X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=42424d9dc8a4a30b95cd7f93905ec5d9e0385ec5;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=4e287b150cdb3e65a168b2775fa566c338f94a03;hpb=412265975277586d03ec183fce0f6e18a022b240;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 4e287b1..42424d9 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,384 +1,844 @@ +/* + * 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 jalview.datamodel.*; + 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 +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class SeqCanvas extends JComponent { - Image img; - Graphics 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; - - int chunkHeight; - int chunkWidth; - - Graphics debugG; - // FeatureRenderer fr = new FeatureRenderer(); - // BlockRenderer br = new BlockRenderer(); - // CpGRenderer cgr = new CpGRenderer(); - - ColourSchemeI cs = new ZappoColourScheme(); - + FeatureRenderer fr; + SequenceRenderer sr; + BufferedImage img; + Graphics2D gg; + int imgWidth; + int imgHeight; + AlignViewport av; + boolean displaySearch = false; + int[] searchResults = null; + boolean fastPaint = false; + int LABEL_WEST; + int LABEL_EAST; + + /** + * Creates a new SeqCanvas object. + * + * @param av DOCUMENT ME! + */ public SeqCanvas(AlignViewport av) { - this.av = av; - setLayout(new BorderLayout()); + this.av = av; + fr = new FeatureRenderer(av); + sr = new SequenceRenderer(av); + setLayout(new BorderLayout()); + PaintRefresher.Register(this, av.alignment); + setBackground(Color.white); } - 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)); - } - } - - -/** - * 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(); + MCview.PDBCanvas pdbCanvas; + public SequenceRenderer getSequenceRenderer() + { + return sr; + } - if (img == null || - imgWidth != getWidth() || - imgHeight != getHeight() || - paintFlag == true) { + public FeatureRenderer getFeatureRenderer() + { + return fr; + } - imgWidth = (getWidth() > 0 ? getWidth() : 1); - imgHeight = (getHeight() > 0 ? getHeight() : 1); + public void setPDBCanvas(MCview.PDBCanvas pc) + { + pdbCanvas = pc; + } - img = createImage(imgWidth,imgHeight); - gg = img.getGraphics(); + public AlignViewport getViewport() + { + return av; + } - // 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()); + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + * @param startx DOCUMENT ME! + * @param endx DOCUMENT ME! + * @param ypos DOCUMENT ME! + */ + 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); + } + } - paintFlag = false; + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + * @param startx DOCUMENT ME! + * @param endx DOCUMENT ME! + * @param ypos DOCUMENT ME! + */ + 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(String.valueOf(value))-av.charWidth/2; + g.drawString(value + "", x, + (ypos + (i * av.charHeight)) - (av.charHeight / 5)); + } + } + } - oldstartx = -1; - oldendx = -1; - oldstarty = -1; - oldendy = -1; + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + * @param startx DOCUMENT ME! + * @param endx DOCUMENT ME! + * @param ypos DOCUMENT ME! + */ + 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(String.valueOf(value), av.charWidth/2, + (ypos + (i * av.charHeight)) - (av.charHeight / 5)); + } + } } - int startx = av.getStartRes(); - int starty = av.getStartSeq(); + /** + * DOCUMENT ME! + * + * @param horizontal DOCUMENT ME! + * @param vertical DOCUMENT ME! + */ + public void fastPaint(int horizontal, int vertical) + { + if (gg == null) + { + return; + } + + gg.copyArea(horizontal * av.charWidth, + vertical * av.charHeight, + imgWidth, + imgHeight, + -horizontal * av.charWidth, + -vertical * av.charHeight); + + 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 + { + er ++; + transX = (er - sr - horizontal) * av.charWidth; + sr = er - horizontal; + } + else if (horizontal < 0) + { + er = sr - horizontal-1; + } + 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); + drawPanel(gg, sr, er, ss, es, sr, ss, 0); + gg.translate(-transX, -transY); + + fastPaint = true; + repaint(); + } - int endx = av.getEndRes(); - int endy = av.getEndSeq(); + /** + * 