trapper: trapperview.cpp Source File

00001 /*******************************************************************************
00002  *                                                                             *
00003  *   Copyright (C) 2003  Erik Sjolund,  (<html>Erik Sj&ouml;lund</html>)       *
00004  *                       Center for Genomics and Bioinformatics,               *
00005  *                       Karolinska Institutet,                                *
00006  *                       Stockholm,                                            *
00007  *                       Sweden                                                *
00008  *                                                                             *
00009  *  Author: Erik Sjolund                                                       *
00010  *  Email: erik.sjolund@adivo.se                                               *
00011  *                                                                             *
00012  *******************************************************************************
00013  */
00014 
00015 // include files for Qt
00016 #include <qprinter.h>
00017 #include <qinputdialog.h>
00018 #include <qlineedit.h>
00019 #include <qstring.h>
00020 #include <qcstring.h>
00021 #include <qvaluelist.h>
00022 #include <qwidget.h>
00023 #include <qdragobject.h>
00024 #include <qclipboard.h>
00025 #include <qapplication.h>
00026 
00027 #include <qpopupmenu.h>
00028 #include <qlabel.h>
00029 #include "trapperconf.h"
00030 #include <qcursor.h>
00031 // application specific includes
00032 #include "trapperview.h"
00033 #include "trapperdoc.h"
00034 
00035 #include "generalmaker.h"
00036 
00037 #include "featuregui.h"
00038 #include "readdata.h"
00039 
00040 #include "viewmode.h"
00041 #include <string>
00042 #include <iostream>
00043 
00044 #include "algomaker.h"
00045 #include "algo.h"
00046 
00047 #include <algorithm>
00048 #include <cstdlib>
00049 #include <vector>
00050 #include "readsinrect.h"
00051 #include <sstream>
00052 #include "destroyer.h"
00053 
00054 using namespace std;
00055 
00056 
00057 /** \brief drag object representing selected reads. Is created when a drag in TrapperView is initiated. */
00058 
00059 class ReadDrag : public QStoredDrag
00060 {
00061 public:
00062   ReadDrag( QPixmap & pixmap, QPoint & hotspot, QWidget * w ) : QStoredDrag("min_mime_type", w) {
00063     setPixmap( pixmap, hotspot );
00064 
00065   } 
00066   ReadDrag( QWidget* w ) : QStoredDrag("min_mime_type", w) { } 
00067   ~ReadDrag(){}
00068   
00069 };
00070 
00071 TrapperView::TrapperView(TrapperDoc* pDoc, QWidget *parent, const char* name, QString _viewMode )
00072   : QScrollView(parent, name,/** wflags**/ WResizeNoErase|WStaticContents|WDestructiveClose/*|WNoAutoErase*/), doc( pDoc )
00073 {
00074 //   cerr << "in TrapperView::TrapperView" << endl;
00075 //   cerr<<"doc: "<<doc<<endl;
00076   viewport()->setAcceptDrops( true );
00077   setDragAutoScroll( true );
00078   allow_dragging = true;
00079   dragging = false;
00080   moving = false;
00081   rubber_band = 0;
00082   last_click_selected_read = false;
00083   last_click_changed_selection = false;
00084   
00085   
00086   if ( _viewMode.isNull() )
00087     {
00088       _viewMode = "closeup";
00089     }
00090 
00091   viewModes = new ViewModes( _viewMode, doc );
00092   
00093   //Ugly business here...
00094   list<string> type_list = GeneralMaker::listRegistered();
00095   for( list<string>::iterator it = type_list.begin(); it != type_list.end(); ++it ) {
00096     zoom_cutoff[ *it ] = 0;
00097   }
00098   zoom_cutoff["DnaStrData"] = 4;
00099   zoom_cutoff["QualityData"] = 4;
00100   zoom_cutoff["ChromatData"] = 8;
00101 
00102 
00103 //   globalRows = 1000;
00104 //   globalBases = 50000;
00105   globalRows = 50;
00106   globalBases = 2000;
00107 //   rowheight = 20;
00108 //   basewidth = 10;
00109   rowheight = 5;
00110   basewidth = 1;
00111   magnifyX = magnifyY = 1;
00112   zoomfactor = 2;
00113   spaceBetweenRows = 0;
00114   center_point = 0;
00115   
00116   fitContentsizeToData();
00117   
00118 
00119   viewport()->setPaletteBackgroundColor(white);
00120   viewport()->setBackgroundMode( Qt::FixedColor );
00121   setCaption( "yes" );
00122   viewport()->setMouseTracking(TRUE);
00123 }
00124 
00125 
00126 TrapperView::~TrapperView()
00127 {
00128  
00129   if ( viewModes ) {
00130     delete viewModes;
00131     viewModes = NULL;
00132   }
00133 }
00134 
00135 void TrapperView::fitContentsizeToData()
00136 {
00137   Database::SecondaryIterator<ReadData>* end_it = new Database::SecondaryIterator<ReadData>( "end", doc, "ReadData" );
00138   int ret_end = end_it->last();
00139   Database::SecondaryIterator<ReadData>* row_it = new Database::SecondaryIterator<ReadData>( "pos", doc, "ReadData" );
00140   int ret_row = row_it->last();
00141   ReadData* r_end = (ret_end != DB_NOTFOUND) ? end_it->answer() : 0;
00142   ReadData* r_row = (ret_row != DB_NOTFOUND) ? row_it->answer() : 0;
00143   if ( r_end ) {
00144     
00145     globalBases = r_end->endPos() + 50;    
00146   }
00147   if ( r_row ) {
00148     
00149     globalRows = r_row->row() + 500;
00150   }
00151   
00152   delete end_it;
00153   delete row_it;
00154   
00155   resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY);
00156  
00157 }
00158 
00159 QString TrapperView::mode()
00160 {
00161     return viewModes->currentViewMode()->name();
00162 }
00163 
00164 TrapperDoc *TrapperView::getDocument() const
00165 {
00166     return doc;
00167 }
00168 
00169 void TrapperView::update(TrapperView* pSender)
00170 {
00171     if(pSender != this)
00172         repaint();
00173 }
00174 
00175 void TrapperView::print(QPrinter *pPrinter)
00176 {
00177     if (pPrinter->setup(this))
00178     {
00179         QPainter p;
00180         p.begin(pPrinter);
00181 
00182         ///////////////////////////////
00183         // TODO: add your printing code here
00184         ///////////////////////////////
00185 
00186         p.end();
00187     }
00188 }
00189 
00190 void TrapperView::closeEvent(QCloseEvent*)
00191 {
00192     // LEAVE THIS EMPTY: THE EVENT FILTER IN THE TrapperApp CLASS TAKES CARE FOR CLOSING
00193     // QWidget closeEvent must be prevented.
