X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=c4424655edc22241d5fc2c48aab764569b5101ea;hb=5ba8b4a50183f8a799069ba7a4dabd4cc2589a5b;hp=f9ab0156721ee9f892cb37be967ef5d761238b9b;hpb=09b64bea954c283bde1d21c0a230f51f1ae89373;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index f9ab015..c442465 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,299 +1,591 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.gui; import java.awt.*; +import java.awt.image.*; import javax.swing.*; -import jalview.datamodel.*; -import jalview.analysis.*; +import jalview.analysis.*; +import jalview.datamodel.*; -public class SeqCanvas extends JPanel +public class SeqCanvas + extends JComponent { - FeatureRenderer fr; - Image img; - Graphics gg; - int imgWidth; - int imgHeight; - - AlignViewport av; + 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; + int LABEL_WEST; + int LABEL_EAST; + + + public SeqCanvas(AlignViewport av) + { + this.av = av; + fr = new FeatureRenderer(av); + sr = new SequenceRenderer(av); + setLayout(new BorderLayout()); + PaintRefresher.Register(this, av.alignment); + setBackground(Color.white); + } - public boolean paintFlag = false; + void drawNorthScale(Graphics g, int startx, int endx, int ypos) + { + int scalestartx = startx - (startx % 10) + 10; - boolean showScores = false; - boolean displaySearch = false; - int [] searchResults = null; + g.setColor(Color.black); - int chunkHeight; - int chunkWidth; + // 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; - public SeqCanvas(AlignViewport av) + // EAST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) { - this.av = av; - fr = new FeatureRenderer(av); - setLayout(new BorderLayout()); - PaintRefresher.Register(this); + 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)); + } } + } - public void drawScale(Graphics g, int startx, int endx,int ypos) { - int scalestartx = startx - startx%10 + 10; + void drawEastScale(Graphics g, int startx, int endx, int ypos) + { + ypos += av.charHeight; - g.setColor(Color.black); + // EAST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) + { + SequenceI seq = av.alignment.getSequenceAt(i); + int index = endx; + int value = -1; - for (int i=scalestartx;i < endx;i+= 10) + while (index > startx) { - String string = String.valueOf(i); - g.drawString(string,(i-startx-1)*av.charWidth,ypos - av.charHeight/2); + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + { + index--; - 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 ); + 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); -/** - * 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. - */ + int sr = av.startRes; + int er = av.endRes; + int ss = av.startSeq; + int es = av.endSeq; + int transX = 0; + int 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.startSeq) + { // ie scrolling too fast, more than a page at a time + ss = av.startSeq; + } + else + { + transY = imgHeight - (vertical * av.charHeight); + } + } + else if (vertical < 0) + { + es = ss - vertical; + + if (es > 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. + */ + + + // Set this to false to force a full panel paint public void paintComponent(Graphics g) { + if (img!=null + && (fastPaint || getWidth() != g.getClipBounds().width + || getHeight() != g.getClipBounds().height)) + { + g.drawImage(img, 0, 0, this); + fastPaint = false; + return; + } + + // this draws the whole of the alignment + imgWidth = getWidth(); + imgHeight = getHeight(); - if (img==null || imgWidth!=getWidth() || imgHeight!=getHeight() || paintFlag) + imgWidth -= (imgWidth % av.charWidth); + imgHeight -= (imgHeight % av.charHeight); + + if ( (imgWidth < 1) || (imgHeight < 1)) { - imgWidth = getWidth(); - imgHeight = getHeight(); - img = createImage(imgWidth,imgHeight); - gg = img.getGraphics(); - gg.setFont(av.getFont()); - paintFlag = false; + return; } + 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 = getWidth()/av.charWidth; - chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; + chunkWidth = getWrappedCanvasWidth(getWidth()); + chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight; av.setChunkHeight(chunkHeight); av.setChunkWidth(chunkWidth); - fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight); - 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); + { + drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, + av.startRes, av.startSeq, 0); + } + g.drawImage(img, 0, 0, this); + } + + 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"); + } - g.drawImage(img,0,0,this); + 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) + public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, + int