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>

Inheritance diagram for TrapperView:

[legend]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 ()
void	slotContextSelect (int i)
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	selectBetweenCols ()
void	selectRows (int start, int stop)
void	selectCols (int start, int stop)
void	findRead ()
void	findTag ()
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)
void	setViewTimeCourse (bool toggle)
void	setNormalizeTimeCourse (bool toggle)
void	scrollToNextCluster (bool forward)
void	setClusterWindow (int window_size)
void	setClusterMinNum (int num)
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
QPopupMenu *	contextSelectMenu
std::set< db_recno_t >	selectedReads
std::map< std::string, int >	zoom_cutoff
int	min_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
bool	time_course
bool	tc_normalize
int	read_cluster_min_num
TR_DNA	read_cluster_window
Private Member Functions
void	drawRubber (QPainter *p)
Private Attributes
QPixmap	dragPixmap
QBitmap	dragBitmap
QPainter	p3
QPoint	mousePressedPoint
QPoint	dragWindowPoint
QRect *	rubber_band
bool	ctrl
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 300 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 73 of file trapperview.cpp.

References allow_dragging, basewidth, center_point, doc, dragging, fitContentsizeToData(), globalBases, globalRows, QString::isNull(), last_click_changed_selection, last_click_selected_read, GeneralMaker::listRegistered(), magnifyX, magnifyY, min_cutoff, moving, read_cluster_min_num, read_cluster_window, rowheight, rubber_band, QScrollView::setDragAutoScroll(), spaceBetweenRows, tc_normalize, time_course, viewModes, QScrollView::viewport(), 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;
  time_course = false;
  tc_normalize = false;

  setFocusPolicy(StrongFocus);
  
  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;
  zoom_cutoff["DnpData"] = 1;
//   min_cutoff = 1;
  min_cutoff = 0.0009765625;


//   globalRows = 1000;
//   globalBases = 50000;
  globalRows = 50;
  globalBases = 2000;
//   rowheight = 20;
//   basewidth = 10;
  rowheight = 5;
  basewidth = 1;
  magnifyX = 8;
  magnifyY = 4;
  zoomfactor = 2;
  spaceBetweenRows = 0;
  center_point = 0;

  read_cluster_min_num = 10;
  read_cluster_window = 100;


  fitContentsizeToData();
  

  viewport()->setPaletteBackgroundColor(white);
  viewport()->setBackgroundMode( Qt::FixedColor );
  setCaption( "yes" );
  viewport()->setMouseTracking(TRUE);
}

TrapperView::~TrapperView

(

)

Destructor for the main view

Definition at line 139 of file trapperview.cpp.

References viewModes.

{
 
  if ( viewModes ) {
    delete viewModes;
    viewModes = NULL;
  }
}

---

Member Function Documentation

TrapperDoc * TrapperView::getDocument

(

)

const

returns a pointer to the document connected to the view

Definition at line 177 of file trapperview.cpp.

References doc.

Referenced by contentsDropEvent(), TrapperApp::eventFilter(), TrapperApp::exportToFile(), TrapperApp::slotCreateClient(), TrapperApp::slotFileClose(), TrapperApp::slotFileSave(), TrapperApp::slotShowStatistics(), TrapperApp::slotTcImport(), and TrapperApp::slotWindowNewWindow().

{
    return doc;
}

void TrapperView::update

(

TrapperView *

pSender

)

gets called to redraw the document contents if it has been modified

Definition at line 182 of file trapperview.cpp.

Referenced by TrapperDoc::updateAllViews().

{
    if(pSender != this)
        repaint();
}

void TrapperView::print

(

QPrinter *

pPrinter

)

contains the implementation for printing functionality and gets called by TrapperApp::slotFilePrint()

Definition at line 188 of file trapperview.cpp.

References QPrinter::setup().

Referenced by TrapperApp::slotFilePrint().

{
    if (pPrinter->setup(this))
    {
        QPainter p;
        p.begin(pPrinter);

        ///////////////////////////////
        // TODO: add your printing code here
        ///////////////////////////////

        p.end();
    }
}

QString TrapperView::mode

(

)

the name of the view mode that the TrapperView is using right now

Definition at line 172 of file trapperview.cpp.

References ViewModes::currentViewMode(), ViewMode::name(), and viewModes.

Referenced by TrapperDoc::changedViewList().

{
    return viewModes->currentViewMode()->name();
}

void TrapperView::zoomIn

(

)

zooms in

Definition at line 1474 of file trapperview.cpp.

References zoomInX(), and zoomInY().

Referenced by TrapperApp::slotZoomIn().

{
  zoomInX();
  zoomInY();
}

void TrapperView::zoomInX

(

)

zooms in X-direction

Definition at line 1480 of file trapperview.cpp.

References basewidth, globalBases, globalRows, magnifyX, magnifyY, QScrollView::resizeContents(), rowheight, QScrollView::setContentsPos(), QScrollView::viewport(), QScrollView::viewportToContents(), QScrollView::visibleWidth(), QPoint::x(), QPoint::y(), and zoomfactor.

Referenced by TrapperApp::slotZoomInX(), and zoomIn().

{
  if ( magnifyX >= 128 ) {
    return;
  }
  
  
  magnifyX *= zoomfactor;
  if ( static_cast<int>(globalBases * magnifyX * basewidth) < 0 ) {
    magnifyX /= zoomfactor;
    return;
  }
  

  
//   QPoint p = viewportToContents(viewport()->rect().topLeft());
  QPoint p = viewportToContents(viewport()->rect().topLeft()) + QPoint(visibleWidth()/2, 0);

  resizeContents(static_cast<int>(globalBases * magnifyX * basewidth), globalRows * rowheight * magnifyY);
//   setContentsPos(p.x()*zoomfactor, p.y());
  setContentsPos(p.x()*zoomfactor - visibleWidth()/2, p.y());

//   updateContents();

}

void TrapperView::zoomInY

(

)

zooms in Y-direction

Definition at line 1506 of file trapperview.cpp.

References basewidth, globalBases, globalRows, magnifyX, magnifyY, QScrollView::resizeContents(), rowheight, QScrollView::setContentsPos(), QScrollView::updateContents(), QScrollView::viewport(), QScrollView::viewportToContents(), QPoint::x(), QPoint::y(), and zoomfactor.

Referenced by TrapperApp::slotZoomInY(), and zoomIn().

{
  if ( magnifyY >= 8 )
    return;
  magnifyY *= zoomfactor;
//   doZoom();

  QPoint p = viewportToContents(viewport()->rect().topLeft());
  
  resizeContents(static_cast<int>(globalBases * magnifyX * basewidth), globalRows * rowheight * magnifyY);
  setContentsPos(p.x(), p.y()*zoomfactor);

  updateContents();
}

void TrapperView::zoomOut

(

)

zooms out

Definition at line 1521 of file trapperview.cpp.

References zoomOutX(), and zoomOutY().

Referenced by TrapperApp::slotZoomOut().

{
  zoomOutX();
  zoomOutY();
}

void TrapperView::zoomOutX

(

)

zooms out X-dir

Definition at line 1527 of file trapperview.cpp.

