->x() ); mousePressedPoint.setY( e->y() ); //RUBBERTEST RubberStart=contentsToViewport(e->pos()); RubberEnd = RubberStart; RubberOn=FALSE; //END RUBBERTEST //MOVINGTEST moveOn = false; //END MOVINGTEST TR_DNA x_dna, y_dna; convertToDnaCoordinates( x_dna, y_dna, e->x(), e->y() ); readsInRect = new ReadsInRect( doc ); // readsInRect->setWindowCoord( x_dna, y_dna, 1, 1 ); /* a rectangle with dimension 1x1 */ readsInRect->setWindowCoord( x_dna, y_dna, 3, 3 ); /* a rectangle with dimension 3x3 */ ReadData * r = readsInRect->first(); if ( r ) {//hit read if ( ctrlclick ) { if ( isSelected( r->getRecno() ) ) { select( r->getRecno(), false ); last_click_selected_read = false; last_click_changed_selection = true; } else { select( r->getRecno(), true); last_click_selected_read = true; last_selected_recno = r->getRecno(); last_click_changed_selection = true; } }//end ctrlclick else {//no ctrlclick if ( isSelected( r->getRecno() ) ) { last_click_selected_read = true; last_selected_recno = r->getRecno(); last_click_changed_selection = false; } else { clearSelected(); select( r->getRecno(), true); last_click_selected_read = true; last_selected_recno = r->getRecno(); last_click_changed_selection = true; } }//end no ctrlclick if ( last_click_selected_read ) dragging = TRUE; }// end hit read else {//didn't hit read // if ( rubber_band != 0 ) { // delete rubber_band; // } // rubber_band = new QRect( mousePressedPoint, mousePressedPoint ); if ( ctrlclick ) { last_click_selected_read = false; last_click_changed_selection = false; }//end ctrlclick else {//no ctrlclick last_click_selected_read = false; if ( selectedReads.size() > 0 ) last_click_changed_selection = true; clearSelected(); //"Rubber band" // if ( rubber_band != 0 ) { // delete rubber_band; // } // if ( leftbutton ) // rubber_band = new QRect( mousePressedPoint, mousePressedPoint ); }//end no ctrlclick if ( rubber_band != 0 ) { delete rubber_band; } if (leftbutton && !last_click_selected_read) { moving = false; rubber_band = new QRect( mousePressedPoint, mousePressedPoint ); } }//end didn't hit read // updateContents();//Removed this because of visual bug... delete readsInRect; // From here on: about Start a drag and painting { dragWindowPoint.setX( size().width() ); dragWindowPoint.setY( size().height() ); QRect re( mousePressedPoint - dragWindowPoint, mousePressedPoint + dragWindowPoint ); dragPixmap.resize( re.size() ); QPainter p2; p2.begin(&dragPixmap, this); dragBitmap.resize( re.size() ); p3.begin(&dragBitmap, this); QBrush brush; brush.setStyle( Qt::SolidPattern ); brush.setColor( Qt::white ); p2.fillRect( 0 , 0 , re.width() , re.height() ,brush) ; brush.setColor( Qt::color0 ); p3.fillRect( 0 , 0 , re.width() , re.height() ,brush) ; QPoint tl = re.topLeft() ; QPoint br = re.bottomRight() ; drawContents_helper(&p2, &p3, tl.x(), tl.y(), br.x() - tl.x() + 1, br.y() - tl.y() + 1, - ( mousePressedPoint.x() - dragWindowPoint.x() ), - ( mousePressedPoint.y() - dragWindowPoint.y() )); //Test: // QPen a_pen; // p2.setPen(a_pen); // p2.drawRect(dragPixmap.rect()); // a_pen.setColor(Qt::color1); // p3.setPen(a_pen); // p3.drawRect(dragPixmap.rect()); //End test dragPixmap.setMask(dragBitmap); p2.end(); p3.end(); } }

void TrapperView::contentsMouseReleaseEvent (  QMouseEvent *  e  )  [protected]

Definition at line 804 of file trapperview.cpp. References clearSelected(), convertToDnaCoordinates(), doc, dragging, drawRubber(), ReadsInRect::first(), last_click_changed_selection, last_click_selected_read, last_selected_recno, moveData(), moveOn, moving, ReadsInRect::next(), readsInRect, rubber_band, RubberEnd, RubberOn, RubberStart, select(), ReadsInRect::setWindowCoord(), TR_DNA, TR_PIX, and y_delta. { dragging = false; //Maybe dragging code here? NO! if ( moving ) { //Moving stuff... moveData(0, y_delta); //MOVINGTEST if(moveOn) { updateContents(); moveOn=FALSE; } //END MOVINGTEST moving = false; } else { //not moving bool ctrlclick = Qt::ControlButton & e->state(); if ( !ctrlclick && last_click_selected_read ) { clearSelected(); select( last_selected_recno, true ); last_click_changed_selection = true; // updateContents(); } if ( last_click_changed_selection ) { updateContents(); } if ( rubber_band != 0 ) { readsInRect = new ReadsInRect( doc ); TR_DNA x_dna, y_dna, w_dna, h_dna, x2_dna, y2_dna; TR_PIX x_pix, y_pix, w_pix, h_pix; QRect norm = rubber_band->normalize(); //RUBBERTEST RubberStart = viewportToContents( RubberStart ); RubberEnd = viewportToContents( RubberEnd ); norm = QRect( RubberStart.x(), RubberStart.y(), RubberEnd.x()-RubberStart.x(), RubberEnd.y()-RubberStart.y() ).normalize(); //END RUBBERTEST rubber_band->setTopLeft( norm.topLeft() ); rubber_band->setBottomRight( norm.bottomRight() ); rubber_band->rect( &x_pix, &y_pix, &w_pix, &h_pix); convertToDnaCoordinates( x_dna, y_dna, x_pix, y_pix ); convertToDnaCoordinates( x2_dna, y2_dna, x_pix + w_pix, y_pix + h_pix); w_dna = x2_dna - x_dna; h_dna = y2_dna - y_dna; readsInRect->setWindowCoord( x_dna, y_dna, w_dna,h_dna ); if ( !ctrlclick) clearSelected(); for ( ReadData * r = readsInRect->first(); r; r = readsInRect->next() ) { select( r->getRecno(), true); } //RUBBERTEST QPainter p(viewport()); p.setPen(QColor(255,255,255)); p.setRasterOp(NotROP); if(RubberOn) { drawRubber(&p); RubberOn=FALSE; } else { RubberEnd=RubberStart; } //END RUBBERTEST delete rubber_band; rubber_band = 0; delete readsInRect; updateContents(); } } moving = false; dragging = false; last_click_changed_selection = false; last_click_selected_read = false; }

void TrapperView::convertToDnaCoordinates (  TR_DNA &  x_dna, TR_DNA &  y_dna, const TR_PIX  cx, const TR_PIX  cy )  [protected]

Definition at line 196 of file trapperview.cpp. References pixelCoordToDna_X(), and pixelCoordToDna_Y(). Referenced by contentsDropEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), and drawContents_helper(). { x_dna = pixelCoordToDna_X(cx); y_dna = pixelCoordToDna_Y(cy); return; }

void TrapperView::convertToPixelCoordinates (  TR_PIX &  x_pix, TR_PIX &  y_pix, TR_DNA  x_dna, TR_DNA  y_dna )  [protected]