00194 }
00195 
00196 void TrapperView::convertToDnaCoordinates( TR_DNA & x_dna, TR_DNA & y_dna, const TR_PIX cx, const TR_PIX cy )
00197 {
00198     x_dna = pixelCoordToDna_X(cx);
00199     y_dna = pixelCoordToDna_Y(cy);
00200     return;
00201 }
00202 
00203 TR_DNA TrapperView::pixelCoordToDna_X( TR_PIX cx )
00204 {
00205 //   if ( basewidth * magnifyX < 1 ) {
00206 //     cerr<<"basewidth: "<<basewidth<<endl;
00207 //     cerr<<"basewidth * magnifyX: "<<basewidth * magnifyX<<endl;
00208 //   }
00209   
00210 
00211   return cx / ( basewidth * magnifyX );
00212 }
00213 
00214 TR_DNA TrapperView::pixelCoordToDna_Y( TR_PIX cy )
00215 {
00216   return cy / ( rowheight * magnifyY );
00217 }
00218 
00219 void TrapperView::convertToPixelCoordinates( TR_PIX & x_pix, TR_PIX & y_pix, TR_DNA x_dna, TR_DNA y_dna )
00220 {
00221     x_pix = dnaCoordToPixel_X(x_dna);
00222     y_pix = dnaCoordToPixel_Y(y_dna);
00223     return;
00224 }
00225 
00226 TR_PIX TrapperView::dnaCoordToPixel_X( TR_DNA x_dna )
00227 {
00228 //   if ( x_dna * basewidth * magnifyX < 1 ) {
00229 //     cerr<<"x_dna: "<<x_dna<<endl;
00230 //     cerr<<"basewidth: "<<basewidth<<endl;
00231 //     cerr<<"x_dna * basewidth * magnifyX: "<<x_dna * basewidth * magnifyX<<endl;
00232 //   }
00233   
00234 
00235   return x_dna * basewidth * magnifyX;
00236 }
00237 
00238 TR_PIX TrapperView::dnaCoordToPixel_Y( TR_DNA y_dna )
00239 {
00240   return y_dna * rowheight * magnifyY;
00241 }
00242 
00243 void TrapperView::paintFeatures( QPainter* p, QPainter * bitmapPainter, db_recno_t readRecno, 
00244                                  TR_PIX x_pix, TR_PIX y_pix, 
00245                                  TR_DNA x_dna_relative, TR_DNA dna_len , 
00246                                  /*TR_PIX*/double width, TR_PIX height, bool selected, int center_relative, 
00247                                  bool overlap, TR_DNA bg, TR_DNA eg )
00248 {
00249   
00250 //   cerr << "  db_recno_t = "<<readRecno
00251 //        << "  x_pix ="<< x_pix
00252 //        << "  y_pix ="<< y_pix
00253 //        << "  x_dna_relative ="<< x_dna_relative
00254 //        << "  dna_len ="<< dna_len
00255 //        << "  width =" << width
00256 //        << "  height ="<<height
00257 //        << endl;
00258   
00259   
00260   Layer * layer;
00261   
00262   p->setPen( Qt::black );
00263   
00264   /* clear away old painted stuff, by painting white in the read rectangle */
00265   QBrush brush;
00266   brush.setStyle( Qt::SolidPattern );
00267   brush.setColor( Qt::white );
00268   p->fillRect( x_pix  , y_pix ,  dna_len*width , height ,brush) ;
00269   
00270   brush.setColor( Qt::color1 );
00271   
00272   if ( bitmapPainter && selected )
00273     bitmapPainter->fillRect( x_pix  , y_pix , dna_len*width , height ,brush) ;
00274   
00275   /*  finished clearing */
00276   
00277   
00278   
00279   
00280   
00281   // we use two pixels in the height to draw the paintReadBorder
00282   y_pix += 1;
00283   height -= 2;
00284   
00285   
00286   
00287   /* starting painting features */
00288   
00289   
00290   TR_PIX heightLayerSum = 0; /* each feature knows how many percent of the total height
00291                                 it may use when painting itself. The variable heightLayerSum stores how much of the
00292                                 total height has already been painted to by other feature layers */
00293   for (layer = viewModes->currentViewMode()->layerList.first(); layer; layer =  viewModes->currentViewMode()->layerList.next() )
00294     {
00295       TR_PIX heightLayer = layer->heightInPix( height );
00296       Database::SecondaryIterator<FeatureData> * it;
00297       for (it  = layer->featureList.first(); it; it = layer->featureList.next() )
00298         {
00299           int cutoff = zoom_cutoff[ it->name() ];
00300           if ( magnifyX < cutoff || magnifyY < cutoff ) continue;
00301           
00302           it->key()->setReadRecno( readRecno );
00303           if ( it->set() == 0 ) {
00304             int ret;
00305             do {
00306 //               if ( readRecno == 654 ) {
00307 //                 cerr<<'\t'<<it->answer()->uniqueName()<<'\t'<<it->answer()->getRecno()<<endl;
00308 //               }
00309               
00310               
00311               it->answer()->gui()->paint( p, x_pix, y_pix + heightLayerSum , x_dna_relative, x_dna_relative + dna_len -1 , width, heightLayer, center_relative );
00312               
00313             } while ( (ret = it->nextdup())  == 0);
00314             
00315             
00316           }
00317           it->closeCursor();
00318         }
00319       heightLayerSum += heightLayer;
00320     }
00321   /* finished painting features */
00322   
00323   
00324   /* paint readBorder, start */
00325   
00326   /* the horisontal border is painted just outside the features,
00327      but the vertical border is painted on the features side, so the 
00328      features lose one pixel of width on the left and right sides */
00329   
00330   QPen oldpen( p->pen() ), newpen( p->pen() );
00331   
00332   if ( selected ) {
00333     newpen.setColor( Qt::red );
00334     if ( moving )
00335       newpen.setStyle( Qt::DashLine);
00336   }
00337   if ( overlap ) {
00338     newpen.setColor(Qt::green);
00339   }
00340   p->setPen(newpen);
00341   
00342   if ( magnifyX < 1.0 ) {
00343     //       cerr<<"x_pix: "<<x_pix<<endl;
00344     //       cerr<<"y_pix: "<<y_pix<<endl;
00345     //       cerr<<"dna_len: "<<dna_len<<endl;
00346     //       cerr<<"width: "<<width<<endl;
00347     //       cerr<<"dna_len * width: "<<dna_len * width<<endl;
00348     //       cerr<<"height: "<<height<<endl;
00349   }
00350   
00351   p->drawRect( x_pix  , y_pix,  dna_len*width  , height ) ;
00352 
00353   //Quality trimming
00354   brush.setStyle( Qt::Dense4Pattern );
00355   brush.setColor( Qt::white );
00356   if ( x_dna_relative < bg ) {
00357     p->fillRect( x_pix  , y_pix,  (bg - x_dna_relative)*width  , height, brush ) ;
00358   }
00359   if ( x_dna_relative + dna_len > eg ) {
00360     int goodlen = eg - x_dna_relative + 1;
00361     if ( goodlen < 0 ) goodlen = 0;
00362     p->fillRect( x_pix + goodlen*width  , y_pix, (dna_len - goodlen )*width, height, brush ) ;
00363   }
00364   
00365 
00366   
00367   p->setPen( oldpen );
00368   
00369   /* finished painting readBorder */
00370 }
00371 
00372 // void TrapperView::drawContents(QPainter* p, int cx, int cy, int cw, int ch)
00373 void TrapperView::drawContents(QPainter* p, TR_PIX cx, TR_PIX cy, TR_PIX cw, TR_PIX ch)
00374 {
00375 //   QPoint qp = viewportToContents(viewport()->rect().topLeft());
00376 //   cerr<<"qp.x(): "<<qp.x()<<endl;
00377 //   cerr<<"qp.y(): "<<qp.y()<<endl;
00378 
00379   drawContents_helper(p, NULL, cx, cy, cw, ch, 0, 0);
00380   paintGrid( p, cx, cy, cw, ch);
00381 }
00382 
00383 void TrapperView::drawContents_helper(QPainter* p,QPainter* bitmapPainter, int cx, int cy, int cw, int ch, int dx, int dy)
00384 {
00385   /* We have the window to paint in pixel coordinates, but the biological data ( the reads ) are stored
00386      in dna coordinates. The pixel coordinates are on a smaler scale than the dna coordinates, so therefore
00387      the pixel coordinates might lay a fraction of a dna coordinate. Thus we seak the minimal overlapping window 
00388      in dna coordinates. */
00389 
00390   if ( moving ) {
00391     assert( bitmapPainter == 0 );
00392     //MOVINGTEST
00393 //     p->setRasterOp(NotROP);
00394     p->setRasterOp(NotXorROP);
00395 //      p->setRasterOp(XorROP);
00396     if ( moveOn ) {
00397       p->drawPixmap(oldMovePoint, dragPixmap);
00398     }
00399     else {
00400       oldMovePoint = contentsToViewport(mousePressedPoint - dragWindowPoint);
00401       p->setRasterOp(NotXorROP);
00402       p->drawPixmap(oldMovePoint, dragPixmap);
00403       
00404     }
00405     
00406 
00407     oldMovePoint = contentsToViewport(mousePressedPoint - dragWindowPoint + QPoint(0, dnaCoordToPixel_Y(pixelCoordToDna_Y(y_delta)) ));
00408     //END MOVINGTEST
00409 //     oldMovePoint = mousePressedPoint - dragWindowPoint + QPoint(0, dnaCoordToPixel_Y(pixelCoordToDna_Y(y_delta)) );
00410     p->drawPixmap(oldMovePoint, dragPixmap);
00411     //MOVINGTEST
00412     moveOn = true;
00413     return;
00414     //END MOVINGTEST
00415   }
00416 
00417   
00418   TR_DNA x_dna, y_dna; /* the dna coordinate of upperleft corner of the overlapping dna window */
00419   TR_DNA x2_dna, y2_dna;
00420   TR_DNA h_dna, w_dna; /* representing the width and height of the overlapping dna window */
00421   
00422   convertToDnaCoordinates( x_dna, y_dna, cx, cy );
00423   convertToDnaCoordinates( x2_dna, y2_dna, cx + cw - 1, cy + ch - 1 );
00424   
00425   /* to be on the safe side that we paint on a rectangle big enough we add some on the edges.