References basewidth, globalBases, globalRows, magnifyX, magnifyY, QScrollView::resizeContents(), rowheight, QScrollView::setContentsPos(), QScrollView::updateContents(), QScrollView::viewport(), QScrollView::viewportToContents(), QScrollView::visibleWidth(), QPoint::x(), QPoint::y(), and zoomfactor.

Referenced by TrapperApp::slotZoomOutX(), and zoomOut().

{

//   if ( magnifyX <= 0.25 ) {
//   if ( magnifyX <= 0.0625 ) {
//   if ( magnifyX <= 0.015625 ) {
//   if ( magnifyX <= 0.0078125 ) {
//   if ( magnifyX <= 0.00390625 ) {
//   if ( magnifyX <= 0.0009765625 ) {
//   if ( magnifyX <= 0.000244140625 ) {
//   if ( magnifyX <= 6.103515625e-05 ) {
//   if ( magnifyX <= 1.52587890625e-05 ) {
  if ( magnifyX <= 7.62939453125e-06 ) {
    return;
  }
  magnifyX /= zoomfactor;


  QPoint p = viewportToContents(viewport()->rect().topLeft()) + QPoint(visibleWidth()/2, 0);

//   if ( globalBases * magnifyX * basewidth < 1 ) {
//     cerr<<"globalBases: "<<globalBases<<endl;
//     cerr<<"globalBases * magnifyX * basewidth: "<<globalBases * magnifyX * basewidth<<endl;
//   }
  resizeContents(static_cast<int>(globalBases * magnifyX * basewidth), globalRows * rowheight * magnifyY);
  setContentsPos(p.x()/zoomfactor - visibleWidth()/2, p.y());

  updateContents();
}

void TrapperView::zoomOutY

(

)

zooms out Y-dir

Definition at line 1557 of file trapperview.cpp.

References basewidth, globalBases, globalRows, magnifyX, magnifyY, QScrollView::resizeContents(), rowheight, QScrollView::setContentsPos(), QScrollView::updateContents(), QScrollView::viewport(), QScrollView::viewportToContents(), QPoint::x(), QPoint::y(), and zoomfactor.

Referenced by TrapperApp::slotZoomOutY(), and zoomOut().

{
  if ( magnifyY <= 1 )
    {
      return;
    }
  magnifyY /= zoomfactor;
//   doZoom();

  QPoint p = viewportToContents(viewport()->rect().topLeft());
  resizeContents(static_cast<int>(globalBases * magnifyX * basewidth), globalRows * rowheight * magnifyY);
  setContentsPos(p.x(), p.y()/zoomfactor);

  updateContents();
}

void TrapperView::selectAll

(

)

selects all

Definition at line 1615 of file trapperview.cpp.

References Database::PrimaryIterator< T >::answer(), clearSelected(), doc, Database::PrimaryIterator< T >::first(), GeneralData::getRecno(), Database::PrimaryIterator< T >::next(), select(), and QScrollView::updateContents().

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 1632 of file trapperview.cpp.

References QInputDialog::getInteger(), selectRows(), and TR_DNA.

Referenced by TrapperApp::slotEditSelectBetween().

{
  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;
  }
  selectRows(start, stop);

}

void TrapperView::selectBetweenCols

(

)

selects between cols

Definition at line 1687 of file trapperview.cpp.

References QInputDialog::getInteger(), selectCols(), and TR_DNA.

Referenced by TrapperApp::slotEditSelectBetweenCols().

{
  bool ok;
  TR_DNA start, stop;
  int res = QInputDialog::getInteger("Select between cols", "Enter start col for selected reads:", 0, 1, numeric_limits<int>::max(), 1,
                                     &ok, 0 );
  if ( ok ) {
    start = res;
  }
  else {
    return;
  }
  
  res = QInputDialog::getInteger("Select between cols", 
                                 "Enter stop col 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;
  }

  selectCols(start, stop);
}

void TrapperView::selectRows	(	int	start,
		int	stop
	)

selects between specified rows

Definition at line 1664 of file trapperview.cpp.

References Database::SecondaryIterator< T >::answer(), clearSelected(), ctrl, doc, GeneralData::getRecno(), Database::SecondaryIterator< T >::key(), Database::SecondaryIterator< T >::next(), ReadData::row(), select(), Database::SecondaryIterator< T >::setRange(), ReadData::setRow(), ReadData::setStartPos(), and QScrollView::updateContents().

Referenced by selectBetween(), and slotContextSelect().

{
  if ( !ctrl )
    clearSelected();

  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::selectCols	(	int	start,
		int	stop
	)

selects between specified cols

Definition at line 1719 of file trapperview.cpp.

References Database::SecondaryIterator< T >::answer(), clearSelected(), ctrl, doc, ReadData::endPos(), GeneralData::getRecno(), Database::SecondaryIterator< T >::key(), Database::SecondaryIterator< T >::next(), select(), ReadData::setEndPos(), Database::SecondaryIterator< T >::setRange(), ReadData::setRow(), ReadData::startPos(), and QScrollView::updateContents().

Referenced by selectBetweenCols(), and slotContextSelect().

{
  if ( !ctrl )
    clearSelected();

  Database::SecondaryIterator<ReadData> row_it( "end", doc, "ReadData" );
  row_it.key()->setRow(0);
  row_it.key()->setEndPos(start);
  
  if ( row_it.setRange() != 0 ) {

    return;
  }
  
  do {
    if ( row_it.answer()->startPos() >= start ) {
      select( row_it.answer()->getRecno(), true );
    }
  }while( row_it.next() == 0 && row_it.answer()->endPos() <= stop );

  updateContents();
  
}

void TrapperView::findRead

(

)

finds a read

Definition at line 1250 of file trapperview.cpp.

References Database::SecondaryIterator< T >::answer(), QString::ascii(), clearSelected(), doc, QInputDialog::getText(), Database::SecondaryIterator< T >::key(), ReadMetaData::name(), Database::SecondaryIterator< T >::next(), ReadMetaData::readRecno, select(), ReadMetaData::setName(), Database::SecondaryIterator< T >::setRange(), and QScrollView::updateContents().

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<ReadMetaData> name_it( "name", doc, "ReadMetaData" );
  name_it.key()->setName( res );
  if ( name_it.setRange() != 0 ) {
    cerr<<"Error, couldn't find "<<res<<" in db"<<endl;
    return;
  }
  clearSelected();

  do {
    select(name_it.answer()->readRecno(), true);
  } while ( name_it.next() == 0 && name_it.answer()->name().find(res.ascii()) < name_it.answer()->name().size() );
//   } while ( name_it.next() == 0 && name_it.answer()->name() == res );
  
  updateContents();
  

//   TR_PIX y = dnaCoordToPixel_Y(name_it.answer()->row());
//   TR_PIX x = dnaCoordToPixel_X(name_it.answer()->startPos());
//   scrollTo(x, y);

}

void TrapperView::findTag

(

)

finds a tag

Definition at line 1285 of file trapperview.cpp.

References Database::SecondaryIterator< T >::answer(), QString::ascii(), clearSelected(), doc, TagData::getInfo(), QInputDialog::getText(), Database::SecondaryIterator< T >::key(), Database::SecondaryIterator< T >::next(), FeatureData::readRecno(), select(), TagData::setInfo(), Database::SecondaryIterator< T >::setRange(), and QScrollView::updateContents().