Definition at line 219 of file trapperview.cpp. References dnaCoordToPixel_X(), and dnaCoordToPixel_Y(). Referenced by drawContents_helper(). { x_pix = dnaCoordToPixel_X(x_dna); y_pix = dnaCoordToPixel_Y(y_dna); return; }

void TrapperView::copy (   )

copies selected data Definition at line 1636 of file trapperview.cpp. References writeSelected(). Referenced by cut(), and TrapperApp::slotEditCopy(). { QByteArray ar; QDataStream str(ar, IO_WriteOnly); writeSelected(str); QClipboard* cb = QApplication::clipboard(); ReadDrag* r = new ReadDrag(this); r->setEncodedData(ar); cb->setData(r, QClipboard::Clipboard); }

void TrapperView::createView (  QString   )  [signal]

void TrapperView::cut (   )

cuts selected data Definition at line 1662 of file trapperview.cpp. References clearSelected(), copy(), Destroyer::destroy(), doc, and selectedReads. Referenced by TrapperApp::slotEditCut(). { copy(); Destroyer d(doc); for( set<db_recno_t>::iterator it = selectedReads.begin(); it != selectedReads.end(); ++it ) { d.destroy(*it); } clearSelected(); updateContents(); }

TR_PIX TrapperView::dnaCoordToPixel_X (  TR_DNA  cx  )  [protected]

Definition at line 226 of file trapperview.cpp. References basewidth, and magnifyX. Referenced by convertToPixelCoordinates(), findRead(), paintGrid(), readSelected(), slotScrollToPos(), and undo(). { // if ( x_dna * basewidth * magnifyX < 1 ) { // cerr<<"x_dna: "<<x_dna<<endl; // cerr<<"basewidth: "<<basewidth<<endl; // cerr<<"x_dna * basewidth * magnifyX: "<<x_dna * basewidth * magnifyX<<endl; // } return x_dna * basewidth * magnifyX; }

TR_PIX TrapperView::dnaCoordToPixel_Y (  TR_DNA  cy  )  [protected]

Definition at line 238 of file trapperview.cpp. References magnifyY, and rowheight. Referenced by convertToPixelCoordinates(), drawContents_helper(), findRead(), paintGrid(), readSelected(), slotScrollToPos(), and undo(). { return y_dna * rowheight * magnifyY; }

void TrapperView::doZoom (   )  [protected]

Definition at line 1339 of file trapperview.cpp. References basewidth, globalBases, globalRows, magnifyX, magnifyY, and rowheight. { // QPoint p = viewportToContents(viewport()->rect().topLeft()); // if ( globalBases * magnifyX * basewidth < 1 ) { // cerr<<"globalBases: "<<globalBases<<endl; // cerr<<"globalBases * magnifyX * basewidth: "<<globalBases * magnifyX * basewidth<<endl; // } resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY); // QPoint p = viewportToContents(viewport()->rect().center()); // center( p.x()* factor , p.y()*factor ); // setContentsPos(p.x()*zoomfactor, p.y()*zoomfactor); // setContentsPos(p.x(), p.y()); updateContents(); }

void TrapperView::drawContents (  QPainter *  p, TR_PIX  cx, TR_PIX  cy, TR_PIX  cw, TR_PIX  ch )  [protected]

Definition at line 373 of file trapperview.cpp. References drawContents_helper(), and paintGrid(). { // QPoint qp = viewportToContents(viewport()->rect().topLeft()); // cerr<<"qp.x(): "<<qp.x()<<endl; // cerr<<"qp.y(): "<<qp.y()<<endl; drawContents_helper(p, NULL, cx, cy, cw, ch, 0, 0); paintGrid( p, cx, cy, cw, ch); }

void TrapperView::drawContents_helper (  QPainter *  p, QPainter *  bitmapPainter, int  cx, int  cy, int  cw, int  ch, int  dx, int  dy )  [protected]

paint a rectangle of the window Parameters: p  where to paint to bmp  where to paint a bitmask, we paint to the bitmask on the same places as we paint to p. cx  x coordinate of rectangle in "content" coordinate system cy  y coordinate of rectangle in "content" coordinate system cw  width of rectangle in "content" coordinate system ch  height of rectangle in "content" coordinate system dx  displace painting with this dy  displace painting with this Definition at line 383 of file trapperview.cpp. References basewidth, center_point, convertToDnaCoordinates(), convertToPixelCoordinates(), dnaCoordToPixel_Y(), doc, dragPixmap, dragWindowPoint, ReadsInRect::first(), isSelected(), magnifyX, magnifyY, mousePressedPoint, moveOn, moving, ReadsInRect::next(), oldMovePoint, paintFeatures(), pixelCoordToDna_Y(), readsInRect, rowheight, rubber_band, ReadsInRect::setWindowCoord(), spaceBetweenRows, TR_DNA, TR_PIX, and y_delta. Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), and drawContents(). { /* We have the window to paint in pixel coordinates, but the biological data ( the reads ) are stored in dna coordinates. The pixel coordinates are on a smaler scale than the dna coordinates, so therefore the pixel coordinates might lay a fraction of a dna coordinate. Thus we seak the minimal overlapping window in dna coordinates. */ if ( moving ) { assert( bitmapPainter == 0 ); //MOVINGTEST // p->setRasterOp(NotROP); p->setRasterOp(NotXorROP); // p->setRasterOp(XorROP); if ( moveOn ) { p->drawPixmap(oldMovePoint, dragPixmap); } else { oldMovePoint = contentsToViewport(mousePressedPoint - dragWindowPoint); p->setRasterOp(NotXorROP); p->drawPixmap(oldMovePoint, dragPixmap); } oldMovePoint = contentsToViewport(mousePressedPoint - dragWindowPoint + QPoint(0, dnaCoordToPixel_Y(pixelCoordToDna_Y(y_delta)) )); //END MOVINGTEST // oldMovePoint = mousePressedPoint - dragWindowPoint + QPoint(0, dnaCoordToPixel_Y(pixelCoordToDna_Y(y_delta)) ); p->drawPixmap(oldMovePoint, dragPixmap); //MOVINGTEST moveOn = true; return; //END MOVINGTEST } TR_DNA x_dna, y_dna; /* the dna coordinate of upperleft corner of the overlapping dna window */ TR_DNA x2_dna, y2_dna; TR_DNA h_dna, w_dna; /* representing the width and height of the overlapping dna window */ convertToDnaCoordinates( x_dna, y_dna, cx, cy ); convertToDnaCoordinates( x2_dna, y2_dna, cx + cw - 1, cy + ch - 1 ); /* to be on the safe side that we paint on a rectangle big enough we add some on the edges. The reason comes from the fact that vertical read border is drawn up on the uttermost pixels of the feature area. */ x_dna -= 10; x2_dna += 10; w_dna = x2_dna - x_dna + 1; h_dna = y2_dna - y_dna + 1; TR_PIX x_pix, y_pix; /* the pixel coordinate of upperleft corner of the overlapping dna window */ convertToPixelCoordinates( x_pix, y_pix, x_dna, y_dna ); TR_PIX cx_paint = x_pix + dx; TR_PIX cy_paint = y_pix + dy; readsInRect = new ReadsInRect( doc ); readsInRect->setWindowCoord( x_dna, y_dna, w_dna,h_dna ); // cerr<<"rowheight*magnifyY - spaceBetweenRows: "<<rowheight*magnifyY - spaceBetweenRows<<endl; int previous_row(-1), previous_end(-1); for ( ReadData * r = readsInRect->first(); r; r = readsInRect->next() ) { // cerr<<r->name()<<'\t'<<r->getRecno()<<endl; bool overlap(false); if ( r->row() == previous_row && (r->startPos() <= previous_end ) ) { overlap = true; } previous_row = r->row(); previous_end = r->endPos(); bool selected = isSelected( r->getRecno() ); /* we just have to paint the part of the read that is visible in the current window. Therefore we seak max and min values */ TR_DNA x1_dna_paint = max( r->startPos(), x_dna ) ; TR_DNA x2_dna_paint = min( r->endPos(), x_dna + w_dna - 1 ) ; TR_PIX x_pix_adjust, y_pix_adjust; convertToPixelCoordinates( x_pix_adjust, y_pix_adjust, x1_dna_paint - x_dna, r->row() - y_dna ); // x_pix += cx; // y_pix += cy; TR_DNA len = x2_dna_paint - x1_dna_paint +1 ; paintFeatures( p, bitmapPainter, r->getRecno(), x_pix_adjust + cx_paint , y_pix_adjust + cy_paint, x1_dna_paint - r->startPos(), len, basewidth*magnifyX, rowheight*magnifyY - spaceBetweenRows , selected, center_point - r->startPos(), overlap, r->beginGood(), r->endGood() ); } delete readsInRect; if ( rubber_band ) { QPen oldpen( p->pen() ); QPen newpen( Qt::black, 0, Qt::DotLine ); p->setPen( newpen ); p->drawRect( *rubber_band ); p->setPen( oldpen ); } }

