package jalview.gui; import java.awt.*; import java.awt.image.*; import javax.swing.*; import jalview.datamodel.*; import jalview.analysis.*; public class SeqCanvas extends JComponent { FeatureRenderer fr; SequenceRenderer sr; BufferedImage img; Graphics2D gg; int imgWidth; int imgHeight; AlignViewport av; boolean showScores = false; boolean displaySearch = false; int [] searchResults = null; int chunkHeight; int chunkWidth; boolean fastPaint = false; public SeqCanvas(AlignViewport av) { this.av = av; fr = new FeatureRenderer(av); sr = new SequenceRenderer(av); setLayout(new BorderLayout()); PaintRefresher.Register(this); } void drawNorthScale(Graphics g, int startx, int endx,int ypos) { int scalestartx = startx - startx % 10 + 10; g.setColor(Color.black); // 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); 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); } } 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); } } } 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; } value = av.alignment.getSequenceAt(i).findPosition(index); break; } if(value!=-1) g.drawString(value + "", 0, ypos + i*av.charHeight - av.charHeight/5); } } public void fastPaint(int horizontal, int vertical) { if (horizontal == 0 && vertical == 0 || gg==null) return; gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth, -vertical * av.charHeight); 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; else if (vertical > 0) // scroll down { ss = es - vertical; if(ss av.endSeq) es = av.endSeq; } gg.translate(transX, transY); 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); fastPaint = true; repaint(); } /** * 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) { g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); if (fastPaint) { g.drawImage(img, 0, 0, this); fastPaint = false; return; } // this draws the whole of the alignment imgWidth = getWidth(); imgHeight = getHeight(); if(imgWidth<1 || imgHeight<1) return; imgWidth -= imgWidth%av.charWidth; imgHeight-= imgHeight%av.charHeight; 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); gg.setColor(Color.white); gg.fillRect(0,0,imgWidth,imgHeight); chunkWidth = getWrappedCanvasWidth( getWidth() ); chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; av.setChunkHeight(chunkHeight); av.setChunkWidth(chunkWidth); 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); g.drawImage(img, 0, 0, this); } int LABEL_WEST, LABEL_EAST; public int getWrappedCanvasWidth(int cwidth) { FontMetrics fm = getFontMetrics(av.getFont()); LABEL_EAST = 0; LABEL_WEST = 0; if(av.scaleRightWrapped) LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" ); if(av.scaleLeftWrapped) LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" ); return (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth; } public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) { AlignmentI al = av.getAlignment(); FontMetrics fm = getFontMetrics(av.getFont()); 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"); int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth; int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; av.endRes = av.startRes + cWidth; int endx = startRes+cWidth-1; int ypos = 2*av.charHeight; while (ypos <= canvasHeight && startRes 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) { Graphics2D g = (Graphics2D)g1; g.setFont(av.getFont()); sr.renderGaps(av.renderGaps); SequenceI nextSeq; /// 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); } } // ///////////////////////////////////// // Now outline any areas if necessary ///////////////////////////////////// SequenceGroup group = av.getSelectionGroup(); java.util.Vector groups = av.alignment.getGroups(); int sx = -1, sy = -1, ex = -1; int groupIndex = -1; if (group == null && groups.size() > 0) { group = (SequenceGroup) groups.elementAt(0); groupIndex = 0; } 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); } while (groupIndex < groups.size()); /// Highlight search Results once all sequences have been drawn ////////////////////////////////////////////////////////// if(displaySearch) { for(int r=0; r= y1 && searchSeq < y2) { SequenceI seq = av.getAlignment().getSequenceAt(searchSeq); int searchStart = seq.findIndex( searchResults[r+1] )-1; int searchEnd = seq.findIndex( searchResults[r+2] )-1; SequenceRenderer ssr = (SequenceRenderer) sr; if(searchStart x2) searchEnd = x2; ssr.drawHighlightedText(seq, searchStart, searchEnd, (searchStart - startx) * av.charWidth, offset + AlignmentUtil.getPixelHeight(starty, searchSeq, av.charHeight), av.charWidth, av.charHeight); } } } } public void highlightSearchResults(int [] results) { // results are in the order sequence, startRes, endRes if(results==null) displaySearch = false; else displaySearch = true; searchResults = results; repaint(); } }