Referenced by TrapperApp::slotEditFindTag().

{
  bool ok;
  QString res = QInputDialog::getText ( "Find tag", "Enter tag name:", QLineEdit::Normal, QString::null, &ok );
  

  if ( ok ) {
    // user entered something and pressed OK
  } else {
    // user pressed Cancel
    return;
  }

  Database::SecondaryIterator<TagData> info_it( "info", doc, "TagData" );
  info_it.key()->setInfo( res );
  if ( info_it.setRange() != 0 ) {
    cerr<<"Error, couldn't find "<<res<<" in db"<<endl;
    return;
  }
  clearSelected();

  do {
    select(info_it.answer()->readRecno(), true);
  } while ( info_it.next() == 0 && info_it.answer()->getInfo().find(res.ascii()) < info_it.answer()->getInfo().size() );
//   } while ( name_it.next() == 0 && name_it.answer()->name() == res );
  
  updateContents();
  

//   TR_PIX y = dnaCoordToPixel_Y(name_it.answer()->row());
//   TR_PIX x = dnaCoordToPixel_X(name_it.answer()->startPos());
//   scrollTo(x, y);

}

void TrapperView::enlarge

(

)

enlarges view

Definition at line 1598 of file trapperview.cpp.

References basewidth, globalBases, globalRows, magnifyX, magnifyY, QScrollView::resizeContents(), rowheight, and QScrollView::updateContents().

Referenced by TrapperApp::slotEnlarge().

{
  globalRows *= 2;
  globalBases = static_cast<int32_t>(globalBases * 1.25);
  resizeContents(static_cast<int>(globalBases * magnifyX * basewidth), globalRows * rowheight * magnifyY);
  updateContents();
}

void TrapperView::shrink

(

)

shrinks view

Definition at line 1606 of file trapperview.cpp.

References basewidth, globalBases, globalRows, magnifyX, magnifyY, QScrollView::resizeContents(), rowheight, and QScrollView::updateContents().

Referenced by TrapperApp::slotShrink().

{
  globalRows = static_cast<int32_t>(globalRows * 0.5);
  globalBases = static_cast<int32_t>(globalBases * 0.8);
  resizeContents(static_cast<int>(globalBases * magnifyX * basewidth), globalRows * rowheight * magnifyY);
  updateContents();
}

void TrapperView::setDragMode

(

bool

status

)

sets pointer mode

Definition at line 1924 of file trapperview.cpp.

References allow_dragging.

Referenced by TrapperApp::slotDragMode(), and TrapperApp::slotNormalMode().

{
  allow_dragging = status;
}

void TrapperView::copy

(

)

copies selected data

Definition at line 1929 of file trapperview.cpp.

References QApplication::clipboard(), QClipboard::setData(), QStoredDrag::setEncodedData(), and 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::paste

(

)

pastes selected data

Definition at line 1942 of file trapperview.cpp.

References QApplication::clipboard(), QClipboard::data(), QMimeSource::encodedData(), readSelected(), and QScrollView::updateContents().

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();
}

void TrapperView::cut

(

)

cuts selected data

Definition at line 1955 of file trapperview.cpp.

References clearSelected(), copy(), Destroyer::destroy(), doc, selectedReads, and QScrollView::updateContents().

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();
  
}

void TrapperView::undo

(

)

undoes last move

Definition at line 1967 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) );
}

TR_DNA TrapperView::mousePressedRow

(

)

gets row position of last mouse press

Definition at line 1972 of file trapperview.cpp.

References mousePressedPoint, pixelCoordToDna_Y(), and QPoint::y().

Referenced by slotContextSelect(), and OptimizeLayoutAlgo::start().

{
  return pixelCoordToDna_Y( mousePressedPoint.y() );
  
  
}

TR_DNA TrapperView::mousePressedCol

(

)

gets col position of last mouse press

Definition at line 1979 of file trapperview.cpp.

References mousePressedPoint, pixelCoordToDna_X(), and QPoint::x().

Referenced by slotContextSelect(), and slotSetCenter().

{
  return pixelCoordToDna_X( mousePressedPoint.x() );
  
}

void TrapperView::sendMsg

(

const QString &

msg

)

Sends out a message

Definition at line 1985 of file trapperview.cpp.

References message().

Referenced by contentsMouseMoveEvent(), and contentsMousePressEvent().

{
  emit message(msg);
}

void TrapperView::setViewTimeCourse

(

bool

toggle

)

sets visualization mode for time course data

Definition at line 1990 of file trapperview.cpp.

References time_course, and QScrollView::updateContents().

Referenced by TrapperApp::slotViewTimeCourse().

{
  if ( time_course != toggle) {
    updateContents();
  }
  time_course = toggle;
}

void TrapperView::setNormalizeTimeCourse

(

bool

toggle

)

sets normalization mode for time course data

Definition at line 1998 of file trapperview.cpp.

References tc_normalize, and QScrollView::updateContents().

Referenced by TrapperApp::slotNormalizeTimeCourse().

{
  if ( tc_normalize != toggle) {
    updateContents();
  }
  tc_normalize = toggle;
}

void TrapperView::scrollToNextCluster

(

bool

forward

)

scrolls to next visible read cluster

Definition at line 2006 of file trapperview.cpp.

References Database::SecondaryIterator< T >::answer(), QScrollView::contentsX(), QScrollView::contentsY(), dnaCoordToPixel_X(), doc, Database::SecondaryIterator< T >::key(), Database::SecondaryIterator< T >::last(), Database::SecondaryIterator< T >::next(), pixelCoordToDna_X(), Database::SecondaryIterator< T >::prev(), read_cluster_min_num, read_cluster_window, scrollTo(), Database::SecondaryIterator< T >::setRange(), ReadData::setStartPos(), ReadData::startPos(), TR_DNA, and QScrollView::visibleWidth().

Referenced by TrapperApp::slotScrollBackwards(), and TrapperApp::slotScrollForward().

{


  Database::SecondaryIterator<ReadData> start_it( "start", doc, "ReadData" );

  TR_DNA start;
  if ( forward ) {
    start = pixelCoordToDna_X( contentsX() + visibleWidth()*3/5 ) + 1;
  }
  else {
    start = pixelCoordToDna_X( contentsX() + visibleWidth()*2/5 );
  }

  while( true ) {
    
    start_it.key()->setStartPos( start );
    

    if ( forward ) {
      if ( start_it.setRange() != 0 ){
        
        return;
      }
      
    }
    else {
      if (start_it.setRange() == 0) {
        if ( start_it.prev() != 0 ) {
          return;
        }
      }
      else {
        if (start_it.last() != 0){
          
        }
      }
    }
    
    
    start = start_it.answer()->startPos();
    TR_DNA stop;
    if ( forward ) {
      stop = start + read_cluster_window;
    }
    else {
      stop = start - read_cluster_window;
    }
    
  
    size_t num_in_win(0);
    
    do {
      num_in_win++;

    }while( ( (forward && start_it.next() == 0) || (!forward && start_it.prev() == 0) ) && 
            ( (forward && start_it.answer()->startPos() < stop) || (!forward && start_it.answer()->startPos() > stop) ) && 
            num_in_win < read_cluster_min_num );
    
    if ( num_in_win == read_cluster_min_num ) {
      //Found a cluster
      scrollTo( dnaCoordToPixel_X(start) - visibleWidth()/2, contentsY() );
      
      return;
    }
    else if ( forward && start_it.answer()->startPos() >= stop ) {
      start++;
    }
    else if ( !forward && start_it.answer()->startPos() <= stop ) {
      start--;
    }
    else {
      return;
    }
    
    
  }
  
  

}

void TrapperView::setClusterWindow

(

int

window_size

)

sets cluster window size

Definition at line 2088 of file trapperview.cpp.