void TrapperView::drawRubber (  QPainter *  p  )  [inline, private]

Definition at line 324 of file trapperview.h. References RubberEnd, and RubberStart. Referenced by contentsMouseMoveEvent(), and contentsMouseReleaseEvent(). { QPen ppen = p->pen(); ppen.setStyle(Qt::DotLine); p->setPen(ppen); p->drawRect( RubberStart.x(), RubberStart.y(), RubberEnd.x()-RubberStart.x(), RubberEnd.y()-RubberStart.y() ); }

void TrapperView::enlarge (   )

enlarges view Definition at line 1364 of file trapperview.cpp. References basewidth, globalBases, globalRows, magnifyX, magnifyY, and rowheight. Referenced by TrapperApp::slotEnlarge(). { globalRows *= 2; globalBases *= 1.25; resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY); updateContents(); }

void TrapperView::findRead (   )

finds a read Definition at line 1087 of file trapperview.cpp. References Database::SecondaryIterator< T >::answer(), clearSelected(), dnaCoordToPixel_X(), dnaCoordToPixel_Y(), doc, GeneralData::getRecno(), Database::SecondaryIterator< T >::key(), ReadData::row(), scrollTo(), select(), Database::SecondaryIterator< T >::set(), ReadData::setName(), ReadData::startPos(), and TR_PIX. Referenced by TrapperApp::slotEditFindRead(). { bool ok; QString res = QInputDialog::getText ( "Find read", "Enter read name:", QLineEdit::Normal, QString::null, &ok ); if ( ok ) { // user entered something and pressed OK } else { // user pressed Cancel return; } Database::SecondaryIterator<ReadData> name_it( "name", doc, "ReadData" ); name_it.key()->setName( res ); if ( name_it.set() != 0 ) { cerr<<"Error, couldn't find "<<res<<" in db"<<endl; return; } clearSelected(); select(name_it.answer()->getRecno(), true); TR_PIX y = dnaCoordToPixel_Y(name_it.answer()->row()); TR_PIX x = dnaCoordToPixel_X(name_it.answer()->startPos()); scrollTo(x, y); }

void TrapperView::fitContentsizeToData (   )  [protected]

Definition at line 135 of file trapperview.cpp. References Database::SecondaryIterator< T >::answer(), basewidth, doc, ReadData::endPos(), globalBases, globalRows, Database::SecondaryIterator< T >::last(), magnifyX, magnifyY, ReadData::row(), and rowheight. Referenced by readSelected(), runAlgo(), and TrapperView(). { Database::SecondaryIterator<ReadData>* end_it = new Database::SecondaryIterator<ReadData>( "end", doc, "ReadData" ); int ret_end = end_it->last(); Database::SecondaryIterator<ReadData>* row_it = new Database::SecondaryIterator<ReadData>( "pos", doc, "ReadData" ); int ret_row = row_it->last(); ReadData* r_end = (ret_end != DB_NOTFOUND) ? end_it->answer() : 0; ReadData* r_row = (ret_row != DB_NOTFOUND) ? row_it->answer() : 0; if ( r_end ) { globalBases = r_end->endPos() + 50; } if ( r_row ) { globalRows = r_row->row() + 500; } delete end_it; delete row_it; resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY); }

TrapperDoc * TrapperView::getDocument (   )  const

returns a pointer to the document connected to the view Definition at line 164 of file trapperview.cpp. References doc. Referenced by contentsDropEvent(), TrapperApp::eventFilter(), TrapperApp::slotCreateClient(), TrapperApp::slotFileClose(), TrapperApp::slotFileSave(), TrapperApp::slotFileSaveAs(), TrapperApp::slotShowStatistics(), TrapperApp::slotWindowNewWindow(), SubsetAlgo::start(), ReadnamesAlgo::start(), and ConsAlgo::start(). { return doc; }

std::vector< std::list< std::string > > TrapperView::getInfo (  const QPoint &  pos  )  [protected]

Definition at line 1145 of file trapperview.cpp. References Database::SecondaryIterator< T >::answer(), ReadData::beginGood(), doc, ReadData::endGood(), ReadData::endPos(), ReadsInRect::first(), FeatureInfo::getPosInfo(), FeatureInfo::getRangeInfo(), GeneralData::getRecno(), FeatureData::info(), Database::SecondaryIterator< T >::key(), GeneralMaker::listRegistered(), ReadData::mate(), ReadData::mateLength(), ReadData::name(), GeneralMaker::newData(), Database::SecondaryIterator< T >::nextdup(), pixelCoordToDna_X(), pixelCoordToDna_Y(), readsInRect, Database::SecondaryIterator< T >::set(), FeatureData::setReadRecno(), ReadsInRect::setWindowCoord(), ReadData::startPos(), ReadData::strand(), and TR_DNA. Referenced by contentsContextMenuEvent(). { vector<list<string> > result; list<string> readResult; list<string> featResult; list<string> generalResult; //Recalc pos TR_DNA row = pixelCoordToDna_Y( pos.y() ); TR_DNA col = pixelCoordToDna_X( pos.x() ); readsInRect = new ReadsInRect( doc ); readsInRect->setWindowCoord( col, row, 1, 1 ); /* a rectangle with dimension 1x1 */ // readsInRect->setWindowCoord( col, row, 3, 3 ); /* a rectangle with dimension 3x3 */ ReadData * r = readsInRect->first(); ostringstream os; if ( r ) { list<string> types = GeneralMaker::listRegistered(); readResult.push_back( "Read info" ); readResult.push_back( r->name() ); os<<"Strand: "<<r->strand(); readResult.push_back( r->strand() ); os.str(""); os<<"Mate: "<<r->mate() << ' ' << r->mateLength(); readResult.push_back( os.str() ); os.str(""); os<<"Begin good: "<<r->beginGood(); readResult.push_back( os.str() ); os.str(""); os<<"End good: "<<r->endGood(); readResult.push_back( os.str() ); os.str(""); os<<"Read index: "<<col - r->startPos(); readResult.push_back( os.str() ); featResult.push_back( "Feature info" ); //Feature stuff for( list<string>::iterator it = types.begin(); it != types.end(); ++it ) { GeneralData * data = GeneralMaker::newData( *it ); FeatureData * fdata = dynamic_cast<FeatureData *>( data ); // fdata is just used to see that the registered string is corresponding to // a feature if ( fdata ) { Database::SecondaryIterator<FeatureData> featIt( "readRecno", doc, it->c_str() ); featIt.key()->setReadRecno( r->getRecno() ); string featInfo; if ( featIt.set() == 0 ) { int ret; do { featInfo = featIt.answer()->info()->getPosInfo( col - r->startPos() ); if ( !featInfo.empty() ) { featResult.push_back( featInfo ); } featInfo = featIt.answer()->info()->getRangeInfo( 0, r->endPos() - r->startPos() ); if ( !featInfo.empty() ) { readResult.push_back( featInfo ); } } while ( (ret = featIt.nextdup()) == 0); } } delete data; } } generalResult.push_back("General info"); os.str(""); os<<"Row: "<<row<<", Col: "<<col; generalResult.push_back( os.str() ); result.push_back(readResult); result.push_back(featResult); result.push_back(generalResult); delete readsInRect; return result; }

