X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=f3e753226f2b5a9073703a25e5132bc8b6b04c01;hb=9be2898dd1635c87539a90de321975f043d005f3;hp=c697d1e5fe5b0eb579e3887a8c6a129d1def9c76;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index c697d1e..f3e7532 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,359 +1,492 @@ package jalview.gui; import java.awt.*; +import java.awt.image.*; import javax.swing.*; -import java.util.*; import jalview.datamodel.*; -import jalview.schemes.*; import jalview.analysis.*; -public class SeqCanvas extends JPanel +public class SeqCanvas extends JComponent { - Image img; - Graphics gg; + FeatureRenderer fr; + SequenceRenderer sr; + BufferedImage img; + Graphics2D gg; int imgWidth; int imgHeight; AlignViewport av; - int pady = 2; - int oldstartx; - int oldstarty; - int oldendx; - int oldendy; - public boolean paintFlag = false; boolean showScores = false; + boolean displaySearch = false; + int [] searchResults = null; int chunkHeight; int chunkWidth; - Graphics debugG; - FeatureRenderer fr = new FeatureRenderer(); - BlockRenderer br = new BlockRenderer(); - CpGRenderer cgr = new CpGRenderer(); + boolean fastPaint = false; - ColourSchemeI cs = new ZappoColourScheme(); public SeqCanvas(AlignViewport av) { this.av = av; + fr = new FeatureRenderer(av); + sr = new SequenceRenderer(av); setLayout(new BorderLayout()); - } - - public void drawScale(int startx, int endx,double charWidth, int charHeight,int ypos) { - int scalestartx = startx - startx%10 + 10; - - gg.setColor(Color.black); - - for (int i=scalestartx;i < endx;i+= 10) { - String string = String.valueOf(i); - gg.drawString(string,(int)((i-startx-1)*charWidth),ypos+15 - charHeight*(2)); - } - } + PaintRefresher.Register(this); + } -/** - * Definitions of startx and endx (hopefully): - * SMJS This is what I'm working towards! - * startx is the first residue (starting at 0) to display. - * endx is the last residue to display (starting at 0). - * starty is the first sequence to display (starting at 0). - * endy is the last sequence to display (starting at 0). - * NOTE 1: The av limits are set in setFont in this class and - * in the adjustment listener in SeqPanel when the scrollbars move. - */ - - public void paintComponent(Graphics g) { - debugG = g; - - AlignmentI da = av.getAlignment(); + void drawNorthScale(Graphics g, int startx, int endx,int ypos) { + int scalestartx = startx - startx % 10 + 10; - if (img == null || - imgWidth != getWidth() || - imgHeight != getHeight() || - paintFlag == true) { + g.setColor(Color.black); - imgWidth = (getWidth() > 0 ? getWidth() : 1); - imgHeight = (getHeight() > 0 ? getHeight() : 1); + // NORTH SCALE + for (int i = scalestartx; i < endx; i += 10) + { + String string = String.valueOf(i); + g.drawString(string, (i - startx - 1) * av.charWidth, + ypos - av.charHeight / 2); - img = createImage(imgWidth,imgHeight); - gg = img.getGraphics(); + g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2, + ypos + 2 - av.charHeight / 2, + (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2); - // SMJS I added this in to update the AV when the size changes - // until I figure out how this should be done - setFont(av.getFont()); + } + } - gg.setFont(av.getFont()); + void drawWestScale(Graphics g, int startx, int endx, int ypos) + { + FontMetrics fm = getFontMetrics(av.getFont()); + ypos+= av.charHeight; + // EAST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) + { + SequenceI seq = av.alignment.getSequenceAt(i); + int index = startx; + int value = -1; + while (index < endx) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + { + index++; + continue; + } + + value = av.alignment.getSequenceAt(i).findPosition(index); + break; + } + if(value!=-1) + { + int x = LABEL_WEST - fm.stringWidth(value+""); + g.drawString(value + "", x, ypos + i*av.charHeight - av.charHeight/5); + } + } + } - paintFlag = false; + void drawEastScale(Graphics g, int startx, int endx, int ypos) +{ + ypos+= av.charHeight; + // EAST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) + { + SequenceI seq = av.alignment.getSequenceAt(i); + int index = endx; + int value = -1; + while (index > startx) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + { + index--; + continue; + } - oldstartx = -1; - oldendx = -1; - oldstarty = -1; - oldendy = -1; + value = av.alignment.getSequenceAt(i).findPosition(index); + break; } + if(value!