References read_cluster_window.

Referenced by TrapperApp::slotClusterWindowChanged().

{
  read_cluster_window = window_size;
}

void TrapperView::setClusterMinNum

(

int

num

)

sets cluster minimum read num size

Definition at line 2094 of file trapperview.cpp.

References read_cluster_min_num.

Referenced by TrapperApp::slotClusterNumChanged().

{
  read_cluster_min_num = num;
}

void TrapperView::slotSwitchToMode

(

int

i

)

[slot]

Definition at line 1130 of file trapperview.cpp.

References TrapperDoc::changedViewList(), doc, ViewModes::setMode(), switchViewMenu, QPopupMenu::text(), QScrollView::updateContents(), and viewModes.

Referenced by contentsContextMenuEvent().

{
    QString viewMode =  switchViewMenu->text(i);
    viewModes->setMode( viewMode );
    doc->changedViewList();
    updateContents();
}

void TrapperView::slotStartAlgo

(

int

i

)

[slot]

Definition at line 1138 of file trapperview.cpp.

References algoMenu, QString::ascii(), clearLastMove(), getSelectedReads(), runAlgo(), QPopupMenu::text(), and QScrollView::updateContents().

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::slotScrollToMouse

(

)

[slot]

Definition at line 1167 of file trapperview.cpp.

References mousePressedPoint, scrollTo(), QPoint::x(), and QPoint::y().

Referenced by contentsContextMenuEvent().

{
  scrollTo(mousePressedPoint.x(), mousePressedPoint.y());

}

void TrapperView::slotScrollToPos

(

)

[slot]

Definition at line 1173 of file trapperview.cpp.

References dnaCoordToPixel_X(), dnaCoordToPixel_Y(), QInputDialog::getInteger(), 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 1205 of file trapperview.cpp.

References center_point, mousePressedCol(), and QScrollView::updateContents().

{
  center_point = mousePressedCol();
//   cerr<<center_point<<endl;
  updateContents();
}

void TrapperView::slotClearCenter

(

)

[slot]

Definition at line 1212 of file trapperview.cpp.

References center_point, and QScrollView::updateContents().

{
  center_point = 0;
  updateContents();
}

void TrapperView::slotContextSelect

(

int

i

)

[slot]

Definition at line 1218 of file trapperview.cpp.

References contextSelectMenu, globalBases, globalRows, mousePressedCol(), mousePressedRow(), selectCols(), selectRows(), and QPopupMenu::text().

Referenced by contentsContextMenuEvent().

{
  QString direction =  contextSelectMenu->text(i);
  int start, stop;

  if ( direction == "above" || direction == "below") {
    if ( direction == "above" ){
      start = 0;
      stop = mousePressedRow();
    }
    else {
      start = mousePressedRow();
      stop = globalRows;
    }
    selectRows(start, stop);
  }
  else {
    assert(direction == "left" || direction == "right");
    if ( direction == "left" ){
      start = 0;
      stop = mousePressedCol();
    }
    else {
      start = mousePressedCol();
      stop = globalBases;
    }
    selectCols(start, stop);
  }
  

}

void TrapperView::contentsDragEnterEvent

(

QDragEnterEvent *

event

)

[protected]

Reimplemented from QScrollView.

Definition at line 1744 of file trapperview.cpp.

{
  event->accept( TRUE );
}

void TrapperView::contentsDropEvent

(

QDropEvent *

event

)

[protected]

Reimplemented from QScrollView.

Definition at line 1760 of file trapperview.cpp.

References convertToDnaCoordinates(), QDropEvent::encodedData(), getDocument(), mousePressedPoint, moveData(), QDropEvent::pos(), readSelected(), QDropEvent::source(), TR_DNA, QScrollView::updateContents(), QPoint::x(), and QPoint::y().

{
//   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]

Reimplemented from QScrollView.

Definition at line 827 of file trapperview.cpp.

References allow_dragging, QRect::bottomRight(), QScrollView::contentsToViewport(), curr_mouse_pos, dragging, dragPixmap, dragWindowPoint, drawContents_helper(), drawRubber(), last_click_selected_read, mousePressedPoint, moving, QRect::normalize(), pixelCoordToDna_X(), pixelCoordToDna_Y(), QMouseEvent::pos(), rubber_band, RubberEnd, RubberOn, sendMsg(), QStoredDrag::setEncodedData(), QPainter::setPen(), QPainter::setRasterOp(), QRect::setSize(), QMouseEvent::state(), QRect::topLeft(), QScrollView::updateContents(), QScrollView::viewport(), writeSelected(), QPoint::x(), QMouseEvent::x(), QPoint::y(), QMouseEvent::y(), 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::contentsMouseReleaseEvent

(

QMouseEvent *

e

)

[protected]

Reimplemented from QScrollView.

Definition at line 913 of file trapperview.cpp.

References QRect::bottomRight(), clearSelected(), convertToDnaCoordinates(), doc, dragging, drawRubber(), ReadsInRect::first(), last_click_changed_selection, last_click_selected_read, last_selected_recno, moveData(), moveOn, moving, ReadsInRect::next(), QRect::normalize(), readsInRect, QRect::rect(), rubber_band, RubberEnd, RubberOn, RubberStart, select(), QRect::setBottomRight(), QRect::setTopLeft(), ReadsInRect::setWindowCoord(), QMouseEvent::state(), QRect::topLeft(), TR_DNA, TR_PIX, QScrollView::updateContents(), QScrollView::viewport(), QScrollView::viewportToContents(), QPoint::x(), QPoint::y(), 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;

    }
//     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() ) {
        last_click_changed_selection = true;//new 071203
        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();
    }

  }
  if ( last_click_changed_selection ) {
    updateContents();
  }

  moving = false;
  dragging = false;
  last_click_changed_selection = false;
  last_click_selected_read = false;
  
}

void TrapperView::contentsContextMenuEvent

(

QContextMenuEvent *

e

)

[protected]

Reimplemented from QScrollView.

Definition at line 1021 of file trapperview.cpp.

References algoMenu, AlgoMaker::algosRegistered(), contextSelectMenu, dragging, QPopupMenu::exec(), getInfo(), infoMenu, QPopupMenu::insertItem(), QPopupMenu::insertSeparator(), TrapperConf::instance(), last_click_changed_selection, last_click_selected_read, moving, QCursor::pos(), QContextMenuEvent::pos(), slotContextSelect(), slotScrollToMouse(), slotScrollToPos(), slotStartAlgo(), slotSwitchToMode(), switchViewMenu, QScrollView::updateContents(), and TrapperConf::viewModeNames().