std::set< db_recno_t > & TrapperView::getSelectedReads (   )  [protected]

Definition at line 1115 of file trapperview.cpp. References selectedReads. Referenced by moveData(), and slotStartAlgo(). { return selectedReads; }

bool TrapperView::isSelected (  db_recno_t  recno  )  [protected]

Definition at line 1134 of file trapperview.cpp. References selectedReads. Referenced by contentsMousePressEvent(), drawContents_helper(), and select(). { return selectedReads.find( recno ) != selectedReads.end(); }

void TrapperView::message (  const QString &   )  [signal]

Referenced by sendMsg(), and TrapperParser::startElement().

QString TrapperView::mode (   )

the name of the view mode that the TrapperView is using right now Definition at line 159 of file trapperview.cpp. References ViewModes::currentViewMode(), ViewMode::name(), and viewModes. Referenced by TrapperDoc::changedViewList(). { return viewModes->currentViewMode()->name(); }

TR_DNA TrapperView::mousePressedCol (   )

gets col position of last mouse press Definition at line 1686 of file trapperview.cpp. References mousePressedPoint, and pixelCoordToDna_X(). Referenced by slotSetCenter(). { return pixelCoordToDna_X( mousePressedPoint.x() ); }

TR_DNA TrapperView::mousePressedRow (   )

gets row position of last mouse press Definition at line 1679 of file trapperview.cpp. References mousePressedPoint, and pixelCoordToDna_Y(). { return pixelCoordToDna_Y( mousePressedPoint.y() ); }

void TrapperView::moveData (  TR_PIX  dx, TR_PIX  dy )  [protected]

Definition at line 549 of file trapperview.cpp. References AlgoMoveParam::get_x_delta(), AlgoMoveParam::get_y_delta(), getSelectedReads(), last_move_x, last_move_y, pixelCoordToDna_X(), pixelCoordToDna_Y(), runAlgo(), and TR_DNA. Referenced by contentsDropEvent(), contentsMouseReleaseEvent(), readSelected(), and undo(). { // cerr<<"PLEASE NOTE: ALGO PARAMS SHOULD BE FIXED!!!"<<endl; TR_DNA col_delta, row_delta; row_delta = pixelCoordToDna_Y( dy ); col_delta = pixelCoordToDna_X( dx); AlgoMoveParam param( col_delta, row_delta ); runAlgo( "Move Reads", getSelectedReads(), &param ); last_move_x = param.get_x_delta(); last_move_y = param.get_y_delta(); }

void TrapperView::paintFeatures (  QPainter *  p, QPainter *  bitmapPainter, db_recno_t  readRecno, TR_PIX  x_pix, TR_PIX  y_pix, TR_DNA  x_dna_relative, TR_DNA  dna_len, double  width, TR_PIX  height, bool  selected, int  center_relative, bool  overlap, TR_DNA  bg, TR_DNA  eg )  [protected]

paint border line around the read rectangle. Then divide the rectangle into layers and paint features of the read into these layers. Parameters: p  where to paint bmp  where to paint a bitmask, we paint to the bitmask on the same places as we paint to p. readRecno  the index of the read in the underlying berkeley db. x_pix  x "content" coordinate of the upperleft corner of the paint area y_pix  y "content" coordinate of the upperleft corner of the paint area x1_dna  x dna coordinate of the left most position to paint seen relative the left side of the read x2_dna  x dna coordinate of the right most position to paint seen relative the left side of the read width  the pixel width of one x dna coordinate height  the pixel width of one x dna coordinate highlight  if true change the read border color Definition at line 243 of file trapperview.cpp. References Database::SecondaryIterator< T >::answer(), Database::SecondaryIterator< T >::closeCursor(), ViewModes::currentViewMode(), Layer::featureList, FeatureData::gui(), Layer::heightInPix(), Database::SecondaryIterator< T >::key(), ViewMode::layerList, magnifyX, magnifyY, moving, Database::SecondaryIterator< T >::name(), Database::SecondaryIterator< T >::nextdup(), FeatureGui::paint(), Database::SecondaryIterator< T >::set(), FeatureData::setReadRecno(), TR_PIX, viewModes, and zoom_cutoff. Referenced by drawContents_helper(). { // cerr << " db_recno_t = "<<readRecno // << " x_pix ="<< x_pix // << " y_pix ="<< y_pix // << " x_dna_relative ="<< x_dna_relative // << " dna_len ="<< dna_len // << " width =" << width // << " height ="<<height // << endl; Layer * layer; p->setPen( Qt::black ); /* clear away old painted stuff, by painting white in the read rectangle */ QBrush brush; brush.setStyle( Qt::SolidPattern ); brush.setColor( Qt::white ); p->fillRect( x_pix , y_pix , dna_len*width , height ,brush) ; brush.setColor( Qt::color1 ); if ( bitmapPainter && selected ) bitmapPainter->fillRect( x_pix , y_pix , dna_len*width , height ,brush) ; /* finished clearing */ // we use two pixels in the height to draw the paintReadBorder y_pix += 1; height -= 2; /* starting painting features */ TR_PIX heightLayerSum = 0; /* each feature knows how many percent of the total height it may use when painting itself. The variable heightLayerSum stores how much of the total height has already been painted to by other feature layers */ for (layer = viewModes->currentViewMode()->layerList.first(); layer; layer = viewModes->currentViewMode()->layerList.next() ) { TR_PIX heightLayer = layer->heightInPix( height ); Database::SecondaryIterator<FeatureData> * it; for (it = layer->featureList.first(); it; it = layer->featureList.next() ) { int cutoff = zoom_cutoff[ it->name() ]; if ( magnifyX < cutoff || magnifyY < cutoff ) continue; it->key()->setReadRecno( readRecno ); if ( it->set() == 0 ) { int ret; do { // if ( readRecno == 654 ) { // cerr<<'\t'<<it->answer()->uniqueName()<<'\t'<<it->answer()->getRecno()<<endl; // } it->answer()->gui()->paint( p, x_pix, y_pix + heightLayerSum , x_dna_relative, x_dna_relative + dna_len -1 , width, heightLayer, center_relative ); } while ( (ret = it->nextdup()) == 0); } it->closeCursor(); } heightLayerSum += heightLayer; } /* finished painting features */ /* paint readBorder, start */ /* the horisontal border is painted just outside the features, but the vertical border is painted on the features side, so the features lose one pixel of width on the left and right sides */ QPen oldpen( p->pen() ), newpen( p->pen() ); if ( selected ) { newpen.setColor( Qt::red ); if ( moving ) newpen.setStyle( Qt::DashLine); } if ( overlap ) { newpen.setColor(Qt::green); } p->setPen(newpen); if ( magnifyX < 1.0 ) { // cerr<<"x_pix: "<<x_pix<<endl; // cerr<<"y_pix: "<<y_pix<<endl; // cerr<<"dna_len: "<<dna_len<<endl; // cerr<<"width: "<<width<<endl; // cerr<<"dna_len * width: "<<dna_len * width<<endl; // cerr<<"height: "<<height<<endl; } p->drawRect( x_pix , y_pix, dna_len*width , height ) ; //Quality trimming brush.setStyle( Qt::Dense4Pattern ); brush.setColor( Qt::white ); if ( x_dna_relative < bg ) { p->fillRect( x_pix , y_pix, (bg - x_dna_relative)*width , height, brush ) ; } if ( x_dna_relative + dna_len > eg ) { int goodlen = eg - x_dna_relative + 1; if ( goodlen < 0 ) goodlen = 0; p->fillRect( x_pix + goodlen*width , y_pix, (dna_len - goodlen )*width, height, brush ) ; } p->setPen( oldpen ); /* finished painting readBorder */ }