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) + { + super.paintComponent(g); - double charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); + sr.renderGaps(av.renderGaps); - chunkWidth = (int)(getWidth()/charWidth); - chunkHeight = (da.getHeight() + 2)*charHeight; + if ( img != null && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) + || (getVisibleRect().height != g.getClipBounds().height))) + { + g.drawImage(img, 0, 0, this); + fastPaint = false; + return; + } - av.setChunkHeight(chunkHeight); - av.setChunkWidth(chunkWidth); - int offy = av.getStartSeq(); + // this draws the whole of the alignment + imgWidth = getWidth(); + imgHeight = getHeight(); - if (oldendx == -1) { - fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight); + imgWidth -= (imgWidth % av.charWidth); + imgHeight -= (imgHeight % av.charHeight); - if (av.getWrapAlignment()) { - startx = (int)(offy/chunkWidth)*chunkWidth; - endx = startx + chunkWidth; - starty = offy%chunkHeight; - endy = starty + da.getHeight(); + if ((imgWidth < 1) || (imgHeight < 1)) + { + return; + } - int ypos = 0; - int rowstart = starty; + 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 (starty == 0) { - ypos = 2*charHeight; - } else if (starty == 1) { - starty = 0; - ypos = charHeight; - } + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, imgHeight); - if (endy > da.getHeight()) { - endy = da.getHeight(); - } - if (endx > da.getWidth()) { - endx = da.getWidth(); - } + 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); + } - if (rowstart < 2) { - drawScale(startx,endx,charWidth,charHeight,ypos); - } + g.drawImage(img, 0, 0, this); - drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos); + if (pdbCanvas != null) + { + pdbCanvas.updateSeqColours(); + } - if (rowstart == 0) { - ypos = ypos + chunkHeight; - } else if (rowstart == 1) { - ypos = ypos + chunkHeight; - } else { - ypos = ypos + chunkHeight - rowstart*charHeight; - } + } - startx += chunkWidth; - endx = startx + chunkWidth; - starty = 0; + /** + * DOCUMENT ME! + * + * @param cwidth DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getWrappedCanvasWidth(int cwidth) + { + FontMetrics fm = getFontMetrics(av.getFont()); - if (endx > da.getWidth()) { - endx = da.getWidth(); - } - // Draw the rest of the panels + LABEL_EAST = 0; + LABEL_WEST = 0; - while (ypos <= getHeight()) { - drawScale(startx,endx,charWidth,charHeight,ypos); - drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos); + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()+"0"); + } - ypos += chunkHeight; - startx += chunkWidth; - endx = startx + chunkWidth; + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } - if (endy > da.getHeight()) { - endy = da.getHeight(); - } + return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + } - if (endx > da.getWidth()) { - endx = da.getWidth(); - } - } - } - else + /** + * Generates a string of zeroes. + * @return String + */ + String getMask() + { + String mask = "0"; + for (int i = av.alignment.getWidth(); i > 0; i /= 10) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - - oldstartx = startx; - oldendx = endx; - oldstarty = starty; - oldendy = endy; - + mask += "0"; } + return mask; } - else if (oldstartx < startx) + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + * @param canvasWidth DOCUMENT ME! + * @param canvasHeight DOCUMENT ME! + * @param startRes DOCUMENT ME! + */ + public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, + int startRes) { - // This is dragging horizontal scrollbar to the right - int delx = (int)((startx - oldstartx) * charWidth); - int delx2 = (int)((oldendx - startx + 1) * charWidth); + AlignmentI al = av.getAlignment(); - gg.copyArea(delx,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),-delx,0); + FontMetrics fm = getFontMetrics(av.getFont()); - 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_EAST = 0; + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()+"0"); + } - oldstartx = startx; - oldendx = endx; + int LABEL_WEST = 0; - } else if (oldstartx > startx) - { - // Horizontal scrollbar pulled to the left + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } - int delx = (int)((oldstartx - startx) * charWidth); - int delx2 = (int)((endx - oldstartx +1) * charWidth); + int hgap = av.charHeight; + if(av.scaleAboveWrapped) + hgap += av.charHeight; - gg.copyArea(0,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),delx,0); + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + int cHeight = av.getAlignment().getHeight() * av.charHeight; - if (oldstartx > endx) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - } else { - drawPanel(gg,startx,oldstartx-1,starty,endy,startx,starty,0); - } + av.setWrappedWidth(cWidth); - oldstartx = startx; - oldendx = endx; + av.endRes = av.startRes + cWidth; - } 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 endx = (startRes + cWidth) - 1; + int ypos = hgap; - if (starty > oldendy) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - } else { - drawPanel(gg,startx,endx,oldendy,endy,startx,starty,0); - } - oldstarty = starty; - oldendy = endy; + while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth())) + { + g.setFont(av.getFont()); + g.setColor(Color.black); - } else if (oldstarty > 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, 0); + drawEastScale(g, startRes, endx, ypos); + g.translate(-(canvasWidth - LABEL_EAST), 0); + } - gg.copyArea(0,0,(int)((endx-startx+1)*charWidth),dely2,0,dely); + g.translate(LABEL_WEST, 0); - if (oldstarty > endy) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - } else { - drawPanel(gg,startx,endx,starty,oldstarty,startx,starty,0); - } + if (av.scaleAboveWrapped) + { + drawNorthScale(g, startRes, endx, ypos); + } - 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 ((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()); - } + 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 (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size()) + { + endx = av.vconsensus.size() - 2; + } - gg.setColor(Color.red); - gg.drawRect( groupX, groupY, groupendX-groupX, groupendY-groupY ); - gg.drawRect( groupX+1, groupY+1, groupendX-groupX-2, groupendY-groupY-2 ); + drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos); - g.drawImage(img,0,0,this); + if(av.showAnnotation) + { + g.translate(0, cHeight + ypos + 3); + if(annotations==null) + annotations = new AnnotationPanel(av); - } + annotations.drawComponent( (Graphics2D) g, startRes, endx + 1); + g.translate(0, -cHeight - ypos); + } + g.setClip(clip); + g.translate(-LABEL_WEST, 0); + ypos += cHeight+getAnnotationHeight()+hgap; + if(av.showAnnotation) + ypos -= 3; + startRes += cWidth; + endx = (startRes + cWidth) - 1; + if (endx > al.getWidth()) + { + endx = al.getWidth(); + } + } + } - 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); -*/ - - g.setFont(av.getFont()); - double charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - RendererI sr = av.getRenderer(); - - - /*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 (sr instanceof SequenceRenderer) - pid = AAFrequency.calculate(tmpseq,x1,x2); + AnnotationPanel annotations; + int getAnnotationHeight() + { + if(!av.showAnnotation) + return 0; - else if (sr instanceof GraphRenderer) - pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0), - av.getAlignment().getSequences(), - av.getPIDWindow(),x1,x2); + if(annotations==null) + annotations = new AnnotationPanel(av); -*/ + return annotations.adjustPanelHeight(); + } - if (y2 > starty && y1 < av.getEndSeq()) + /** + * DOCUMENT ME! + * + * @param g1 DOCUMENT ME! + * @param x1 DOCUMENT ME! + * @param x2 DOCUMENT ME! + * @param y1 DOCUMENT ME! + * @param y2 DOCUMENT ME! + * @param startx DOCUMENT ME! + * @param starty DOCUMENT ME! + * @param offset DOCUMENT ME! + */ + + float aaRatio = 2f/3f; + public void increaseAARatio() { - 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())); + aaRatio += .025; + if(aaRatio>1) + aaRatio = 1; + + repaint(); } - SequenceI nextSeq; - SequenceGroup group; - for (int i = y1 ; i < y2 ;i++) + public void decreaseAARation() { - 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"); - } -*/ - nextSeq = av.getAlignment().getSequenceAt(i); - group = av.alignment.findGroup( nextSeq ); - if( group!