{
  if ( last_click_changed_selection ) {
    updateContents();
  }
  moving = false;
  dragging = 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 InfoPopup(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());
  }

  //Info is copied to clipboard through InfoPopup class

  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();
  contextSelectMenu = new QPopupMenu( this );
  Q_CHECK_PTR( contextSelectMenu );
  
  contextSelectMenu->insertItem("above");
  contextSelectMenu->insertItem("below");
  contextSelectMenu->insertItem("left");
  contextSelectMenu->insertItem("right");
  connect( contextSelectMenu, SIGNAL( activated( int ) ),
           this, SLOT( slotContextSelect( int ) ) );
  contextMenu->insertItem( "&Select all", contextSelectMenu );
  

//   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;
  delete contextSelectMenu;
}

void TrapperView::contentsMousePressEvent

(

QMouseEvent *

e

)

[protected]

Reimplemented from QScrollView.

Definition at line 676 of file trapperview.cpp.

References QPainter::begin(), QRect::bottomRight(), clearSelected(), QScrollView::contentsToViewport(), convertToDnaCoordinates(), ctrl, doc, dragBitmap, dragging, dragPixmap, dragWindowPoint, drawContents_helper(), QPainter::end(), QPainter::fillRect(), GeneralData::getRecno(), QRect::height(), isSelected(), last_click_changed_selection, last_click_selected_read, last_selected_recno, mousePressedPoint, moveOn, moving, p3, pixelCoordToDna_X(), pixelCoordToDna_Y(), QMouseEvent::pos(), readsInRect, QPixmap::resize(), rubber_band, RubberEnd, RubberOn, RubberStart, select(), selectedReads, sendMsg(), QBrush::setColor(), QPixmap::setMask(), QBrush::setStyle(), QPoint::setX(), QPoint::setY(), QRect::size(), QMouseEvent::state(), QMouseEvent::stateAfter(), QRect::topLeft(), TR_DNA, QRect::width(), QPoint::x(), QMouseEvent::x(), QPoint::y(), QMouseEvent::y(), y_delta, and y_delta_previous.

{
  setFocus();

  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 ) {
    ctrl = true;
  }
  else {
    ctrl = false;
  }
  
  

  
  
  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
  if ( last_click_selected_read )//"if" added 071203
  {
    cerr<<"filling pixmap..."<<endl;
    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() ));
    
    dragPixmap.setMask(dragBitmap);

    p2.end();
    p3.end();
  }
}

void TrapperView::contentsDragMoveEvent

(

QDragMoveEvent *

)

[protected]

Reimplemented from QScrollView.

Definition at line 1749 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::closeEvent

(

QCloseEvent *

)

[protected, virtual]

Definition at line 203 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::doZoom

(

)

[protected]

Definition at line 1573 of file trapperview.cpp.

References basewidth, globalBases, globalRows, magnifyX, magnifyY, QScrollView::resizeContents(), rowheight, and QScrollView::updateContents().

{
//   QPoint p = viewportToContents(viewport()->rect().topLeft());

//   if ( globalBases * magnifyX * basewidth < 1 ) {
//     cerr<<"globalBases: "<<globalBases<<endl;
//     cerr<<"globalBases * magnifyX * basewidth: "<<globalBases * magnifyX * basewidth<<endl;
//   }
  resizeContents(static_cast<int>(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::scrollTo	(	TR_PIX	x,
		TR_PIX	y
	)			[protected]

Definition at line 1590 of file trapperview.cpp.

References QScrollView::setContentsPos().

Referenced by scrollToNextCluster(), slotScrollToMouse(), and slotScrollToPos().

{
  setContentsPos( x, y );
//   updateContents();
  
}

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

Definition at line 470 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 480 of file trapperview.cpp.

References basewidth, center_point, QScrollView::contentsToViewport(), convertToDnaCoordinates(), convertToPixelCoordinates(), dnaCoordToPixel_Y(), doc, dragPixmap, dragWindowPoint, QPainter::drawPixmap(), QPainter::drawRect(), ReadsInRect::first(), isSelected(), magnifyX, magnifyY, mousePressedPoint, moveOn, moving, ReadsInRect::next(), oldMovePoint, paintFeatures(), QPainter::pen(), pixelCoordToDna_Y(), readsInRect, rowheight, rubber_band, QPainter::setPen(), QPainter::setRasterOp(), 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, 0, r->endPos() - 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 );    
    
  }

  return;
  
  
}

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 256 of file trapperview.cpp.

References Database::SecondaryIterator< T >::answer(), Database::SecondaryIterator< T >::closeCursor(), ViewModes::currentViewMode(), dnaCoordToPixel_X(), doc, QPainter::drawRect(), Layer::featureList, QPainter::fillRect(), FeatureData::gui(), Layer::heightInPix(), Database::SecondaryIterator< T >::key(), ViewMode::layerList, magnifyX, magnifyY, min_cutoff, moving, Database::SecondaryIterator< T >::name(), Database::SecondaryIterator< T >::nextdup(), FeatureGui::paint(), QPainter::pen(), rowheight, Database::SecondaryIterator< T >::set(), QBrush::setColor(), QColor::setNamedColor(), QPainter::setPen(), FeatureData::setReadRecno(), QBrush::setStyle(), spaceBetweenRows, TrapperVector< T >::stlVector(), tc_normalize, ReadMetaData::tc_vec, time_course, TR_PIX, viewModes, and zoom_cutoff.

Referenced by drawContents_helper().

{

  int pix_len = static_cast<int>(dna_len*width);
  if ( pix_len < 1 ) {
    pix_len = 1;
  }
  
  
  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 ,  pix_len , height ,brush) ;
  
  brush.setColor( Qt::color1 );
  
  if ( bitmapPainter && selected )
    bitmapPainter->fillRect( x_pix  , y_pix , pix_len , height ,brush) ;
  
  /*  finished clearing */
  
  
  
  
  
  // we use two pixels in the height to draw the paintReadBorder
  y_pix += 1;
  height -= 2;
  
  
  
  /* starting painting features */
  
  if ( !time_course  ) {
  
    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<SpatialFeatureData> * it;
      for (it  = layer->featureList.first(); it; it = layer->featureList.next() ) {

        if ( magnifyX < min_cutoff || magnifyY < min_cutoff ) continue;
        int cutoff = zoom_cutoff[ it->name() ];
        if ( magnifyX < cutoff || magnifyY < cutoff ) continue;
        
        it->key()->setReadRecno( readRecno );
        if ( it->set() == 0 ) {
          int ret;
          do {
            
            
            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;
    }
  }
  else  {
    
    //TIME COURSE
    Database::SecondaryIterator<ReadMetaData> read_meta_it( "readRecno", doc, "ReadMetaData" );
    //   assert( read_it.setFromRecno(readRecno) == 0 );
    read_meta_it.key()->setReadRecno( readRecno );
    assert(read_meta_it.set() == 0 );
    if ( read_meta_it.answer()->tc_vec.stlVector().size() != 0 ) {
    

      Database::PrimaryIterator<ReadData> read_it( doc, "ReadData" );
      assert( read_it.setFromRecno(readRecno) == 0 );
      