void TrapperView::paintGrid (  QPainter *  p, TR_PIX  cx, TR_PIX  cy, TR_PIX  cw, TR_PIX  ch )  [protected]

paint some extra dots in the background of the window. These will move along when the user scrolls. Nice to have some visual feedback of movement when there are no reads in the window Definition at line 505 of file trapperview.cpp. References center_point, dnaCoordToPixel_X(), dnaCoordToPixel_Y(), pixelCoordToDna_X(), pixelCoordToDna_Y(), and rowheight. Referenced by drawContents(). { p->setPen( Qt::black ); // int toprow=cy/rowheight; // int bottomrow=(cy+ch+rowheight-1)/rowheight; int local_rowheight = 100; int toprow=cy/local_rowheight; int bottomrow=(cy+ch+local_rowheight-1)/local_rowheight; int colwidth=100; int leftcol=cx/colwidth; int rightcol=(cx+cw+colwidth-1)/colwidth; for (int r=toprow; r<=bottomrow; r++) { // int py=r*rowheight; int py=r*local_rowheight - dnaCoordToPixel_Y(1)/2; for (int c=leftcol; c<=rightcol; c++) { int px=c*colwidth + dnaCoordToPixel_X(1)/2; p->drawLine(px, py, px+2, py); } } QFont f; f.setPointSize(10); p->setFont(f); int viewport_toprow=contentsY()/local_rowheight - 2; if (viewport_toprow <0 ) viewport_toprow = 0; int viewport_bottomrow=(cy+ch+local_rowheight-1)/local_rowheight + 1; int viewport_leftcol=contentsX()/colwidth; int viewport_rightcol=(contentsX() + contentsWidth() +colwidth-1)/colwidth; for( int i = viewport_leftcol; i < viewport_rightcol; i++ ) { p->drawText( i*colwidth + dnaCoordToPixel_X(1)/2, 10, QString().setNum(pixelCoordToDna_X( i*colwidth )) ); } for( int i = viewport_toprow; i < viewport_bottomrow; i++ ) { p->drawText( 0, i*local_rowheight, QString().setNum(pixelCoordToDna_Y( i*local_rowheight )) ); } bottomrow=(cy+ch+rowheight-1)/rowheight; int center_x = dnaCoordToPixel_X(center_point) + dnaCoordToPixel_X(1)/2; p->drawLine(center_x, 0, center_x, bottomrow*rowheight ); }

void TrapperView::paste (   )

pastes selected data Definition at line 1649 of file trapperview.cpp. References readSelected(). Referenced by TrapperApp::slotEditPaste(). { QClipboard* cb = QApplication::clipboard(); QMimeSource* r = cb->data(QClipboard::Clipboard); QByteArray ar(r->encodedData("min_mime_type")); QDataStream str(ar, IO_ReadOnly); readSelected(str); updateContents(); }

TR_DNA TrapperView::pixelCoordToDna_X (  TR_PIX  x_dna  )  [protected]

Definition at line 203 of file trapperview.cpp. References basewidth, and magnifyX. Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), convertToDnaCoordinates(), getInfo(), mousePressedCol(), moveData(), and paintGrid(). { // if ( basewidth * magnifyX < 1 ) { // cerr<<"basewidth: "<<basewidth<<endl; // cerr<<"basewidth * magnifyX: "<<basewidth * magnifyX<<endl; // } return cx / ( basewidth * magnifyX ); }

TR_DNA TrapperView::pixelCoordToDna_Y (  TR_PIX  y_dna  )  [protected]

Definition at line 214 of file trapperview.cpp. References magnifyY, and rowheight. Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), convertToDnaCoordinates(), drawContents_helper(), getInfo(), mousePressedRow(), moveData(), and paintGrid(). { return cy / ( rowheight * magnifyY ); }

void TrapperView::print (  QPrinter *  pPrinter  )

contains the implementation for printing functionality and gets called by TrapperApp::slotFilePrint() Definition at line 175 of file trapperview.cpp. Referenced by TrapperApp::slotFilePrint(). { if (pPrinter->setup(this)) { QPainter p; p.begin(pPrinter); /////////////////////////////// // TODO: add your printing code here /////////////////////////////// p.end(); } }

void TrapperView::readSelected (  QDataStream &  data_stream  )  [protected]

Definition at line 1571 of file trapperview.cpp. References clearLastMove(), clearSelected(), Database::Creator< T >::create(), Database::Creator< T >::data(), dnaCoordToPixel_X(), dnaCoordToPixel_Y(), doc, fitContentsizeToData(), moveData(), GeneralData::readStream(), select(), FeatureData::setReadRecno(), and TR_DNA. Referenced by contentsDropEvent(), and paste(). { //Read from stream clearSelected(); db_recno_t recno(0); //Keep track of lowest row and start pos, and transpose the pasted reads there TR_DNA rowmin(numeric_limits<TR_DNA>::max()); TR_DNA colmin(numeric_limits<TR_DNA>::max()); while ( !data_stream.atEnd() ) { //Read data type char* data_type; data_stream>>data_type;//must delete this myself according to Qt docs string type(data_type); //Create Creator for general data with Data type name to constructor Database::Creator<GeneralData> a_creator(doc, type); //Read stream using readStream on Creators data() pointer a_creator.data()->readStream(data_stream); if ( ReadData* data = dynamic_cast<ReadData*>(a_creator.data())) {/* type is ReadData*/ //Creator::create(false) and save read recno recno = a_creator.create(false); select(recno, true); if ( data->row() < rowmin ) { rowmin = data->row(); } if ( data->startPos() < colmin ) { colmin = data->startPos(); } } else { //Type is feature, but let's do a sanity check FeatureData* data = dynamic_cast<FeatureData*>(a_creator.data()); assert( data ); assert( recno != 0 ); //Set feature's read recno to saved recno data->setReadRecno(recno); //Creator::create() a_creator.create(false); } delete data_type; } fitContentsizeToData(); moveData( -dnaCoordToPixel_X(colmin - 1), -dnaCoordToPixel_Y(rowmin - 1) ); clearLastMove(); }

void TrapperView::runAlgo (  const std::string &  AlgoType, std::set< db_recno_t > &  recnoList, AlgoParam *  param = 0 )  [protected]