00426      The reason comes from the fact that vertical read border is drawn up on the uttermost pixels
00427      of the feature area. */
00428    x_dna -= 10;
00429    x2_dna += 10;
00430   
00431   w_dna = x2_dna - x_dna + 1;
00432   h_dna = y2_dna - y_dna + 1;
00433   
00434   
00435   
00436   
00437   TR_PIX x_pix, y_pix; /* the pixel coordinate of upperleft corner of the overlapping dna window */
00438   convertToPixelCoordinates( x_pix, y_pix, x_dna, y_dna );
00439   
00440   TR_PIX cx_paint = x_pix + dx;
00441   TR_PIX cy_paint = y_pix + dy;
00442 
00443 
00444   
00445   readsInRect = new ReadsInRect( doc );
00446 
00447 
00448   readsInRect->setWindowCoord( x_dna, y_dna,  w_dna,h_dna );
00449 //   cerr<<"rowheight*magnifyY - spaceBetweenRows: "<<rowheight*magnifyY - spaceBetweenRows<<endl;
00450   int previous_row(-1), previous_end(-1);
00451   for ( ReadData * r = readsInRect->first(); r; r = readsInRect->next() )
00452     {
00453 //       cerr<<r->name()<<'\t'<<r->getRecno()<<endl;
00454       
00455       bool overlap(false);
00456       if ( r->row() == previous_row && (r->startPos() <= previous_end ) ) {
00457         overlap = true;
00458       }
00459       previous_row = r->row();
00460       previous_end = r->endPos();
00461       
00462       bool selected = isSelected( r->getRecno() );
00463       
00464       /* we just have to paint the part of the read that is visible in the current window.
00465          Therefore we seak max and min values 
00466           */
00467       
00468       TR_DNA x1_dna_paint = max( r->startPos(), x_dna    ) ;
00469       TR_DNA x2_dna_paint = min( r->endPos(), x_dna + w_dna - 1  ) ;
00470       
00471       TR_PIX x_pix_adjust, y_pix_adjust;
00472       convertToPixelCoordinates( x_pix_adjust, y_pix_adjust, x1_dna_paint - x_dna, r->row() - y_dna );
00473       
00474       // x_pix += cx;
00475       //            y_pix += cy;
00476       
00477       TR_DNA len = x2_dna_paint - x1_dna_paint +1 ;
00478       
00479       paintFeatures( p, bitmapPainter, r->getRecno(), 
00480                      x_pix_adjust + cx_paint , y_pix_adjust + cy_paint,  
00481                      x1_dna_paint - r->startPos(), len, 
00482                      basewidth*magnifyX, rowheight*magnifyY - spaceBetweenRows , selected, center_point - r->startPos(), 
00483                      overlap, r->beginGood(), r->endGood() );
00484 
00485     }
00486 
00487 
00488   delete readsInRect;
00489 
00490 
00491 
00492 
00493   if ( rubber_band ) {
00494     QPen oldpen( p->pen() );
00495     QPen newpen( Qt::black, 0, Qt::DotLine );
00496     
00497     p->setPen( newpen );
00498     p->drawRect( *rubber_band );
00499     p->setPen( oldpen );    
00500     
00501   }
00502   
00503 }
00504 
00505 void TrapperView::paintGrid(QPainter* p, TR_PIX cx, TR_PIX cy, TR_PIX cw, TR_PIX ch)
00506 {
00507   p->setPen( Qt::black );
00508 
00509 //   int toprow=cy/rowheight;
00510 //   int bottomrow=(cy+ch+rowheight-1)/rowheight;
00511   int local_rowheight = 100;
00512   int toprow=cy/local_rowheight;
00513   int bottomrow=(cy+ch+local_rowheight-1)/local_rowheight;
00514   int colwidth=100;
00515   int leftcol=cx/colwidth;
00516   int rightcol=(cx+cw+colwidth-1)/colwidth;
00517   for (int r=toprow; r<=bottomrow; r++) {
00518 //     int py=r*rowheight;
00519     int py=r*local_rowheight - dnaCoordToPixel_Y(1)/2;
00520     for (int c=leftcol; c<=rightcol; c++) {
00521       int px=c*colwidth + dnaCoordToPixel_X(1)/2;
00522       p->drawLine(px, py, px+2, py);
00523       
00524     }
00525   }
00526   QFont f;
00527   f.setPointSize(10);
00528   p->setFont(f);
00529   int viewport_toprow=contentsY()/local_rowheight - 2;
00530   if (viewport_toprow <0 ) viewport_toprow = 0;
00531   
00532   int viewport_bottomrow=(cy+ch+local_rowheight-1)/local_rowheight + 1;
00533   int viewport_leftcol=contentsX()/colwidth;
00534   int viewport_rightcol=(contentsX() + contentsWidth() +colwidth-1)/colwidth;
00535 
00536 
00537   for( int i = viewport_leftcol; i < viewport_rightcol; i++ ) {
00538     p->drawText( i*colwidth + dnaCoordToPixel_X(1)/2, 10, QString().setNum(pixelCoordToDna_X( i*colwidth )) );
00539   }
00540   for( int i = viewport_toprow; i < viewport_bottomrow; i++ ) {
00541     p->drawText( 0, i*local_rowheight, QString().setNum(pixelCoordToDna_Y( i*local_rowheight )) );    
00542   }
00543 
00544   bottomrow=(cy+ch+rowheight-1)/rowheight;
00545   int center_x = dnaCoordToPixel_X(center_point) + dnaCoordToPixel_X(1)/2;
00546   p->drawLine(center_x, 0, center_x, bottomrow*rowheight );
00547 }
00548 
00549 void TrapperView::moveData(TR_PIX dx, TR_PIX dy)
00550 {
00551 //     cerr<<"PLEASE NOTE: ALGO PARAMS SHOULD BE FIXED!!!"<<endl;
00552   TR_DNA col_delta, row_delta;
00553   row_delta = pixelCoordToDna_Y( dy );
00554   col_delta = pixelCoordToDna_X( dx);
00555 
00556   AlgoMoveParam param( col_delta, row_delta );
00557   
00558   runAlgo( "Move Reads", getSelectedReads(), &param );
00559 
00560   last_move_x = param.get_x_delta();
00561   last_move_y = param.get_y_delta();
00562   
00563   
00564 }
00565 
00566 void TrapperView::clearLastMove()
00567 {
00568   last_move_x = last_move_y = 0;
00569 }
00570 
00571 
00572 void TrapperView::contentsMousePressEvent(QMouseEvent* e)
00573 {
00574   QString msg = "Row: " + QString().setNum(pixelCoordToDna_Y(e->y())) + ", col: " + QString().setNum(pixelCoordToDna_X(e->x()));
00575   sendMsg( msg );
00576 
00577   y_delta = 0;
00578   y_delta_previous = 0;
00579   
00580   bool ctrlclick = Qt::ControlButton & e->state();
00581   bool leftbutton = Qt::LeftButton & e->stateAfter();
00582 
00583 //   if ( ctrlclick )
00584 //     cerr<<"ctrlclick!!!!!!!!!!!!!! "<<endl;
00585   
00586   
00587   mousePressedPoint.setX( e->x() );
00588   mousePressedPoint.setY( e->y() );