      //     int tc_len = dnaCoordToPixel_X( read_it.answer()->tc_vec.stlVector().size() );
      int tc_len = dnaCoordToPixel_X( read_it.answer()->endPos() - read_it.answer()->startPos() + 1 );
      int start_tc_pix = dnaCoordToPixel_X( read_it.answer()->startPos() ) + 1;
      int stop_tc_pix = start_tc_pix + tc_len;
      //     if ( r_end && cx + cw > start_tc_pix && cx < stop_tc_pix ) {
      //Part of time course needs to be drawn
      
      //Paint new TC
      int numpoints = read_meta_it.answer()->tc_vec.stlVector().size();
      if ( numpoints > 0 ) {
        
        
        int pix_per_point = tc_len/numpoints;
        
        //       int start_paint_index = max(0, (cx - start_tc_pix)/numpoints - 10);
        //       int stop_paint_index = min(numpoints, (cx + cw)/numpoints);
        int start_paint_index = 0;
        int stop_paint_index = numpoints;
        
        
        
        //Need to find the max tc value for each read for normalization
        double max_tc(0.000001);
        if ( tc_normalize ) {
          bool foundmax(false);
          for( size_t i = 0; i < read_meta_it.answer()->tc_vec.stlVector().size(); i++ ) {
            if ( read_meta_it.answer()->tc_vec.stlVector()[i] > max_tc ) {
              max_tc = read_meta_it.answer()->tc_vec.stlVector()[i];
              foundmax = true;
            }
          }
          if ( !foundmax ) {
            max_tc = 1;
          }
        }
        
        QBrush brush;
        for( int i = start_paint_index; i < stop_paint_index && i < numpoints; i++ ) {
          brush.setStyle( Qt::SolidPattern );
          QColor tc_color;
          double tc_val = read_meta_it.answer()->tc_vec.stlVector()[i];
          if ( ( tc_normalize && tc_val/max_tc < 0.125 ) || ( !tc_normalize && tc_val < 1) ) {
            tc_color.setNamedColor("#0000FF");
          }
          else if ( ( tc_normalize && tc_val/max_tc < 0.250 ) || ( !tc_normalize && tc_val < 2 ) ) {
            tc_color.setNamedColor("#00BFFF");
          }
          else if ( ( tc_normalize && tc_val/max_tc < 0.375 ) || ( !tc_normalize && tc_val < 5 ) ) {
            tc_color.setNamedColor("#20B2AA");
          }
          else if ( ( tc_normalize && tc_val/max_tc < 0.500 ) || ( !tc_normalize && tc_val < 10 ) ) {
            tc_color.setNamedColor("#32CD32");
          }
          else if ( ( tc_normalize && tc_val/max_tc < 0.625 ) || ( !tc_normalize && tc_val < 100 ) ) {
            tc_color.setNamedColor("#FFD700");
          }
          else if ( ( tc_normalize && tc_val/max_tc < 0.750 ) || ( !tc_normalize && tc_val < 500 ) ) {
            tc_color.setNamedColor("#FFA500");
          }
          else if ( ( tc_normalize && tc_val/max_tc < 0.875 ) || ( !tc_normalize && tc_val < 1000 ) ) {
            tc_color.setNamedColor("#FF4500");
          }
          else {
            tc_color.setNamedColor("#FF0000");
          }
          
          brush.setColor( tc_color );
          p->fillRect( start_tc_pix + i* pix_per_point, read_it.answer()->row()*rowheight*magnifyY + 2, pix_per_point, rowheight*magnifyY - spaceBetweenRows - 2,brush) ;
          
        }
        
      }
    }
    
  }
  
  //     }
  
  //END TIME COURSE
  
  
  
  

  /* 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);
  
  
  p->drawRect( x_pix  , y_pix,  pix_len, height ) ;

  //Quality trimming
  brush.setStyle( Qt::Dense4Pattern );
  brush.setColor( Qt::white );
  if ( x_dna_relative < bg ) {
    p->fillRect( x_pix  , y_pix,  static_cast<int>((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( static_cast<int>(x_pix + goodlen*width), y_pix, static_cast<int>((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 606 of file trapperview.cpp.

References center_point, QScrollView::contentsY(), dnaCoordToPixel_X(), dnaCoordToPixel_Y(), QPainter::drawLine(), QPainter::drawText(), pixelCoordToDna_X(), pixelCoordToDna_Y(), rowheight, QPainter::setFont(), QPainter::setPen(), and QFont::setPointSize().

Referenced by drawContents().

{
  p->setPen( Qt::black );

  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;

  //Coordinates
  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;
  for( int i = leftcol; i <= 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 )) );    
  }

  return;
  

  //Grid
  for (int r=toprow; r<=bottomrow; r++) {
    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);
      
    }
  }
  

  //Chromat line
  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::convertToPixelCoordinates	(	TR_PIX &	x_pix,
		TR_PIX &	y_pix,
		TR_DNA	x_dna,
		TR_DNA	y_dna
	)			[protected]

Definition at line 232 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::convertToDnaCoordinates	(	TR_DNA &	x_dna,
		TR_DNA &	y_dna,
		const TR_PIX	cx,
		const TR_PIX	cy
	)			[protected]

Definition at line 209 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;
}

TR_PIX TrapperView::dnaCoordToPixel_X

(

TR_DNA

cx

)

[protected]

Definition at line 239 of file trapperview.cpp.

References basewidth, and magnifyX.

Referenced by convertToPixelCoordinates(), paintFeatures(), paintGrid(), readSelected(), scrollToNextCluster(), 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 static_cast<TR_PIX>(x_dna * basewidth * magnifyX);
}

TR_PIX TrapperView::dnaCoordToPixel_Y

(

TR_DNA

cy

)

[protected]

Definition at line 251 of file trapperview.cpp.

References magnifyY, and rowheight.

Referenced by convertToPixelCoordinates(), drawContents_helper(), paintGrid(), readSelected(), slotScrollToPos(), and undo().

{
  return y_dna * rowheight * magnifyY;
}

TR_DNA TrapperView::pixelCoordToDna_X

(

TR_PIX

x_dna

)

[protected]

Definition at line 216 of file trapperview.cpp.

References basewidth, and magnifyX.

Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), convertToDnaCoordinates(), getInfo(), mousePressedCol(), moveData(), paintGrid(), and scrollToNextCluster().

{
//   if ( basewidth * magnifyX < 1 ) {
//     cerr<<"basewidth: "<<basewidth<<endl;
//     cerr<<"basewidth * magnifyX: "<<basewidth * magnifyX<<endl;
//   }
  

  return static_cast<TR_DNA>(cx / ( basewidth * magnifyX ));
}

TR_DNA TrapperView::pixelCoordToDna_Y

(

TR_PIX

y_dna

)

[protected]

Definition at line 227 of file trapperview.cpp.

References magnifyY, and rowheight.

Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), convertToDnaCoordinates(), drawContents_helper(), getInfo(), mousePressedRow(), moveData(), and paintGrid().

{
  return cy / ( rowheight * magnifyY );
}

std::set< db_recno_t > & TrapperView::getSelectedReads

(

)

[protected]

Definition at line 1321 of file trapperview.cpp.