Definition at line 1236 of file trapperview.cpp. References TrapperDoc::addAlgorithm(), doc, fitContentsizeToData(), AlgoMaker::newAlgo(), TrapperDoc::removeAlgorithm(), selectedReads, and Algo::start(). Referenced by moveData(), and slotStartAlgo(). { if (selectedReads.size() > 0 ) { Algo * algo = AlgoMaker::newAlgo( AlgoType, doc , recnoList, param ); doc->addAlgorithm( algo ); algo->start(); doc->removeAlgorithm( algo );//POSSIBLE MEMORY LEAK!!!!!!!!! delete algo;//To avoid memory leak... updateContents(); fitContentsizeToData(); } }

void TrapperView::scrollTo (  TR_PIX  x, TR_PIX  y )  [protected]

Definition at line 1356 of file trapperview.cpp. Referenced by findRead(), slotScrollToMouse(), and slotScrollToPos(). { setContentsPos( x, y ); updateContents(); }

void TrapperView::select (  db_recno_t  recno, bool  status )  [protected]

Definition at line 1120 of file trapperview.cpp. References clearLastMove(), isSelected(), and selectedReads. Referenced by contentsMousePressEvent(), contentsMouseReleaseEvent(), findRead(), readSelected(), selectAll(), and selectBetween(). { RecnoMap::iterator pos; if ( status == true && !isSelected(recno) ) { selectedReads.insert( recno ); clearLastMove(); } else if ( ( pos = selectedReads.find( recno )) != selectedReads.end() ) { selectedReads.erase( pos ); clearLastMove(); } }

void TrapperView::selectAll (   )

selects all Definition at line 1381 of file trapperview.cpp. References Database::PrimaryIterator< T >::answer(), clearSelected(), doc, Database::PrimaryIterator< T >::first(), GeneralData::getRecno(), Database::PrimaryIterator< T >::next(), and select(). Referenced by TrapperApp::slotEditSelectAll(). { clearSelected(); Database::PrimaryIterator<ReadData> iter( doc, "ReadData" ); if ( iter.first() == 0 ) { do { select( iter.answer()->getRecno(), true ); } while ( iter.next() == 0 ); } updateContents(); }

void TrapperView::selectBetween (   )

selects between rows Definition at line 1398 of file trapperview.cpp. References Database::SecondaryIterator< T >::answer(), clearSelected(), doc, GeneralData::getRecno(), Database::SecondaryIterator< T >::key(), Database::SecondaryIterator< T >::next(), ReadData::row(), select(), Database::SecondaryIterator< T >::setRange(), ReadData::setRow(), ReadData::setStartPos(), and TR_DNA. Referenced by TrapperApp::slotEditSelectBetween(). { clearSelected(); bool ok; TR_DNA start, stop; int res = QInputDialog::getInteger("Select between rows", "Enter start row for selected reads:", 0, 1, numeric_limits<int>::max(), 1, &ok, 0 ); if ( ok ) { start = res; } else { return; } res = QInputDialog::getInteger("Select between rows", "Enter stop row for selected reads:", 0, 1, numeric_limits<int>::max(), 1, &ok, 0 ); if ( ok ) { stop = res; if ( start > stop ) { TR_DNA tmp = start; start = stop; stop = tmp; } } else { return; } Database::SecondaryIterator<ReadData> row_it( "pos", doc, "ReadData" ); row_it.key()->setRow(start); row_it.key()->setStartPos(0); if ( row_it.setRange() != 0 ) { return; } do { select( row_it.answer()->getRecno(), true ); }while( row_it.next() == 0 && row_it.answer()->row() <= stop ); updateContents(); }

void TrapperView::sendMsg (  const QString &  msg  )

Sends out a message Definition at line 1692 of file trapperview.cpp. References message(). Referenced by contentsMouseMoveEvent(), and contentsMousePressEvent(). { emit message(msg); }

void TrapperView::setDragMode (  bool  status  )

sets pointer mode Definition at line 1631 of file trapperview.cpp. References allow_dragging. Referenced by TrapperApp::slotActivatedWindow(), TrapperApp::slotDragMode(), and TrapperApp::slotNormalMode(). { allow_dragging = status; }

void TrapperView::shrink (   )

shrinks view Definition at line 1372 of file trapperview.cpp. References basewidth, globalBases, globalRows, magnifyX, magnifyY, and rowheight. Referenced by TrapperApp::slotShrink(). { globalRows *= 0.5; globalBases *= 0.8; resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY); updateContents(); }

void TrapperView::slotClearCenter (   )  [slot]

Definition at line 1081 of file trapperview.cpp. References center_point. Referenced by contentsContextMenuEvent(). { center_point = 0; updateContents(); }

void TrapperView::slotScrollToMouse (   )  [slot]

Definition at line 1036 of file trapperview.cpp. References mousePressedPoint, and scrollTo(). Referenced by contentsContextMenuEvent(). { scrollTo(mousePressedPoint.x(), mousePressedPoint.y()); }

void TrapperView::slotScrollToPos (   )  [slot]

Definition at line 1042 of file trapperview.cpp. References dnaCoordToPixel_X(), dnaCoordToPixel_Y(), scrollTo(), and TR_PIX. Referenced by contentsContextMenuEvent(). { bool ok; int res = QInputDialog::getInteger( "Scroll to position", "Enter row:", 0, 0, numeric_limits<int>::max(), 1, &ok, 0 ); if ( ok ) { // user entered something and pressed OK } else { // user pressed Cancel return; } TR_PIX y = dnaCoordToPixel_Y(res); res = QInputDialog::getInteger( "Scroll to position", "Enter column:", 0, 0, numeric_limits<int>::max(), 1, &ok, 0 ); if ( ok ) { // user entered something and pressed OK } else { // user pressed Cancel return; } TR_PIX x = dnaCoordToPixel_X(res); scrollTo(x, y); }

void TrapperView::slotSetCenter (   )  [slot]

Definition at line 1074 of file trapperview.cpp. References center_point, and mousePressedCol(). Referenced by contentsContextMenuEvent(). { center_point = mousePressedCol(); // cerr<<center_point<<endl; updateContents(); }

void TrapperView::slotStartAlgo (  int  i  )  [slot]

Definition at line 1008 of file trapperview.cpp. References algoMenu, clearLastMove(), getSelectedReads(), and runAlgo(). Referenced by contentsContextMenuEvent(). { QString algoStr = algoMenu->text(i); /* Right now the Algo constructor takes a list of db_recno_t. We create such a list from the keys in the map, selectedReads. Todo: To make the code prettier: is it be possible to pass the map iterators to the constructor of the list? Instead of our manual forloop. */ // std::list< db_recno_t > alist = getSelectedReads(); // Algo * algo = AlgoMaker::newAlgo( algoStr.ascii(), doc , alist ); // doc->addAlgorithm( algo ); // algo->start(); // doc->removeAlgorithm( algo );//POSSIBLE MEMORY LEAK!!!!!!!!! // updateContents(); ViewParam param(this); updateContents(); runAlgo( algoStr.ascii(), getSelectedReads(), &param ); //To be on the safe side... clearLastMove(); }

void TrapperView::slotSwitchToMode (  int  i  )  [slot]