00589 
00590   
00591   //RUBBERTEST
00592   RubberStart=contentsToViewport(e->pos());
00593   RubberEnd = RubberStart;
00594   RubberOn=FALSE;
00595   //END RUBBERTEST
00596 
00597   //MOVINGTEST
00598   moveOn = false;
00599   //END MOVINGTEST
00600 
00601   TR_DNA x_dna, y_dna;
00602   convertToDnaCoordinates( x_dna, y_dna, e->x(), e->y() );
00603   
00604   readsInRect = new ReadsInRect( doc );
00605 //   readsInRect->setWindowCoord( x_dna, y_dna, 1, 1 );  /* a rectangle with dimension 1x1 */
00606   readsInRect->setWindowCoord( x_dna, y_dna, 3, 3 );  /* a rectangle with dimension 3x3 */
00607   ReadData * r = readsInRect->first(); 
00608   if ( r ) {//hit read
00609     if ( ctrlclick ) {
00610       if ( isSelected( r->getRecno() ) ) {
00611         select( r->getRecno(), false );
00612         last_click_selected_read = false;
00613         last_click_changed_selection = true;
00614       }
00615       else {
00616         select( r->getRecno(), true);
00617         last_click_selected_read = true;
00618         last_selected_recno = r->getRecno();
00619         last_click_changed_selection = true;
00620       }
00621     }//end ctrlclick
00622     else {//no ctrlclick
00623       if ( isSelected( r->getRecno() ) ) {
00624         last_click_selected_read = true;
00625         last_selected_recno = r->getRecno();
00626         last_click_changed_selection = false;
00627       }
00628       else {
00629         clearSelected();
00630         select( r->getRecno(), true);       
00631         last_click_selected_read = true;        
00632         last_selected_recno = r->getRecno();
00633         last_click_changed_selection = true;
00634       }
00635       
00636     }//end no ctrlclick
00637     if ( last_click_selected_read )
00638       dragging = TRUE; 
00639   }// end hit read
00640   else {//didn't hit read
00641 //     if ( rubber_band != 0 ) {
00642 //       delete rubber_band;
00643 //     }
00644 //     rubber_band = new QRect( mousePressedPoint, mousePressedPoint );
00645     if ( ctrlclick ) {
00646       last_click_selected_read = false;
00647       last_click_changed_selection = false;
00648     }//end ctrlclick
00649     else {//no ctrlclick
00650       last_click_selected_read = false;
00651       if ( selectedReads.size() > 0 )
00652         last_click_changed_selection = true;
00653         
00654       clearSelected();
00655 
00656       //"Rubber band"
00657 //       if ( rubber_band != 0 ) {
00658 //         delete rubber_band;
00659 //       }
00660 //       if ( leftbutton )
00661 //         rubber_band = new QRect( mousePressedPoint, mousePressedPoint );
00662       
00663       
00664     }//end no ctrlclick
00665     if ( rubber_band != 0 ) {
00666       delete rubber_band;
00667     }
00668     if (leftbutton && !last_click_selected_read) {
00669       moving = false;
00670       rubber_band = new QRect( mousePressedPoint, mousePressedPoint );
00671     }
00672     
00673   }//end didn't hit read
00674 
00675 //   updateContents();//Removed this because of visual bug...
00676   delete readsInRect;
00677   
00678   // From here on: about Start a drag and painting
00679   {
00680     dragWindowPoint.setX( size().width()      );
00681     dragWindowPoint.setY( size().height() );
00682     QRect re( mousePressedPoint - dragWindowPoint, mousePressedPoint + dragWindowPoint );
00683     
00684     
00685     dragPixmap.resize( re.size() );
00686     QPainter p2;
00687     p2.begin(&dragPixmap, this);
00688     dragBitmap.resize( re.size()  );
00689     p3.begin(&dragBitmap, this);
00690     QBrush brush;
00691     brush.setStyle( Qt::SolidPattern );
00692     brush.setColor( Qt::white );
00693     p2.fillRect( 0  , 0 , re.width() , re.height() ,brush) ;
00694     brush.setColor( Qt::color0 );
00695     
00696     p3.fillRect( 0  , 0 , re.width() , re.height() ,brush) ;
00697     
00698     QPoint tl = re.topLeft() ;
00699     QPoint br = re.bottomRight() ;
00700     
00701     drawContents_helper(&p2, &p3, tl.x(), tl.y(), br.x() - tl.x() + 1, br.y() - tl.y() + 1, 
00702                         - ( mousePressedPoint.x() - dragWindowPoint.x() ),  - ( mousePressedPoint.y() - dragWindowPoint.y() ));
00703     
00704     //Test:
00705 //     QPen a_pen;
00706 //     p2.setPen(a_pen);
00707 //     p2.drawRect(dragPixmap.rect());
00708 //     a_pen.setColor(Qt::color1);
00709 //     p3.setPen(a_pen);
00710 //     p3.drawRect(dragPixmap.rect());
00711     //End test
00712     dragPixmap.setMask(dragBitmap);
00713 
00714     p2.end();
00715     p3.end();
00716   }
00717 }
00718 
00719 
00720 void TrapperView::contentsMouseMoveEvent(QMouseEvent* e)
00721 {
00722   QString msg = "Row: " + QString().setNum(pixelCoordToDna_Y(e->y())) + ", col: " + QString().setNum(pixelCoordToDna_X(e->x()));
00723   sendMsg( msg );
00724 
00725   bool nobutton = Qt::NoButton & e->state();
00726 
00727   if ( nobutton ) {
00728     moving = false;
00729     return;
00730   }
00731   
00732 
00733   if ( allow_dragging && dragging ) {
00734 //   if ( dragging ) {
00735 //     cerr<<"Dragging..."<<endl;
00736 
00737     ReadDrag *d = new ReadDrag( dragPixmap, dragWindowPoint, this );
00738 //     QCString ar("hej");
00739     QByteArray ar;
00740     QDataStream data_stream(ar, IO_WriteOnly);
00741     writeSelected(data_stream);
00742 
00743     d->setEncodedData(ar);
00744     d->dragCopy(); // do NOT delete d.
00745     dragging = FALSE;
00746     moving = false;
00747     last_click_selected_read = false;
00748 //     cerr<<"Stopped dragging"<<endl;
00749   }
00750   else if ( last_click_selected_read ) {
00751 //   else if ( !selectedReads.empty() ) {
00752     //"Normal" moving
00753     moving = true;
00754     
00755     curr_mouse_pos = e->pos();//Don't really need this??