References selectedReads.

Referenced by moveData(), and slotStartAlgo().

{
  return selectedReads;
}

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

Definition at line 1326 of file trapperview.cpp.

References clearLastMove(), isSelected(), and selectedReads.

Referenced by contentsMousePressEvent(), contentsMouseReleaseEvent(), findRead(), findTag(), readSelected(), selectAll(), selectCols(), and selectRows().

{
  RecnoMap::iterator pos;
  if ( status == true && !isSelected(recno) ) {
    selectedReads.insert( recno );
    clearLastMove();
  }
  else if ( ( pos = selectedReads.find( recno )) != selectedReads.end() ) {
    selectedReads.erase( pos );
    clearLastMove();
  }
  
}

bool TrapperView::isSelected

(

db_recno_t

recno

)

[protected]

Definition at line 1340 of file trapperview.cpp.

References selectedReads.

Referenced by contentsMousePressEvent(), drawContents_helper(), and select().

{
  return selectedReads.find( recno ) != selectedReads.end();
}

void TrapperView::clearSelected

(

)

[protected]

Definition at line 1345 of file trapperview.cpp.

References clearLastMove(), and selectedReads.

Referenced by contentsMousePressEvent(), contentsMouseReleaseEvent(), cut(), findRead(), findTag(), readSelected(), selectAll(), selectCols(), and selectRows().

{
  selectedReads.clear();
  clearLastMove();
}

std::vector< std::list< std::string > > TrapperView::getInfo

(

const QPoint &

pos

)

[protected]

Definition at line 1351 of file trapperview.cpp.

References Database::SecondaryIterator< T >::answer(), ReadMetaData::beginGood(), doc, ReadMetaData::endGood(), ReadData::endPos(), GeneralData::getRecno(), Database::SecondaryIterator< T >::key(), GeneralMaker::listRegistered(), ReadMetaData::mate(), ReadMetaData::mateLength(), ReadMetaData::name(), GeneralMaker::newData(), pixelCoordToDna_X(), pixelCoordToDna_Y(), readsInRect, Database::SecondaryIterator< T >::set(), FeatureData::setReadRecno(), ReadData::startPos(), TrapperVector< T >::stlVector(), ReadMetaData::strand(), ReadMetaData::tc_vec, TR_DNA, QPoint::x(), and QPoint::y().

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 ) {
    Database::SecondaryIterator<ReadMetaData> read_m_it( "readRecno", doc, "ReadMetaData" );
    
    read_m_it.key()->setReadRecno( r->getRecno() );
    
    assert(read_m_it.set() == 0);


    list<string> types = GeneralMaker::listRegistered();
    readResult.push_back( "Read info" );
    readResult.push_back( read_m_it.answer()->name() );
    
    os<<"TC:";
    for( size_t i = 0; i < read_m_it.answer()->tc_vec.stlVector().size(); i++ ) {
      os<<' '<<read_m_it.answer()->tc_vec.stlVector()[i];
    }
    readResult.push_back( os.str() );

    os.str("");
    os<<"Strand: "<<read_m_it.answer()->strand();
    readResult.push_back( os.str() );
    os.str("");
    os<<"Mate: "<<read_m_it.answer()->mate() << ' ' << read_m_it.answer()->mateLength();
    readResult.push_back( os.str() );
    os.str("");
    os<<"Begin good: "<<read_m_it.answer()->beginGood();
    readResult.push_back( os.str() );
    os.str("");
    os<<"End good: "<<read_m_it.answer()->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 );
      SpatialFeatureData * fdata = dynamic_cast<SpatialFeatureData *>( data );
      // fdata is just used to see that the registered string is corresponding to
      // a feature
      if ( fdata ) {
        Database::SecondaryIterator<SpatialFeatureData> 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;
}

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

Definition at line 1457 of file trapperview.cpp.

References TrapperDoc::addAlgorithm(), doc, fitContentsizeToData(), AlgoMaker::newAlgo(), TrapperDoc::removeAlgorithm(), selectedReads, and QScrollView::updateContents().

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::writeSelected

(

QDataStream &

data_stream

)

[protected]

Definition at line 1796 of file trapperview.cpp.

References Database::PrimaryIterator< T >::answer(), doc, GeneralMaker::listRegistered(), GeneralMaker::newData(), selectedReads, Database::PrimaryIterator< T >::setFromRecno(), 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::readSelected

(

QDataStream &

data_stream

)

[protected]

Definition at line 1864 of file trapperview.cpp.

References QDataStream::atEnd(), 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::moveData	(	TR_PIX	dx,
		TR_PIX	dy
	)			[protected]

Definition at line 653 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::fitContentsizeToData

(

)

[protected]

Definition at line 148 of file trapperview.cpp.

References Database::SecondaryIterator< T >::answer(), basewidth, doc, ReadData::endPos(), globalBases, globalRows, Database::SecondaryIterator< T >::last(), magnifyX, magnifyY, QScrollView::resizeContents(), 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(static_cast<int>(globalBases * magnifyX * basewidth), globalRows * rowheight * magnifyY);
 
}

void TrapperView::clearLastMove

(

)

[protected]

Definition at line 670 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::drawRubber

(

QPainter *

p

)

[inline, private]

Definition at line 356 of file trapperview.h.

References QPainter::drawRect(), QPainter::pen(), RubberEnd, RubberStart, QPainter::setPen(), QPen::setStyle(), QPoint::x(), and QPoint::y().

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::createView

(

QString

)

[signal]

void TrapperView::message

(

const QString &

)

[signal]

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

---

Friends And Related Function Documentation

friend class TrapperDoc [friend]

Definition at line 119 of file trapperview.h.

Referenced by TrapperParser::startElement().

---

Member Data Documentation

TR_PIX TrapperView::basewidth [protected]

Definition at line 281 of file trapperview.h.

Referenced by dnaCoordToPixel_X(), doZoom(), drawContents_helper(), enlarge(), fitContentsizeToData(), pixelCoordToDna_X(), shrink(), TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

TR_PIX TrapperView::spaceBetweenRows [protected]

Definition at line 282 of file trapperview.h.

Referenced by drawContents_helper(), paintFeatures(), and TrapperView().

TR_PIX TrapperView::rowheight [protected]

Definition at line 283 of file trapperview.h.

Referenced by dnaCoordToPixel_Y(), doZoom(), drawContents_helper(), enlarge(), fitContentsizeToData(), paintFeatures(), paintGrid(), pixelCoordToDna_Y(), shrink(), TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

TR_DNA TrapperView::globalRows [protected]

Definition at line 284 of file trapperview.h.

Referenced by doZoom(), enlarge(), fitContentsizeToData(), shrink(), slotContextSelect(), TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

TR_DNA TrapperView::globalBases [protected]

Definition at line 284 of file trapperview.h.

Referenced by doZoom(), enlarge(), fitContentsizeToData(), shrink(), slotContextSelect(), TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

TR_DNA TrapperView::center_point [protected]

Definition at line 285 of file trapperview.h.

Referenced by drawContents_helper(), paintGrid(), slotClearCenter(), slotSetCenter(), and TrapperView().

TrapperDoc* TrapperView::doc [protected]

Definition at line 287 of file trapperview.h.