Definition at line 1000 of file trapperview.cpp. References TrapperDoc::changedViewList(), doc, ViewModes::setMode(), switchViewMenu, and viewModes. Referenced by contentsContextMenuEvent(). { QString viewMode = switchViewMenu->text(i); viewModes->setMode( viewMode ); doc->changedViewList(); updateContents(); }

void TrapperView::undo (   )

undoes last move Definition at line 1674 of file trapperview.cpp. References dnaCoordToPixel_X(), dnaCoordToPixel_Y(), last_move_x, last_move_y, and moveData(). Referenced by TrapperApp::slotEditUndo(). { moveData( -dnaCoordToPixel_X(last_move_x), -dnaCoordToPixel_Y(last_move_y) ); }

void TrapperView::update (  TrapperView *  pSender  )

gets called to redraw the document contents if it has been modified Definition at line 169 of file trapperview.cpp. Referenced by TrapperDoc::updateAllViews(). { if(pSender != this) repaint(); }

void TrapperView::writeSelected (  QDataStream &  data_stream  )  [protected]

Definition at line 1503 of file trapperview.cpp. References Database::SecondaryIterator< T >::answer(), Database::PrimaryIterator< T >::answer(), doc, Database::SecondaryIterator< T >::key(), GeneralMaker::listRegistered(), GeneralMaker::newData(), Database::SecondaryIterator< T >::nextdup(), selectedReads, Database::SecondaryIterator< T >::set(), Database::PrimaryIterator< T >::setFromRecno(), FeatureData::setReadRecno(), FeatureData::writeStream(), and ReadData::writeStream(). Referenced by contentsMouseMoveEvent(), and copy(). { //Write to stream //Get registered types list<string> type_list = GeneralMaker::listRegistered(); //Loop over selected reads for( set<db_recno_t>::iterator recno_it = selectedReads.begin(); recno_it != selectedReads.end(); ++recno_it ) { //Get recno db_recno_t recno(*recno_it); //Create primary iterator for ReadData with new Database::PrimaryIterator<ReadData>* read_it = new Database::PrimaryIterator<ReadData>(doc, "ReadData"); //Set iterator from recno read_it->setFromRecno(recno); //Write dataname to stream - null terminated, right?? Must check size stuff... data_stream<<"ReadData"; //write ReadData to stream using writeStream read_it->answer()->writeStream(data_stream); //Delete primary readiterator delete read_it; //Loop over types for( list<string>::iterator type_it = type_list.begin(); type_it != type_list.end(); ++type_it ) { GeneralData * data = GeneralMaker::newData( *type_it ); FeatureData * fdata = dynamic_cast<FeatureData *>( data ); // fdata is just used to see that the registered string is corresponding to // a feature if ( fdata ) {/* Can cast type to feature */ //Create secondary feature iterator Database::SecondaryIterator<FeatureData> featIt( "readRecno", doc, type_it->c_str() ); //Set iterator key read recno featIt.key()->setReadRecno( recno ); if ( featIt.set() == 0 ) {//Read has such feature int ret; do { //write feat name to stream data_stream<<type_it->c_str(); //write FeatureData to stream using writeStream featIt.answer()->writeStream(data_stream); } while ((ret = featIt.nextdup())== 0); } } delete data; } } }

void TrapperView::zoomIn (   )

zooms in Definition at line 1253 of file trapperview.cpp. References zoomInX(), and zoomInY(). Referenced by TrapperApp::slotZoomIn(). { zoomInX(); zoomInY(); }

void TrapperView::zoomInX (   )

zooms in X-direction Definition at line 1259 of file trapperview.cpp. References basewidth, globalBases, globalRows, magnifyX, magnifyY, rowheight, and zoomfactor. Referenced by TrapperApp::slotZoomInX(), and zoomIn(). { if ( magnifyX >= 128 ) return; magnifyX *= zoomfactor; // doZoom(); QPoint p = viewportToContents(viewport()->rect().topLeft()); // if ( globalBases * magnifyX * basewidth < 1 ) { // cerr<<"globalBases: "<<globalBases<<endl; // cerr<<"globalBases * magnifyX * basewidth: "<<globalBases * magnifyX * basewidth<<endl; // } resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY); setContentsPos(p.x()*zoomfactor, p.y()); updateContents(); }

void TrapperView::zoomInY (   )

zooms in Y-direction Definition at line 1280 of file trapperview.cpp. References basewidth, globalBases, globalRows, magnifyX, magnifyY, rowheight, and zoomfactor. Referenced by TrapperApp::slotZoomInY(), and zoomIn(). { if ( magnifyY >= 128 ) return; magnifyY *= zoomfactor; // doZoom(); QPoint p = viewportToContents(viewport()->rect().topLeft()); resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY); setContentsPos(p.x(), p.y()*zoomfactor); updateContents(); }

void TrapperView::zoomOut (   )

zooms out Definition at line 1295 of file trapperview.cpp. References zoomOutX(), and zoomOutY(). Referenced by TrapperApp::slotZoomOut(). { zoomOutX(); zoomOutY(); }

void TrapperView::zoomOutX (   )

zooms out X-dir Definition at line 1301 of file trapperview.cpp. References basewidth, globalBases, globalRows, magnifyX, magnifyY, rowheight, and zoomfactor. Referenced by TrapperApp::slotZoomOutX(), and zoomOut(). { // if ( magnifyX <= 1 ) if ( magnifyX <= 0.25 ) { return; } magnifyX /= zoomfactor; // doZoom(); QPoint p = viewportToContents(viewport()->rect().topLeft()); // if ( globalBases * magnifyX * basewidth < 1 ) { // cerr<<"globalBases: "<<globalBases<<endl; // cerr<<"globalBases * magnifyX * basewidth: "<<globalBases * magnifyX * basewidth<<endl; // } resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY); setContentsPos(p.x()/zoomfactor, p.y()); updateContents(); }

void TrapperView::zoomOutY (   )

zooms out Y-dir Definition at line 1323 of file trapperview.cpp. References basewidth, globalBases, globalRows, magnifyX, magnifyY, rowheight, and zoomfactor. Referenced by TrapperApp::slotZoomOutY(), and zoomOut(). { if ( magnifyY <= 1 ) { return; } magnifyY /= zoomfactor; // doZoom(); QPoint p = viewportToContents(viewport()->rect().topLeft()); resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY); setContentsPos(p.x(), p.y()/zoomfactor); updateContents(); }

---

Friends And Related Function Documentation

friend class TrapperDoc [friend]

Definition at line 119 of file trapperview.h. Referenced by TrapperParser::startElement().

---

Member Data Documentation

QPopupMenu* TrapperView::algoMenu [protected]

Definition at line 276 of file trapperview.h. Referenced by contentsContextMenuEvent(), and slotStartAlgo().

bool TrapperView::allow_dragging [protected]

Definition at line 298 of file trapperview.h. Referenced by contentsMouseMoveEvent(), setDragMode(), and TrapperView().