00756 //     y_delta = pixelCoordToDna_Y( (curr_mouse_pos - mousePressedPoint).y() );
00757     y_delta = (curr_mouse_pos - mousePressedPoint).y();
00758 
00759     if ( pixelCoordToDna_Y( y_delta) == pixelCoordToDna_Y( y_delta_previous ) ) {
00760 //       moving = false;
00761       return;
00762     }
00763     
00764     y_delta_previous = y_delta;
00765 
00766     //MOVINGTEST
00767 
00768     QPainter p(viewport());
00769     drawContents_helper(&p, 0,0,0,0,0,0,0);
00770     return;
00771     //END MOVINGTEST
00772     
00773     updateContents();
00774   }
00775   else if ( rubber_band != 0 ) {
00776 
00777     //RUBBERTEST
00778     QPainter p(viewport());
00779     p.setPen(QColor(255,255,255));
00780     p.setRasterOp(NotROP);
00781     if(RubberOn) drawRubber(&p);
00782     RubberEnd= contentsToViewport(e->pos());
00783     drawRubber(&p);
00784     RubberOn=TRUE;
00785     return;
00786     //END RUBBERTEST
00787     
00788     curr_mouse_pos = e->pos();
00789     
00790     QRect oldband = rubber_band->normalize();
00791 
00792     rubber_band->setSize( QSize( curr_mouse_pos.x() - mousePressedPoint.x(),
00793                                  curr_mouse_pos.y() - mousePressedPoint.y() ) );
00794     
00795 //     updateContents();
00796     QPoint margin( 1, 1 );
00797     QRect norm = rubber_band->normalize();
00798     
00799     updateContents( QRect( norm.topLeft() - margin, norm.bottomRight() + margin ).unite( QRect(oldband.topLeft() - margin, oldband.bottomRight() + margin ) ) );
00800   }
00801   
00802 }
00803 
00804 void TrapperView::contentsMouseReleaseEvent(QMouseEvent* e)
00805 {
00806   dragging = false;
00807   //Maybe dragging code here? NO!
00808   
00809   if ( moving ) {
00810     //Moving stuff...
00811     moveData(0, y_delta);
00812 
00813     
00814 
00815     //MOVINGTEST
00816     if(moveOn) 
00817       {
00818         updateContents();
00819         moveOn=FALSE;
00820       }    
00821     //END MOVINGTEST
00822 
00823     moving = false;
00824   }
00825   else { //not moving
00826     
00827     bool ctrlclick = Qt::ControlButton & e->state();
00828 
00829     if ( !ctrlclick && last_click_selected_read ) {
00830       clearSelected();
00831       select( last_selected_recno, true );
00832       last_click_changed_selection = true;
00833 //       updateContents();
00834     }
00835     if ( last_click_changed_selection ) {
00836       updateContents();
00837     }
00838     
00839 
00840     if ( rubber_band != 0 ) {
00841       
00842       readsInRect = new ReadsInRect( doc );
00843       
00844       TR_DNA x_dna, y_dna, w_dna, h_dna, x2_dna, y2_dna;
00845       TR_PIX x_pix, y_pix, w_pix, h_pix;
00846       
00847       QRect norm = rubber_band->normalize();
00848       //RUBBERTEST
00849       RubberStart = viewportToContents( RubberStart );
00850       RubberEnd = viewportToContents( RubberEnd );
00851       
00852       norm = QRect(
00853                 RubberStart.x(),
00854                 RubberStart.y(),
00855                 RubberEnd.x()-RubberStart.x(),
00856                 RubberEnd.y()-RubberStart.y()
00857                 ).normalize();
00858       //END RUBBERTEST
00859 
00860       rubber_band->setTopLeft( norm.topLeft() );      
00861       rubber_band->setBottomRight( norm.bottomRight() );      
00862 
00863       rubber_band->rect( &x_pix, &y_pix, &w_pix, &h_pix);
00864       convertToDnaCoordinates( x_dna, y_dna, x_pix, y_pix );
00865       convertToDnaCoordinates( x2_dna, y2_dna, x_pix + w_pix, y_pix + h_pix);
00866       
00867       w_dna = x2_dna - x_dna;
00868       h_dna = y2_dna - y_dna;
00869 
00870 
00871       readsInRect->setWindowCoord( x_dna, y_dna,  w_dna,h_dna );
00872       if ( !ctrlclick) 
00873         clearSelected();
00874       
00875       for ( ReadData * r = readsInRect->first(); r; r = readsInRect->next() ) {
00876         select( r->getRecno(), true);
00877       }
00878       //RUBBERTEST
00879       QPainter p(viewport());
00880       p.setPen(QColor(255,255,255));
00881       p.setRasterOp(NotROP);
00882       if(RubberOn) 
00883         {
00884           drawRubber(&p);
00885           RubberOn=FALSE;
00886         }
00887       else
00888         {
00889           RubberEnd=RubberStart;
00890         }
00891       //END RUBBERTEST
00892       
00893       delete rubber_band;
00894       rubber_band = 0;
00895       delete readsInRect;
00896       updateContents();
00897     }
00898 
00899   }
00900   moving = false;
00901   dragging = false;
00902   last_click_changed_selection = false;
00903   last_click_selected_read = false;
00904   
00905 }
00906 
00907 void TrapperView::contentsContextMenuEvent( QContextMenuEvent * e )
00908 {
00909   if ( last_click_changed_selection ) {
00910     updateContents();
00911   }
00912   moving = false;
00913   last_click_selected_read = false;
00914   last_click_changed_selection = false;
00915   
00916   QPopupMenu* contextMenu = new QPopupMenu( this );
00917   Q_CHECK_PTR( contextMenu );
00918   QLabel *caption = new QLabel( "<font color=darkblue><u><b>"
00919                                 "Context Menu</b></u></font>", this );
00920   caption->setAlignment( Qt::AlignCenter );
00921   contextMenu->insertItem( caption );
00922   
00923 
00924   
00925 
00926   //Algo stuff
00927   algoMenu = new QPopupMenu( this );
00928   Q_CHECK_PTR( algoMenu );
00929   list<string> algos = AlgoMaker::algosRegistered();
00930   list<string>::iterator stIt;
00931   
00932   for (stIt = algos.begin() ; stIt != algos.end(); ++stIt )
00933     {
00934       algoMenu->insertItem (  stIt->c_str()  );
00935     }
00936   connect( algoMenu, SIGNAL( activated( int ) ),
00937            this, SLOT( slotStartAlgo( int ) ) );
00938   contextMenu->insertItem( "&Operations", algoMenu );
00939   
00940 
00941 
00942   //Info stuff
00943   infoMenu = new QPopupMenu(this);
00944 
00945   vector<list<string> > infos = getInfo( e->pos() );
00946   QPtrList<QPopupMenu> infolist;
00947   infolist.setAutoDelete( true );
00948   
00949   for( size_t i = 0; i < infos.size(); i++ ) {
00950     stIt = infos[i].begin();
00951     if ( stIt == infos[i].end() ) continue;
00952     infolist.append(new QPopupMenu(this));
00953     ++stIt;
00954 
00955     for ( ; stIt != infos[i].end(); ++stIt ) {
00956 //       infoMenu->insertItem (  stIt->c_str()  );
00957 
00958       infolist.last()->insertItem (  stIt->c_str()  );
00959     }
00960 
00961     
00962     infoMenu->insertItem(infos[i].begin()->c_str(), infolist.last());
00963   }
00964 
00965   //No connecting here, 'cause only info...
00966   contextMenu->insertItem( "&Info", infoMenu );
00967 
00968 
00969   //Viewmode stuff
00970   switchViewMenu = new QPopupMenu( this );
00971   Q_CHECK_PTR( switchViewMenu );
00972   TrapperConf * conf = TrapperConf::instance();
00973   QStringList names = conf->viewModeNames();
00974   
00975   QStringList::Iterator it = names.begin();
00976   for ( ; it != names.end(); ++it )
00977     {
00978       switchViewMenu->insertItem ( *it );
00979     }
00980   connect( switchViewMenu, SIGNAL( activated( int ) ),
00981            this, SLOT( slotSwitchToMode( int ) ) );
00982   contextMenu->insertItem( "&Switch to viewmode", switchViewMenu );
00983 
00984 
00985   contextMenu->insertSeparator();
00986   contextMenu->insertItem("Set chromat center", this, SLOT(slotSetCenter()));
00987   contextMenu->insertItem("Clear chromat center", this, SLOT(slotClearCenter()));
00988 
00989   contextMenu->insertSeparator();
00990   contextMenu->insertItem("Scroll Here", this, SLOT(slotScrollToMouse()) );
00991   contextMenu->insertItem("Scroll to pos", this, SLOT(slotScrollToPos()) );
00992 
00993   contextMenu->exec( QCursor::pos() );
00994   delete contextMenu;
00995   delete switchViewMenu;//Previous memory leak??