=-1) + g.drawString(value + "", 0, ypos + i*av.charHeight - av.charHeight/5); + } - int startx = av.getStartRes(); - int starty = av.getStartSeq(); +} - int endx = av.getEndRes(); - int endy = av.getEndSeq(); - double charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - chunkWidth = (int)(getWidth()/charWidth); - chunkHeight = (da.getHeight() + 2)*charHeight; - av.setChunkHeight(chunkHeight); - av.setChunkWidth(chunkWidth); - int offy = av.getStartSeq(); +public void fastPaint(int horizontal, int vertical) +{ + if (horizontal == 0 && vertical == 0 || gg==null) + return; - if (oldendx == -1) { - fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight); + gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth, + -vertical * av.charHeight); - /* if (av.getWrapAlignment() == true) { - startx = (int)(offy/chunkWidth)*chunkWidth; - endx = startx + chunkWidth; - starty = offy%chunkHeight; - endy = starty + da.getHeight(); + int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, + transX = 0, transY = 0; + if (horizontal > 0) // scrollbar pulled right, image to the left + { + transX = (er - sr - horizontal) * av.charWidth; + sr = er - horizontal; + } + else if (horizontal < 0) + er = sr - horizontal; - int ypos = 0; - int rowstart = starty; + else if (vertical > 0) // scroll down + { + ss = es - vertical; + if(ss av.endSeq) + es = av.endSeq; + } - if (starty == 0) { - ypos = 2*charHeight; - } else if (starty == 1) { - starty = 0; - ypos = charHeight; - } - if (endy > da.getHeight()) { - endy = da.getHeight(); - } + gg.translate(transX, transY); - if (endx > da.getWidth()) { - endx = da.getWidth(); - } + gg.setColor(Color.white); + gg.fillRect(0,0, (er-sr+1)*av.charWidth, (es-ss)*av.charHeight); + drawPanel(gg, sr, er, ss, es, sr, ss, 0); + gg.translate( -transX, -transY); - if (rowstart < 2) { - drawScale(startx,endx,charWidth,charHeight,ypos); - } + fastPaint = true; + repaint(); - drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos); +} - if (rowstart == 0) { - ypos = ypos + chunkHeight; - } else if (rowstart == 1) { - ypos = ypos + chunkHeight; - } else { - ypos = ypos + chunkHeight - rowstart*charHeight; - } +/** + * Definitions of startx and endx (hopefully): + * SMJS This is what I'm working towards! + * startx is the first residue (starting at 0) to display. + * endx is the last residue to display (starting at 0). + * starty is the first sequence to display (starting at 0). + * endy is the last sequence to display (starting at 0). + * NOTE 1: The av limits are set in setFont in this class and + * in the adjustment listener in SeqPanel when the scrollbars move. + */ - startx += chunkWidth; - endx = startx + chunkWidth; - starty = 0; + public void paint(Graphics g) + { + g.setColor(Color.white); + g.fillRect(0, 0, getWidth(), getHeight()); - if (endx > da.getWidth()) { - endx = da.getWidth(); - } - // Draw the rest of the panels + if (fastPaint) + { + g.drawImage(img, 0, 0, this); + fastPaint = false; + return; + } - while (ypos <= getHeight()) { - drawScale(startx,endx,charWidth,charHeight,ypos); - drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos); + // this draws the whole of the alignment + imgWidth = getWidth(); + imgHeight = getHeight(); + if(imgWidth==0 || imgHeight==0) + return; - ypos += chunkHeight; - startx += chunkWidth; - endx = startx + chunkWidth; + imgWidth -= imgWidth%av.charWidth; + imgHeight-= imgHeight%av.charHeight; - if (endy > da.getHeight()) { - endy = da.getHeight(); - } + img = new BufferedImage(imgWidth,imgHeight,BufferedImage.TYPE_INT_RGB); + gg = (Graphics2D)img.getGraphics(); + gg.setFont(av.getFont()); + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON); - if (endx > da.getWidth()) { - endx = da.getWidth(); - } + gg.setColor(Color.white); + gg.fillRect(0,0,imgWidth,imgHeight); - } - } else*/ { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); + chunkWidth = getWrappedCanvasWidth( getWidth() ); + chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; - oldstartx = startx; - oldendx = endx; - oldstarty = starty; - oldendy = endy; + av.setChunkHeight(chunkHeight); + av.setChunkWidth(chunkWidth); - } - } - else if (oldstartx < startx) - { - // This is dragging horizontal scrollbar to the right + if (av.getWrapAlignment()) + drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes); + else + drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0); - int delx = (int)((startx - oldstartx) * charWidth); - int delx2 = (int)((oldendx - startx + 1) * charWidth); + g.drawImage(img, 0, 0, this); - gg.copyArea(delx,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),-delx,0); + } - if (startx > oldendx) - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - else - drawPanel(gg,oldendx+1,endx,starty,endy,startx,starty,0); + int LABEL_WEST, LABEL_EAST; + public int getWrappedCanvasWidth(int