=null ) - { - r.drawSequence(g, group.cs, nextSeq, - x1, - x2, - (int) ( (x1 - startx) * charWidth), - offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()), - charWidth, charHeight, - false, group.getDisplayBoxes(), group.getDisplayText(), group.getColourText(), - null, i); - } - else - { - r.drawSequence(g, cs, nextSeq, - x1, - x2, - (int) ( (x1 - startx) * charWidth), - offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()), - charWidth,charHeight, - showScores, av.getShowBoxes(), av.getShowText(), av.getColourText(), - null, i); - - } - + aaRatio -= .025; + if(aaRatio<0) + aaRatio = 0; + repaint(); } - } - public int groupX, groupY, groupendX, groupendY; + 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()); + SequenceI nextSeq, dna = null; + int aaHeight = av.charHeight, dnaHeight = av.charHeight; + Font dnafont = null, aafont = av.getFont(); - public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) { - g.setColor(c); - g.fillRect(x1,y1,width,height); - } + /* if (av.getShowTranslation()) + { + aaHeight = (int) (av.getCharHeight() * aaRatio); + dnaHeight = (int) (av.getCharHeight() * (1 - aaRatio)); + java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform(); + transform.scale(1f / 3f, 1); + dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(), + dnaHeight); + dnafont = dnafont.deriveFont(transform); + + aafont = new Font(av.getFont().getName(), av.getFont().getStyle(), + aaHeight); + transform = new java.awt.geom.AffineTransform(); + transform.scale(1 / aaRatio, 1); + aafont = aafont.deriveFont(transform); + } +*/ - public int getChunkWidth() { - return chunkWidth; - } + ColourSchemeI cs = av.getGlobalColourScheme(); + + /// First draw the sequences + ///////////////////////////// + for (int i = y1; i < y2; i++) + { + nextSeq = av.alignment.getSequenceAt(i); + g.setFont(aafont); + /* if(av.getShowTranslation()) + { + dna = nextSeq; + StringBuffer sb = new StringBuffer(); + for(int r = 0; r 0)) + { + group = (SequenceGroup) av.alignment.getGroups().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 + ((i - starty) * av.charHeight); + ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - + 1; + + if(sx+ex<0 || sx>imgWidth) + { + continue; + } + + if ( (sx <= (x2-x1)*av.charWidth) && + 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) + { + if (sx >= 0 && sx < imgWidth) + g.drawLine(sx, oldY, sx, sy); + + if (sx + ex < imgWidth) + g.drawLine(sx + ex, oldY, sx + ex, sy); + + if (sx < 0) + { + ex += sx; + sx = 0; + } + + if (sx + ex > imgWidth) + ex = imgWidth; + + else if (sx + ex >= (x2 - x1 + 1) * av.charWidth) + ex = (x2 - x1 + 1) * av.charWidth; + + 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 + ( (i - starty) * av.charHeight); + if (sx >= 0 && sx < imgWidth) + g.drawLine(sx, oldY, sx, sy); + + if (sx + ex < imgWidth) + g.drawLine(sx + ex, oldY, sx + ex, sy); + + if (sx < 0) + { + ex += sx; + sx = 0; + } + + if (sx + ex > imgWidth) + ex = imgWidth; + else if (sx + ex >= (x2 - x1 + 1) * av.charWidth) + ex = (x2 - x1 + 1) * av.charWidth; + + 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; + } + + inGroup = false; + } + + groupIndex++; + + if (groupIndex >= av.alignment.getGroups().size()) + { + break; + } + + group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex); + } + while (groupIndex < av.alignment.getGroups().size()); + } + + /// Highlight search Results once all sequences have been drawn + ////////////////////////////////////////////////////////// + if (displaySearch) + { + for (int r = 0; r < searchResults.length; r += 3) + { + int searchSeq = searchResults[r]; + + 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; + + if (searchStart < x1) + { + searchStart = x1; + } + + if (searchEnd > x2) + { + searchEnd = x2; + } + + ssr.drawHighlightedText(seq, searchStart, searchEnd, + (searchStart - startx) * av.charWidth, + offset + ((searchSeq - starty) * av.charHeight), + av.charWidth, av.charHeight); + } + } + } + } + /** + * DOCUMENT ME! + * + * @param results DOCUMENT ME! + */ + public void highlightSearchResults(int[] results) + { + // results are in the order sequence, startRes, endRes + if (results == null) + { + displaySearch = false; + } + else + { + displaySearch = true; + } + + searchResults = results; + + repaint(); + } }