00996   delete algoMenu;
00997   delete infoMenu;
00998 }
00999 
01000 void TrapperView::slotSwitchToMode( int i )
01001 {
01002     QString viewMode =  switchViewMenu->text(i);
01003     viewModes->setMode( viewMode );
01004     doc->changedViewList();
01005     updateContents();
01006 }
01007 
01008 void TrapperView::slotStartAlgo( int i )
01009 {
01010   QString algoStr =  algoMenu->text(i);
01011   
01012   /* Right now the Algo constructor takes a list of db_recno_t.
01013      We create such a list from the keys in the map, selectedReads.
01014      
01015      Todo: To make the code prettier: is it be possible to
01016      pass the map iterators to the constructor of the list?
01017      Instead of our manual forloop.
01018   */
01019   
01020   
01021   //     std::list< db_recno_t > alist = getSelectedReads();
01022   //     Algo * algo = AlgoMaker::newAlgo( algoStr.ascii(), doc , alist );
01023   //     doc->addAlgorithm( algo );
01024   //     algo->start();
01025   //     doc->removeAlgorithm( algo );//POSSIBLE MEMORY LEAK!!!!!!!!!
01026   //     updateContents();
01027   
01028   ViewParam param(this);
01029 
01030   updateContents();
01031   runAlgo( algoStr.ascii(), getSelectedReads(), &param );
01032   //To be on the safe side...
01033   clearLastMove();
01034 }
01035 
01036 void TrapperView::slotScrollToMouse()
01037 {
01038   scrollTo(mousePressedPoint.x(), mousePressedPoint.y());
01039 
01040 }
01041 
01042 void TrapperView::slotScrollToPos()
01043 {
01044   bool ok;
01045   int res = QInputDialog::getInteger(
01046                                      "Scroll to position", "Enter row:", 0, 0, numeric_limits<int>::max(), 1,
01047                                      &ok, 0 );
01048   
01049   if ( ok ) {
01050     // user entered something and pressed OK
01051   } else {
01052     // user pressed Cancel
01053     return;
01054   }
01055   TR_PIX y = dnaCoordToPixel_Y(res);
01056 
01057   res = QInputDialog::getInteger(
01058                                  "Scroll to position", "Enter column:", 0, 0, numeric_limits<int>::max(), 1,
01059                                  &ok, 0 );
01060   
01061   if ( ok ) {
01062     // user entered something and pressed OK
01063   } else {
01064     // user pressed Cancel
01065     return;
01066   }
01067 
01068   TR_PIX x = dnaCoordToPixel_X(res);
01069   
01070   scrollTo(x, y);
01071 
01072 }
01073 
01074 void TrapperView::slotSetCenter()
01075 {
01076   center_point = mousePressedCol();
01077 //   cerr<<center_point<<endl;
01078   updateContents();
01079 }
01080 
01081 void TrapperView::slotClearCenter()
01082 {
01083   center_point = 0;
01084   updateContents();
01085 }
01086 
01087 void TrapperView::findRead()
01088 {
01089   bool ok;
01090   QString res = QInputDialog::getText ( "Find read", "Enter read name:", QLineEdit::Normal, QString::null, &ok );
01091   
01092 
01093   if ( ok ) {
01094     // user entered something and pressed OK
01095   } else {
01096     // user pressed Cancel
01097     return;
01098   }
01099 
01100   Database::SecondaryIterator<ReadData> name_it( "name", doc, "ReadData" );
01101   name_it.key()->setName( res );
01102   if ( name_it.set() != 0 ) {
01103     cerr<<"Error, couldn't find "<<res<<" in db"<<endl;
01104     return;
01105   }
01106   clearSelected();
01107   select(name_it.answer()->getRecno(), true);
01108   TR_PIX y = dnaCoordToPixel_Y(name_it.answer()->row());
01109   TR_PIX x = dnaCoordToPixel_X(name_it.answer()->startPos());
01110   scrollTo(x, y);
01111 
01112 }
01113 
01114 
01115 std::set<db_recno_t>& TrapperView::getSelectedReads()
01116 {
01117   return selectedReads;
01118 }
01119 
01120 void TrapperView::select( db_recno_t recno, bool status )
01121 {
01122   RecnoMap::iterator pos;
01123   if ( status == true && !isSelected(recno) ) {
01124     selectedReads.insert( recno );
01125     clearLastMove();
01126   }
01127   else if ( ( pos = selectedReads.find( recno )) != selectedReads.end() ) {
01128     selectedReads.erase( pos );
01129     clearLastMove();
01130   }
01131   
01132 }
01133 
01134 bool TrapperView::isSelected( db_recno_t recno )
01135 {
01136   return selectedReads.find( recno ) != selectedReads.end();
01137 }
01138 
01139 void TrapperView::clearSelected()
01140 {
01141   selectedReads.clear();
01142   clearLastMove();
01143 }
01144 
01145 std::vector<std::list<std::string > > TrapperView::getInfo( const QPoint& pos )
01146 {
01147   vector<list<string> > result;
01148   list<string> readResult;
01149   list<string> featResult;
01150   list<string> generalResult;
01151   
01152   //Recalc pos
01153   TR_DNA row = pixelCoordToDna_Y( pos.y() );
01154   TR_DNA col = pixelCoordToDna_X( pos.x() );
01155 
01156   readsInRect = new ReadsInRect( doc );
01157   readsInRect->setWindowCoord( col, row, 1, 1 );  /* a rectangle with dimension 1x1 */
01158 //   readsInRect->setWindowCoord( col, row, 3, 3 );  /* a rectangle with dimension 3x3 */
01159   ReadData * r = readsInRect->first();
01160 
01161   ostringstream os;
01162   if ( r ) {
01163     list<string> types = GeneralMaker::listRegistered();
01164     readResult.push_back( "Read info" );
01165     readResult.push_back( r->name() );
01166     
01167     os<<"Strand: "<<r->strand();
01168     readResult.push_back( r->strand() );
01169     os.str("");
01170     os<<"Mate: "<<r->mate() << ' ' << r->mateLength();
01171     readResult.push_back( os.str() );
01172     os.str("");
01173     os<<"Begin good: "<<r->beginGood();
01174     readResult.push_back( os.str() );
01175     os.str("");
01176     os<<"End good: "<<r->endGood();
01177     readResult.push_back( os.str() );
01178     os.str("");
01179     os<<"Read index: "<<col - r->startPos();
01180     readResult.push_back( os.str() );
01181     
01182 
01183     featResult.push_back( "Feature info" );
01184     
01185     //Feature stuff
01186     for( list<string>::iterator it = types.begin(); it != types.end(); ++it ) {
01187       GeneralData * data = GeneralMaker::newData( *it );
01188       FeatureData * fdata = dynamic_cast<FeatureData *>( data );
01189       // fdata is just used to see that the registered string is corresponding to
01190       // a feature
01191       if ( fdata ) {
01192         Database::SecondaryIterator<FeatureData> featIt( "readRecno", doc, it->c_str() );
01193         
01194         featIt.key()->setReadRecno( r->getRecno() );
01195         
01196         string featInfo;
01197         
01198         if ( featIt.set() == 0 ) {
01199 
01200           int ret;
01201           do {
01202             
01203             featInfo = featIt.answer()->info()->getPosInfo( col - r->startPos() );
01204             if ( !featInfo.empty() ) {
01205               featResult.push_back( featInfo );
01206             }
01207             featInfo = featIt.answer()->info()->getRangeInfo( 0, r->endPos() - r->startPos() );
01208             if ( !featInfo.empty() ) {
01209               readResult.push_back( featInfo );
01210             }
01211             
01212             
01213           } while ( (ret = featIt.nextdup())  == 0);
01214         }
01215       }
01216       
01217       delete data;
01218       
01219     }
01220 
01221     
01222   }
01223   generalResult.push_back("General info");
01224   os.str("");
01225   os<<"Row: "<<row<<", Col: "<<col;
01226   generalResult.push_back( os.str() );
01227   
01228   result.push_back(readResult);
01229   result.push_back(featResult);
01230   result.push_back(generalResult);
01231   
01232   delete readsInRect;
01233   return result;
01234 }
01235 
01236 void TrapperView::runAlgo( const std::string& AlgoType, std::set< db_recno_t >& recnoList, AlgoParam* param )
01237 {
01238   
01239   if (selectedReads.size() > 0 ) {
01240     
01241     Algo * algo = AlgoMaker::newAlgo( AlgoType, doc , recnoList, param );
01242     doc->addAlgorithm( algo );
01243     algo->start();
01244     doc->removeAlgorithm( algo );//POSSIBLE MEMORY LEAK!!!!!!!!!