cwidth) + { + FontMetrics fm = getFontMetrics(av.getFont()); + LABEL_EAST = 0; + LABEL_WEST = 0; - oldstartx = startx; - oldendx = endx; + if(av.scaleRightWrapped) + LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" ); - } else if (oldstartx > startx) - { - // Horizontal scrollbar pulled to the left + if(av.scaleLeftWrapped) + LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" ); - int delx = (int)((oldstartx - startx) * charWidth); - int delx2 = (int)((endx - oldstartx +1) * charWidth); + return (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth; + } - gg.copyArea(0,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),delx,0); + public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) + { + AlignmentI al = av.getAlignment(); - if (oldstartx > endx) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - } else { - drawPanel(gg,startx,oldstartx-1,starty,endy,startx,starty,0); - } + FontMetrics fm = getFontMetrics(av.getFont()); - oldstartx = startx; - oldendx = endx; + int LABEL_EAST = 0; + if(av.scaleRightWrapped) + LABEL_EAST = fm.stringWidth( al.getWidth()+"000" ); + int LABEL_WEST = 0; + if(av.scaleLeftWrapped) + LABEL_WEST = fm.stringWidth(al.getWidth()+"0"); - } else if (oldstarty < starty) { - // Vertical scrollbar down - int dely = AlignmentUtil.getPixelHeight(oldstarty,starty,charHeight); - int dely2 = AlignmentUtil.getPixelHeight(starty,oldendy,charHeight); - gg.copyArea(0,dely,(int)((endx-startx+1)*charWidth),dely2,0,-dely); + int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth; + int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; - if (starty > oldendy) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - } else { - drawPanel(gg,startx,endx,oldendy,endy,startx,starty,0); - } + int endx = startRes+cWidth-1; + int ypos = 2*av.charHeight; - oldstarty = starty; - oldendy = endy; + while (ypos <= canvasHeight && startRes starty) { + if(av.scaleLeftWrapped) + drawWestScale(g, startRes, endx, ypos); - // Vertical scrollbar up - int dely = AlignmentUtil.getPixelHeight(endy,oldendy,charHeight); - int dely2 = AlignmentUtil.getPixelHeight(oldstarty,endy,charHeight); + if(av.scaleRightWrapped) + { + g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0); + drawEastScale(g, startRes, endx, ypos); + g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0); + } - gg.copyArea(0,0,(int)((endx-startx+1)*charWidth),dely2,0,dely); + g.translate(LABEL_WEST,0); + if(av.scaleAboveWrapped) + drawNorthScale(g, startRes, endx, ypos); - if (oldstarty > endy) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - } else { - drawPanel(gg,startx,endx,starty,oldstarty,startx,starty,0); - } - oldstarty = starty; - oldendy = endy; - } + // When printing we have an extra clipped region, + // the Printable page which we need to account for here + Shape clip = g.getClip(); + if(clip==null) + g.setClip(0, 0, cWidth*av.charWidth, canvasHeight); + else + g.setClip(0, + (int)clip.getBounds().getY(), + cWidth*av.charWidth, + (int)clip.getBounds().getHeight() + ); - if ((oldendy -oldstarty) > (int)((getWidth() / av.getCharWidth()))) { - System.out.println("LIMITS ERROR LIMITS ERROR"); - System.out.println("Corrds " + (oldendy-oldstarty) + " " + (int)(getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth()); - } + drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos); + g.setClip(clip); + g.translate(-LABEL_WEST,0); + ypos += cHeight; + startRes += cWidth; + endx = startRes + cWidth - 1; - g.drawImage(img,0,0,this); + if (endx > al.getWidth()) + endx = al.getWidth(); + } } + synchronized public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { - - public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { - -/* - System.out.println("drawPanel called with g = " + g); - System.out.println(" x1 = " + x1); - System.out.println(" x2 = " + x2); - System.out.println(" y1 = " + y1); - System.out.println(" y2 = " + y2); - System.out.println(" startx = " + startx); - System.out.println(" starty = " + starty); -*/ - + Graphics2D g = (Graphics2D)g1; g.setFont(av.getFont()); - double charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - - // Vector pid = av.calcNewConsensus(); + sr.renderGaps(av.renderGaps); - RendererI sr = av.getRenderer(); -/* Vector tmpseq = new Vector(); + SequenceI nextSeq; - for (int i = 0; i < av.getAlignment().getHeight(); i++) { - if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i))) { - tmpseq.addElement(av.getAlignment().getSequenceAt(i)); - } + /// First draw the sequences + ///////////////////////////// + for (int i = y1 ; i < y2 ;i++) + { + nextSeq = av.alignment.getSequenceAt(i); + + sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2, + (x1 - startx) * av.charWidth, + offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight), + av.charWidth,av.charHeight); + + if(av.showSequenceFeatures) + { + fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2, + (x1 - startx) * av.charWidth, + offset + + AlignmentUtil.getPixelHeight(starty, i, av.charHeight), + av.charWidth, av.charHeight); + } } + // + ///////////////////////////////////// - if (sr instanceof SequenceRenderer) { - pid = AAFrequency.calculate(tmpseq,x1,x2); - - } else if (sr instanceof GraphRenderer) { - pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0), - av.getAlignment().getSequences(), - av.getPIDWindow(),x1,x2); + // Now outline any areas if necessary + ///////////////////////////////////// + SequenceGroup group = av.getSelectionGroup(); + java.util.Vector groups = av.alignment.getGroups(); - }*/ - - if (y2 > starty && y1 < av.getEndSeq()) { - - fillBackground(g, - Color.white, - (int)((x1-startx)*charWidth), - offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()), - (int)((x2-x1+1)*charWidth), - offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight())); + int sx = -1, sy = -1, ex = -1; + int groupIndex = -1; + if (group == null && groups.size() > 0) + { + group = (SequenceGroup) groups.elementAt(0); + groupIndex = 0; } - for (int i = y1 ; i < y2 ;i++) { + if (group != null) + do + { + int oldY = -1; + int i = 0; + boolean inGroup = false; + int top=-1, bottom =-1; + for (i = y1; i < y2; i++) + { + sx = (group.getStartRes() - startx) * av.charWidth; + sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); + ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1; + + if (sx < getWidth() + && ex > 0 + && group.sequences.contains(av.alignment.getSequenceAt(i))) + { + if (bottom == -1 && + !group.sequences.contains(av.alignment.getSequenceAt(i + 1))) + bottom = sy + av.charHeight ; + + if (!inGroup) + { + if (top == -1 && i==0 || + !group.sequences.contains(av.alignment.getSequenceAt(i - 1))) + top = sy; + + + oldY = sy; + inGroup = true; + if (group == av.getSelectionGroup()) + { + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,3f}, 0f )); + g.setColor(Color.RED); + } + else + { + g.setStroke(new BasicStroke()); + g.setColor(group.getOutlineColour()); + } + } + } + else + { + if (inGroup) + { + g.drawLine(sx, oldY, sx, sy ); + g.drawLine(sx+ex, oldY, sx+ex, sy ); + + if (top != -1) + { + g.drawLine(sx, top, sx + ex, top); + top =-1; + } + if (bottom != -1) + { + g.drawLine(sx, bottom, sx + ex, bottom); + bottom = -1; + } + + + inGroup = false; + } + } + } + + if (inGroup) + { + + if(top!=-1) + { + g.drawLine(sx, top, sx + ex, top); + top =-1; + } + if(bottom!=-1) + { + g.drawLine(sx, bottom-1, sx + ex, bottom-1); + bottom = -1; + + } + sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); + g.drawLine(sx, oldY, sx, sy ); + g.drawLine(sx+ex, oldY, sx+ex, sy ); + inGroup = false; + } + groupIndex++; + if (groupIndex >= groups.size()) + break; + + group = (SequenceGroup) groups.elementAt(groupIndex); - RendererI r = sr; - - /* if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) { - r = fr; - System.out.println("use feature renderer"); - // } else if ( i == 0) { - // r = br; - } else if (av.getAlignment().getSequenceAt(i).getName().equals("CpG")) { - r = cgr; - System.out.println("cg renderer"); - }*/ + } + while (groupIndex < groups.size()); - r.drawSequence(g,cs,av.getAlignment().getSequenceAt(i), - x1, - x2, - (int)((x1-startx)*charWidth), - offset + AlignmentUtil.getPixelHeight(starty,i,av.getCharHeight()), - charWidth, - charHeight,showScores,av.getShowBoxes(),av.getShowText(),null,i,av); + /// Highlight search Results once all sequences have been drawn + ////////////////////////////////////////////////////////// + if(displaySearch) + { + for(int r=0; r= y1 && searchSeq < y2) + { + SequenceRenderer ssr = (SequenceRenderer) sr; + if(searchStart x2) + searchEnd = x2; + ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq), + searchStart, + searchEnd, + (searchStart - startx) * av.charWidth, + offset + + AlignmentUtil.getPixelHeight(starty, searchSeq, + av.charHeight), + av.charWidth, + av.charHeight); + } + } } + } - public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) { - g.setColor(c); - g.fillRect(x1,y1,width,height); - } + public void highlightSearchResults(int [] results) + { + // results are in the order sequence, startRes, endRes + if(results==null) + displaySearch = false; + else + displaySearch = true; - public int getChunkWidth() { - return chunkWidth; + searchResults = results; + + repaint(); } + }