startRes) { - AlignmentI da = av.getAlignment(); + AlignmentI al = av.getAlignment(); - int cWidth = canvasWidth/av.charWidth; - int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; + FontMetrics fm = getFontMetrics(av.getFont()); - int endx = startRes+cWidth-1; - int ypos = 2*av.charHeight; + int LABEL_EAST = 0; - while (ypos <= canvasHeight) - { - drawScale(g, startRes, endx, ypos); - drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos); + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(al.getWidth() + "000"); + } - ypos += cHeight; - startRes += cWidth; - endx = startRes + cWidth - 1; + int LABEL_WEST = 0; - if (endx > da.getWidth()) - endx = da.getWidth(); - } + 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; - public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { + int endx = (startRes + cWidth) - 1; + int ypos = 2 * av.charHeight; + while ( (ypos <= canvasHeight) && (startRes < av.alignment.getWidth())) + { + g.setColor(Color.black); - g.setFont(av.getFont()); - RendererI sr = av.getRenderer(); + if (av.scaleLeftWrapped) + { + drawWestScale(g, startRes, endx, ypos); + } - /*Vector pid = av.getConsensus(false); - Vector tmpseq = new Vector(); - for (int i = 0; i < av.getAlignment().getHeight(); i++) - if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i))) - tmpseq.addElement(av.getAlignment().getSequenceAt(i)); + if (av.scaleRightWrapped) + { + g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0); + drawEastScale(g, startRes, endx, ypos); + g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0); + } - if (sr instanceof SequenceRenderer) - pid = AAFrequency.calculate(tmpseq,x1,x2); + g.translate(LABEL_WEST, 0); - else if (sr instanceof GraphRenderer) - pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0), - av.getAlignment().getSequences(), - av.getPIDWindow(),x1,x2); + if (av.scaleAboveWrapped) + { + drawNorthScale(g, startRes, endx, ypos); + } -*/ + // When printing we have an extra clipped region, + // the Printable page which we need to account for here + Shape clip = g.getClip(); - /* if (y2 > starty && y1 < av.getEndSeq()) - { - fillBackground(g, - Color.red, - (x1-startx)*charWidth, - offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()), - (x2-x1+1)*charWidth, - offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight())); - }*/ + 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()); + } + + 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; + + 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) + { + 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++) + for (int i = y1; i < y2; i++) { - nextSeq = av.getAlignment().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,null, i); - - 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, null, 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 sx = -1; + int sy = -1; + int ex = -1; int groupIndex = -1; - if (group == null && groups.size() > 0) + + 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; + int 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; - - if (group.sequences.contains(av.alignment.getSequenceAt(i)) - && sx < getWidth() - && ex > 0) + 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.setColor(Color.RED.brighter()); + { + 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.drawRect(sx, oldY, ex, (sy - oldY)); + 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) { - sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); - g.drawRect(sx, oldY, ex, (sy - oldY)); + 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) + if (displaySearch) { - for(int r=0; r= y1 && searchSeq < y2) + if ( (searchSeq >= 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; - ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq), - searchStart, - searchEnd, + + if (searchStart < x1) + { + searchStart = x1; + } + + if (searchEnd > x2) + { + searchEnd = x2; + } + + ssr.drawHighlightedText(seq, searchStart, searchEnd, (searchStart - startx) * av.charWidth, offset + - AlignmentUtil.getPixelHeight(starty, searchSeq, - av.charHeight), - av.charWidth, - av.charHeight); + 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 int getChunkWidth() { - return chunkWidth; - } - - public void highlightSearchResults(int [] results) + public void highlightSearchResults(int[] results) { // results are in the order sequence, startRes, endRes - if(results==null) + if (results == null) + { displaySearch = false; + } else + { displaySearch = true; + } searchResults = results; - paintFlag = true; repaint(); } - - }