Referenced by contentsMousePressEvent(), contentsMouseReleaseEvent(), cut(), drawContents_helper(), findRead(), findTag(), fitContentsizeToData(), getDocument(), getInfo(), paintFeatures(), readSelected(), runAlgo(), scrollToNextCluster(), selectAll(), selectCols(), selectRows(), slotSwitchToMode(), TrapperView(), and writeSelected().

QLabel* TrapperView::lab [protected]

Definition at line 288 of file trapperview.h.

double TrapperView::magnifyX [protected]

Definition at line 290 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 291 of file trapperview.h.

Referenced by dnaCoordToPixel_Y(), doZoom(), drawContents_helper(), enlarge(), fitContentsizeToData(), paintFeatures(), pixelCoordToDna_Y(), shrink(), TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

int TrapperView::zoomfactor [protected]

Definition at line 292 of file trapperview.h.

Referenced by TrapperView(), zoomInX(), zoomInY(), zoomOutX(), and zoomOutY().

ViewModes* TrapperView::viewModes [protected]

Definition at line 293 of file trapperview.h.

Referenced by mode(), paintFeatures(), slotSwitchToMode(), TrapperView(), and ~TrapperView().

QPopupMenu* TrapperView::switchViewMenu [protected]

Definition at line 294 of file trapperview.h.

Referenced by contentsContextMenuEvent(), and slotSwitchToMode().

QPopupMenu* TrapperView::algoMenu [protected]

Definition at line 295 of file trapperview.h.

Referenced by contentsContextMenuEvent(), and slotStartAlgo().

QPopupMenu* TrapperView::infoMenu [protected]

Definition at line 296 of file trapperview.h.

Referenced by contentsContextMenuEvent().

QPopupMenu* TrapperView::contextSelectMenu [protected]

Definition at line 297 of file trapperview.h.

Referenced by contentsContextMenuEvent(), and slotContextSelect().

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 313 of file trapperview.h.

Referenced by clearSelected(), contentsMousePressEvent(), cut(), getSelectedReads(), isSelected(), runAlgo(), select(), and writeSelected().

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

Definition at line 314 of file trapperview.h.

Referenced by paintFeatures(), and TrapperView().

int TrapperView::min_cutoff [protected]

Definition at line 315 of file trapperview.h.

Referenced by paintFeatures(), and TrapperView().

ReadsInRect* TrapperView::readsInRect [protected]

Definition at line 317 of file trapperview.h.

Referenced by contentsMousePressEvent(), contentsMouseReleaseEvent(), drawContents_helper(), and getInfo().

bool TrapperView::dragging [protected]

Definition at line 318 of file trapperview.h.

Referenced by contentsContextMenuEvent(), contentsMouseMoveEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), and TrapperView().

bool TrapperView::allow_dragging [protected]

Definition at line 319 of file trapperview.h.

Referenced by contentsMouseMoveEvent(), setDragMode(), and TrapperView().

bool TrapperView::moving [protected]

Definition at line 320 of file trapperview.h.

Referenced by contentsContextMenuEvent(), contentsMouseMoveEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), drawContents_helper(), paintFeatures(), and TrapperView().

bool TrapperView::last_click_selected_read [protected]

Definition at line 321 of file trapperview.h.

Referenced by contentsContextMenuEvent(), contentsMouseMoveEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), and TrapperView().

bool TrapperView::last_click_changed_selection [protected]

Definition at line 322 of file trapperview.h.

Referenced by contentsContextMenuEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), and TrapperView().

db_recno_t TrapperView::last_selected_recno [protected]

Definition at line 323 of file trapperview.h.

Referenced by contentsMousePressEvent(), and contentsMouseReleaseEvent().

QPoint TrapperView::curr_mouse_pos [protected]

Definition at line 324 of file trapperview.h.

Referenced by contentsMouseMoveEvent().

TR_PIX TrapperView::y_delta [protected]

Definition at line 325 of file trapperview.h.

Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), and drawContents_helper().

TR_PIX TrapperView::y_delta_previous [protected]

Definition at line 326 of file trapperview.h.

Referenced by contentsMouseMoveEvent(), and contentsMousePressEvent().

TR_DNA TrapperView::last_move_x [protected]

Definition at line 328 of file trapperview.h.

Referenced by clearLastMove(), moveData(), and undo().

TR_DNA TrapperView::last_move_y [protected]

Definition at line 329 of file trapperview.h.

Referenced by clearLastMove(), moveData(), and undo().

bool TrapperView::time_course [protected]

Definition at line 331 of file trapperview.h.

Referenced by paintFeatures(), setViewTimeCourse(), and TrapperView().

bool TrapperView::tc_normalize [protected]

Definition at line 332 of file trapperview.h.

Referenced by paintFeatures(), setNormalizeTimeCourse(), and TrapperView().

int TrapperView::read_cluster_min_num [protected]

Definition at line 334 of file trapperview.h.

Referenced by scrollToNextCluster(), setClusterMinNum(), and TrapperView().

TR_DNA TrapperView::read_cluster_window [protected]

Definition at line 335 of file trapperview.h.

Referenced by scrollToNextCluster(), setClusterWindow(), and TrapperView().

QPixmap TrapperView::dragPixmap [private]

Definition at line 339 of file trapperview.h.

Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), and drawContents_helper().

QBitmap TrapperView::dragBitmap [private]

Definition at line 340 of file trapperview.h.

Referenced by contentsMousePressEvent().

QPainter TrapperView::p3 [private]

Definition at line 341 of file trapperview.h.

Referenced by contentsMousePressEvent().

QPoint TrapperView::mousePressedPoint [private]

Definition at line 342 of file trapperview.h.

Referenced by contentsDropEvent(), contentsMouseMoveEvent(), contentsMousePressEvent(), drawContents_helper(), mousePressedCol(), mousePressedRow(), and slotScrollToMouse().

QPoint TrapperView::dragWindowPoint [private]

Definition at line 343 of file trapperview.h.

Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), and drawContents_helper().

QRect* TrapperView::rubber_band [private]

Definition at line 344 of file trapperview.h.

Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), drawContents_helper(), and TrapperView().

bool TrapperView::ctrl [private]

Definition at line 345 of file trapperview.h.

Referenced by contentsMousePressEvent(), selectCols(), and selectRows().

QPoint TrapperView::RubberStart [private]

Definition at line 348 of file trapperview.h.

Referenced by contentsMousePressEvent(), contentsMouseReleaseEvent(), and drawRubber().

QPoint TrapperView::RubberEnd [private]

Definition at line 348 of file trapperview.h.

Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), contentsMouseReleaseEvent(), and drawRubber().

bool TrapperView::RubberOn [private]

Definition at line 349 of file trapperview.h.

Referenced by contentsMouseMoveEvent(), contentsMousePressEvent(), and contentsMouseReleaseEvent().

QPoint TrapperView::oldMovePoint [private]

Definition at line 350 of file trapperview.h.

Referenced by drawContents_helper().

bool TrapperView::moveOn [private]

Definition at line 351 of file trapperview.h.

Referenced by contentsMousePressEvent(), contentsMouseReleaseEvent(), and drawContents_helper().

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

• trapperview.h
• trapperview.cpp

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