TR_PIX TrapperView::basewidth [protected]

Definition at line 262 of file trapperview.h. Referenced by dnaCoordToPixel_X(), doZoom(), drawContents_helper(), enlarge(), fitContentsizeToData(), pixelCoordToDna_X(), shrink(), TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

TR_DNA TrapperView::center_point [protected]

Definition at line 266 of file trapperview.h. Referenced by drawContents_helper(), paintGrid(), slotClearCenter(), slotSetCenter(), and TrapperView().

QPoint TrapperView::curr_mouse_pos [protected]

Definition at line 303 of file trapperview.h. Referenced by contentsMouseMoveEvent().

TrapperDoc* TrapperView::doc [protected]

Definition at line 268 of file trapperview.h. Referenced by contentsMousePressEvent(), contentsMouseReleaseEvent(), cut(), drawContents_helper(), findRead(), fitContentsizeToData(), getDocument(), getInfo(), readSelected(), runAlgo(), selectAll(), selectBetween(), slotSwitchToMode(), TrapperView(), and writeSelected().

QBitmap TrapperView::dragBitmap [private]

Definition at line 312 of file trapperview.h. Referenced by contentsMousePressEvent().

bool TrapperView::dragging [protected]

Definition at line 297 of file trapperview.h. Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), and TrapperView().

QPixmap TrapperView::dragPixmap [private]

Definition at line 311 of file trapperview.h. Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), and drawContents_helper().

QPoint TrapperView::dragWindowPoint [private]

Definition at line 315 of file trapperview.h. Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), and drawContents_helper().

TR_DNA TrapperView::globalBases [protected]

Definition at line 265 of file trapperview.h. Referenced by doZoom(), enlarge(), fitContentsizeToData(), shrink(), TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

TR_DNA TrapperView::globalRows [protected]

Definition at line 265 of file trapperview.h. Referenced by doZoom(), enlarge(), fitContentsizeToData(), shrink(), TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

QPopupMenu* TrapperView::infoMenu [protected]

Definition at line 277 of file trapperview.h. Referenced by contentsContextMenuEvent().

QLabel* TrapperView::lab [protected]

Definition at line 269 of file trapperview.h.

bool TrapperView::last_click_changed_selection [protected]

Definition at line 301 of file trapperview.h. Referenced by contentsContextMenuEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), and TrapperView().

bool TrapperView::last_click_selected_read [protected]

Definition at line 300 of file trapperview.h. Referenced by contentsContextMenuEvent(), contentsMouseMoveEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), and TrapperView().

TR_DNA TrapperView::last_move_x [protected]

Definition at line 307 of file trapperview.h. Referenced by clearLastMove(), moveData(), and undo().

TR_DNA TrapperView::last_move_y [protected]

Definition at line 308 of file trapperview.h. Referenced by clearLastMove(), moveData(), and undo().

db_recno_t TrapperView::last_selected_recno [protected]

Definition at line 302 of file trapperview.h. Referenced by contentsMousePressEvent(), and contentsMouseReleaseEvent().

double TrapperView::magnifyX [protected]

Definition at line 271 of file trapperview.h. Referenced by dnaCoordToPixel_X(), doZoom(), drawContents_helper(), enlarge(), fitContentsizeToData(), paintFeatures(), pixelCoordToDna_X(), shrink(), TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

u_int16_t TrapperView::magnifyY [protected]

Definition at line 272 of file trapperview.h. Referenced by dnaCoordToPixel_Y(), doZoom(), drawContents_helper(), enlarge(), fitContentsizeToData(), paintFeatures(), pixelCoordToDna_Y(), shrink(), TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

QPoint TrapperView::mousePressedPoint [private]

Definition at line 314 of file trapperview.h. Referenced by contentsDropEvent(), contentsMouseMoveEvent(), contentsMousePressEvent(), drawContents_helper(), mousePressedCol(), mousePressedRow(), and slotScrollToMouse().

bool TrapperView::moveOn [private]

Definition at line 322 of file trapperview.h. Referenced by contentsMousePressEvent(), contentsMouseReleaseEvent(), and drawContents_helper().

bool TrapperView::moving [protected]

Definition at line 299 of file trapperview.h. Referenced by contentsContextMenuEvent(), contentsMouseMoveEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), drawContents_helper(), paintFeatures(), and TrapperView().

QPoint TrapperView::oldMovePoint [private]

Definition at line 321 of file trapperview.h. Referenced by drawContents_helper().

QPainter TrapperView::p3 [private]

Definition at line 313 of file trapperview.h. Referenced by contentsMousePressEvent().

ReadsInRect* TrapperView::readsInRect [protected]

Definition at line 296 of file trapperview.h. Referenced by contentsMousePressEvent(), contentsMouseReleaseEvent(), drawContents_helper(), and getInfo().

TR_PIX TrapperView::rowheight [protected]

Definition at line 264 of file trapperview.h. Referenced by dnaCoordToPixel_Y(), doZoom(), drawContents_helper(), enlarge(), fitContentsizeToData(), paintGrid(), pixelCoordToDna_Y(), shrink(), TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

QRect* TrapperView::rubber_band [private]

Definition at line 316 of file trapperview.h. Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), drawContents_helper(), and TrapperView().

QPoint TrapperView::RubberEnd [private]

Definition at line 319 of file trapperview.h. Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), and drawRubber().

bool TrapperView::RubberOn [private]

Definition at line 320 of file trapperview.h. Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), and contentsMouseReleaseEvent().

QPoint TrapperView::RubberStart [private]

Definition at line 319 of file trapperview.h. Referenced by contentsMousePressEvent(), contentsMouseReleaseEvent(), and drawRubber().

std::set<db_recno_t> TrapperView::selectedReads [protected]

The index values ( of type db_recno_t ) of all selected reads. Just some thoughts about implemantion: Right now they are stored as an STL map but there are other alternatives of how to implement this: Maybe an STL bitset or STL vector<bool> or maybe store it in a berkeley db. If you want to select all possible reads, 4^32, then you would lower your memory consumption if used a bitset. And going with a berkeley db you would have even lower memory demands. 040315: Changed selectedReads into std::set --EA Definition at line 293 of file trapperview.h. Referenced by clearSelected(), contentsMousePressEvent(), cut(), getSelectedReads(), isSelected(), runAlgo(), select(), and writeSelected().

TR_PIX TrapperView::spaceBetweenRows [protected]

Definition at line 263 of file trapperview.h. Referenced by drawContents_helper(), and TrapperView().

QPopupMenu* TrapperView::switchViewMenu [protected]

Definition at line 275 of file trapperview.h. Referenced by contentsContextMenuEvent(), and slotSwitchToMode().

ViewModes* TrapperView::viewModes [protected]

Definition at line 274 of file trapperview.h. Referenced by mode(), paintFeatures(), slotSwitchToMode(), TrapperView(), and ~TrapperView().

TR_PIX TrapperView::y_delta [protected]

Definition at line 304 of file trapperview.h. Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), and drawContents_helper().

TR_PIX TrapperView::y_delta_previous [protected]

Definition at line 305 of file trapperview.h. Referenced by contentsMouseMoveEvent(), and contentsMousePressEvent().

std::map<std::string, int> TrapperView::zoom_cutoff [protected]

Definition at line 294 of file trapperview.h. Referenced by paintFeatures(), and TrapperView().

int TrapperView::zoomfactor [protected]

Definition at line 273 of file trapperview.h. Referenced by TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

---

The documentation for this class was generated from the following files:

• trapperview.h
• trapperview.cpp

---