01245     delete algo;//To avoid memory leak...
01246     
01247     updateContents();
01248     fitContentsizeToData();
01249   }
01250   
01251 }
01252 
01253 void TrapperView::zoomIn()
01254 {
01255   zoomInX();
01256   zoomInY();
01257 }
01258 
01259 void TrapperView::zoomInX()
01260 {
01261   if ( magnifyX >= 128 )
01262     return;
01263   
01264   magnifyX *= zoomfactor;
01265 //   doZoom();
01266   
01267   QPoint p = viewportToContents(viewport()->rect().topLeft());
01268 //   if ( globalBases * magnifyX * basewidth < 1 ) {
01269 //     cerr<<"globalBases: "<<globalBases<<endl;
01270 //     cerr<<"globalBases * magnifyX * basewidth: "<<globalBases * magnifyX * basewidth<<endl;
01271 //   }
01272 
01273   resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY);
01274   setContentsPos(p.x()*zoomfactor, p.y());
01275 
01276   updateContents();
01277 
01278 }
01279 
01280 void TrapperView::zoomInY()
01281 {
01282   if ( magnifyY >= 128 )
01283     return;
01284   magnifyY *= zoomfactor;
01285 //   doZoom();
01286 
01287   QPoint p = viewportToContents(viewport()->rect().topLeft());
01288   
01289   resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY);
01290   setContentsPos(p.x(), p.y()*zoomfactor);
01291 
01292   updateContents();
01293 }
01294 
01295 void TrapperView::zoomOut()
01296 {
01297   zoomOutX();
01298   zoomOutY();
01299 }
01300 
01301 void TrapperView::zoomOutX()
01302 {
01303 //   if ( magnifyX <= 1 )
01304   if ( magnifyX <= 0.25 )
01305     {
01306       return;
01307     }
01308   magnifyX /= zoomfactor;
01309 //   doZoom();
01310 
01311   QPoint p = viewportToContents(viewport()->rect().topLeft());
01312 
01313 //   if ( globalBases * magnifyX * basewidth < 1 ) {
01314 //     cerr<<"globalBases: "<<globalBases<<endl;
01315 //     cerr<<"globalBases * magnifyX * basewidth: "<<globalBases * magnifyX * basewidth<<endl;
01316 //   }
01317   resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY);
01318   setContentsPos(p.x()/zoomfactor, p.y());
01319 
01320   updateContents();
01321 }
01322 
01323 void TrapperView::zoomOutY()
01324 {
01325   if ( magnifyY <= 1 )
01326     {
01327       return;
01328     }
01329   magnifyY /= zoomfactor;
01330 //   doZoom();
01331 
01332   QPoint p = viewportToContents(viewport()->rect().topLeft());
01333   resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY);
01334   setContentsPos(p.x(), p.y()/zoomfactor);
01335 
01336   updateContents();
01337 }
01338 
01339 void TrapperView::doZoom()
01340 {
01341 //   QPoint p = viewportToContents(viewport()->rect().topLeft());
01342 
01343 //   if ( globalBases * magnifyX * basewidth < 1 ) {
01344 //     cerr<<"globalBases: "<<globalBases<<endl;
01345 //     cerr<<"globalBases * magnifyX * basewidth: "<<globalBases * magnifyX * basewidth<<endl;
01346 //   }
01347   resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY);
01348   //     QPoint p = viewportToContents(viewport()->rect().center());
01349   //     center( p.x()* factor , p.y()*factor );
01350 //   setContentsPos(p.x()*zoomfactor, p.y()*zoomfactor);
01351 //   setContentsPos(p.x(), p.y());
01352   updateContents();
01353   
01354 }
01355 
01356 void TrapperView::scrollTo(TR_PIX x, TR_PIX y)
01357 {
01358   setContentsPos( x, y );
01359   updateContents();
01360   
01361 }
01362 
01363 
01364 void TrapperView::enlarge()
01365 {
01366   globalRows *= 2;
01367   globalBases *= 1.25;
01368   resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY);
01369   updateContents();
01370 }
01371 
01372 void TrapperView::shrink()
01373 {
01374   globalRows *= 0.5;
01375   globalBases *= 0.8;
01376   resizeContents(globalBases * magnifyX * basewidth , globalRows * rowheight * magnifyY);
01377   updateContents();
01378 }
01379 
01380 
01381 void TrapperView::selectAll()
01382 {
01383   clearSelected();
01384   Database::PrimaryIterator<ReadData> iter( doc, "ReadData" );
01385   
01386   if ( iter.first() == 0 ) {
01387   
01388     do {
01389       select( iter.answer()->getRecno(), true );
01390       
01391     } while ( iter.next() == 0 );
01392     
01393   }
01394   updateContents();
01395 
01396 }
01397 
01398 void TrapperView::selectBetween()
01399 {
01400   clearSelected();
01401   bool ok;
01402   TR_DNA start, stop;
01403   int res = QInputDialog::getInteger("Select between rows", "Enter start row for selected reads:", 0, 1, numeric_limits<int>::max(), 1,
01404                                      &ok, 0 );
01405   if ( ok ) {
01406     start = res;
01407   }
01408   else {
01409     return;
01410   }
01411   
01412   res = QInputDialog::getInteger("Select between rows", 
01413                                  "Enter stop row for selected reads:", 
01414                                  0, 1, numeric_limits<int>::max(), 1,
01415                                  &ok, 0 );
01416   if ( ok ) {
01417     stop = res;
01418     if ( start > stop ) {
01419       TR_DNA tmp = start;
01420       start = stop;
01421       stop = tmp;
01422     }
01423   }
01424   else {
01425     return;
01426   }
01427 
01428   Database::SecondaryIterator<ReadData> row_it( "pos", doc, "ReadData" );
01429   row_it.key()->setRow(start);
01430   row_it.key()->setStartPos(0);
01431   
01432   if ( row_it.setRange() != 0 ) {
01433 
01434     return;
01435   }
01436   
01437   do {
01438     select( row_it.answer()->getRecno(), true );
01439   }while( row_it.next() == 0 && row_it.answer()->row() <= stop );
01440 
01441   updateContents();
01442 
01443 }
01444 
01445 
01446 
01447 /* todo: check this: maybe unused */
01448 void TrapperView::contentsDragEnterEvent(QDragEnterEvent* event)
01449 {
01450 //   cerr << "in TrapperView::dragEnterEvent" << endl;
01451   event->accept(
01452                 TRUE
01453                 );
01454 }
01455 
01456 void TrapperView::contentsDragMoveEvent ( QDragMoveEvent* e )
01457 {
01458   
01459 //   e->setPoint( QPoint( mousePressedPoint.x(), e->pos().y() ) );
01460 
01461 //   cerr << "in TrapperView::dragMoveEvent" << endl;  
01462 //   cerr<<"x(): "<<e->pos().x()<<endl;
01463 //   cerr<<"y(): "<<e->pos().y()<<endl;
01464  
01465 }
01466 
01467 void TrapperView::contentsDropEvent(QDropEvent* event)
01468 {
01469 //   cerr << "in TrapperView::dropEvent" << endl;
01470 
01471  QPoint deltaMovement = event->pos() - mousePressedPoint;
01472  TR_DNA x_dna_movDelta;
01473  TR_DNA y_dna_movDelta;
01474 
01475  convertToDnaCoordinates( x_dna_movDelta, y_dna_movDelta, deltaMovement.x(), deltaMovement.y() );
01476 //  cerr << "dropped happened with delta x=" << x_dna_movDelta << " y=" << y_dna_movDelta << endl; 
01477  
01478  TrapperView* w = dynamic_cast<TrapperView*>( event->source() );
01479 
01480  if ( !w) {
01481    //Drop from another app...
01482    return;
01483  }
01484  
01485 
01486  assert(w);
01487  
01488  if ( w->getDocument() == this->getDocument() ) {
01489 
01490    moveData( deltaMovement.x(), deltaMovement.y() );
01491  }
01492  else {
01493    QByteArray ar( event->encodedData("min_mime_type") );
01494    QDataStream data_stream(ar, IO_ReadOnly);
01495    
01496    readSelected(data_stream);
01497    updateContents();
01498  }
01499  
01500 
01501 }
01502 
01503 void TrapperView::writeSelected(QDataStream& data_stream)
01504 {
01505   //Write to stream
01506 
01507   
01508   //Get registered types
01509   
01510   list<string> type_list = GeneralMaker::listRegistered();
01511   
01512   
01513   //Loop over selected reads
01514   for( set<db_recno_t>::iterator recno_it = selectedReads.begin(); recno_it != selectedReads.end(); ++recno_it ) {
01515     //Get recno
01516     db_recno_t recno(*recno_it);
01517     
01518     //Create primary iterator for ReadData with new
01519     Database::PrimaryIterator<ReadData>* read_it = new Database::PrimaryIterator<ReadData>(doc, "ReadData");
01520     
01521     //Set iterator from recno
01522     read_it->setFromRecno(recno);
01523     
01524     //Write dataname to stream - null terminated, right?? Must check size stuff...
01525     data_stream<<"ReadData";
01526     
01527     //write ReadData to stream using writeStream
01528     read_it->answer()->writeStream(data_stream);
01529     
01530     //Delete primary readiterator
01531     delete read_it;
01532     
01533     //Loop over types
01534     for( list<string>::iterator type_it = type_list.begin(); type_it != type_list.end(); ++type_it ) {
01535       
01536       GeneralData * data = GeneralMaker::newData( *type_it );
01537       FeatureData * fdata = dynamic_cast<FeatureData *>( data );
01538       // fdata is just used to see that the registered string is corresponding to
01539       // a feature
01540       if ( fdata ) {/* Can cast type to feature */
01541         //Create secondary feature iterator
01542         Database::SecondaryIterator<FeatureData> featIt( "readRecno", doc, type_it->c_str() );
01543         
01544         //Set iterator key read recno
01545         featIt.key()->setReadRecno( recno );
01546         
01547         if ( featIt.set() == 0 ) {//Read has such feature
01548           int ret;
01549           do {
01550             
01551             //write feat name to stream
01552             data_stream<<type_it->c_str();
01553             
01554             //write FeatureData to stream using writeStream
01555             featIt.answer()->writeStream(data_stream);
01556             
01557           } while ((ret = featIt.nextdup())== 0);
01558           
01559         }
01560         
01561       }
01562       
01563       delete data;
01564       
01565     }
01566     
01567   }
01568   
01569 }
01570 
01571 void TrapperView::readSelected(QDataStream& data_stream)
01572 {
01573   //Read from stream
01574   clearSelected();
01575   
01576   db_recno_t recno(0);
01577 
01578   //Keep track of lowest row and start pos, and transpose the pasted reads there
01579 
01580   TR_DNA rowmin(numeric_limits<TR_DNA>::max());
01581   TR_DNA colmin(numeric_limits<TR_DNA>::max());
01582 
01583   while ( !data_stream.atEnd() ) {
01584     
01585     //Read data type
01586     char* data_type;
01587     
01588     data_stream>>data_type;//must delete this myself according to Qt docs
01589     
01590     string type(data_type);
01591     
01592     //Create Creator for general data with Data type name to constructor
01593     Database::Creator<GeneralData> a_creator(doc, type);
01594     
01595     //Read stream using readStream on Creators data() pointer
01596     a_creator.data()->readStream(data_stream);
01597     
01598     if ( ReadData* data = dynamic_cast<ReadData*>(a_creator.data())) {/* type is ReadData*/
01599       
01600       //Creator::create(false) and save read recno
01601       recno = a_creator.create(false);
01602       select(recno, true);
01603       if ( data->row() < rowmin ) {
01604         rowmin = data->row();
01605       }
01606       if ( data->startPos() < colmin ) {
01607         colmin = data->startPos();
01608       }
01609       
01610     }
01611     else {
01612       //Type is feature, but let's do a sanity check
01613       FeatureData* data = dynamic_cast<FeatureData*>(a_creator.data());
01614       assert( data  );
01615       assert( recno != 0 );
01616       
01617       //Set feature's read recno to saved recno
01618       data->setReadRecno(recno);
01619       
01620       //Creator::create()
01621       a_creator.create(false);
01622     }
01623     
01624     delete data_type;
01625   }
01626   fitContentsizeToData();
01627   moveData( -dnaCoordToPixel_X(colmin - 1), -dnaCoordToPixel_Y(rowmin - 1) );
01628   clearLastMove();
01629 }
01630 
01631 void TrapperView::setDragMode(bool status)
01632 {
01633   allow_dragging = status;
01634 }
01635 
01636 void TrapperView::copy()
01637 {
01638   QByteArray ar;
01639   QDataStream str(ar, IO_WriteOnly);
01640   
01641   writeSelected(str);
01642   QClipboard* cb = QApplication::clipboard();
01643   ReadDrag* r = new ReadDrag(this);
01644   r->setEncodedData(ar);
01645   cb->setData(r, QClipboard::Clipboard);
01646   
01647 }
01648 
01649 void TrapperView::paste()
01650 {
01651   
01652   QClipboard* cb = QApplication::clipboard();
01653   QMimeSource* r = cb->data(QClipboard::Clipboard);
01654 
01655   QByteArray ar(r->encodedData("min_mime_type"));
01656   QDataStream str(ar, IO_ReadOnly);
01657   
01658   readSelected(str);
01659   updateContents();
01660 }
01661 
01662 void TrapperView::cut()
01663 {
01664   copy();
01665   Destroyer d(doc);
01666   for( set<db_recno_t>::iterator it = selectedReads.begin(); it != selectedReads.end(); ++it ) {
01667     d.destroy(*it);
01668   }
01669   clearSelected();
01670   updateContents();
01671   
01672 }
01673 
01674 void TrapperView::undo()
01675 {
01676   moveData( -dnaCoordToPixel_X(last_move_x), -dnaCoordToPixel_Y(last_move_y) );
01677 }
01678 
01679 TR_DNA TrapperView::mousePressedRow()
01680 {
01681   return pixelCoordToDna_Y( mousePressedPoint.y() );
01682   
01683   
01684 }
01685 
01686 TR_DNA TrapperView::mousePressedCol()
01687 {
01688   return pixelCoordToDna_X( mousePressedPoint.x() );
01689   
01690 }
01691 
01692 void TrapperView::sendMsg( const QString& msg)
01693 {
01694   emit message(msg);
01695 }
01696