X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=42424d9dc8a4a30b95cd7f93905ec5d9e0385ec5;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=00b4e954f52b9a614f6eec87a7ae011260ca57a3;hpb=a11e13d8fffacf8115a4d83e4254bf94a87d6600;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 00b4e95..42424d9 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,478 +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.awt.event.*; -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 { - ColourSchemeI globalColorScheme = null; - 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; + FeatureRenderer fr; + SequenceRenderer sr; + BufferedImage img; + Graphics2D gg; + int imgWidth; + int imgHeight; + AlignViewport av; boolean displaySearch = false; - int [] searchResults = null; - - int chunkHeight; - int chunkWidth; - - + 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); + } + MCview.PDBCanvas pdbCanvas; + public SequenceRenderer getSequenceRenderer() + { + return sr; } - public void drawScale(int startx, int endx,int charWidth, int charHeight,int ypos) { - int scalestartx = startx - startx%10 + 10; + public FeatureRenderer getFeatureRenderer() + { + return fr; + } - gg.setColor(Color.black); + public void setPDBCanvas(MCview.PDBCanvas pc) + { + pdbCanvas = pc; + } - 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)); - } - } + public AlignViewport getViewport() + { + return av; + } -/** - * 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. - */ + /** + * 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; - public void paintComponent(Graphics g) { + g.setColor(Color.black); - AlignmentI da = av.getAlignment(); + // 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); + } + } - if (img == null || - imgWidth != getWidth() || - imgHeight != getHeight() - || paintFlag) + /** + * 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; - imgWidth = (getWidth() > 0 ? getWidth() : 1); - imgHeight = (getHeight() > 0 ? getHeight() : 1); - - img = createImage(imgWidth,imgHeight); - gg = img.getGraphics(); + // 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)); + } + } + } - gg.setFont(av.getFont()); + /** + * 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; - oldstartx = -1; - oldendx = -1; - oldstarty = -1; - oldendy = -1; - paintFlag = false; - } + // EAST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) + { + SequenceI seq = av.alignment.getSequenceAt(i); + int index = endx; + int value = -1; - int startx = av.getStartRes(); - int starty = av.getStartSeq(); + while (index > startx) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + { + index--; - int endx = av.getEndRes(); - int endy = av.getEndSeq(); + continue; + } - int charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); + value = av.alignment.getSequenceAt(i).findPosition(index); - chunkWidth = getWidth()/charWidth; - chunkHeight = (da.getHeight() + 2)*charHeight; + break; + } - av.setChunkHeight(chunkHeight); - av.setChunkWidth(chunkWidth); + if (value != -1) + { + g.drawString(String.valueOf(value), av.charWidth/2, + (ypos + (i * av.charHeight)) - (av.charHeight / 5)); + } + } + } - int offy = av.getStartSeq(); + /** + * DOCUMENT ME! + * + * @param horizontal DOCUMENT ME! + * @param vertical DOCUMENT ME! + */ + public void fastPaint(int horizontal, int vertical) + { + if (gg == null) + { + return; + } - if (oldendx == -1) { - fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight); + 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 (av.getWrapAlignment()) { - startx = (int)(offy/chunkWidth)*chunkWidth; - endx = startx + chunkWidth; - starty = offy%chunkHeight; - endy = starty + da.getHeight(); + if (es > av.endSeq) + { + es = av.endSeq; + } + } - int ypos = 0; - int rowstart = starty; + gg.translate(transX, transY); + drawPanel(gg, sr, er, ss, es, sr, ss, 0); + gg.translate(-transX, -transY); - if (starty == 0) { - ypos = 2*charHeight; - } else if (starty == 1) { - starty = 0; - ypos = charHeight; - } + fastPaint = true; + repaint(); + } - if (endy > da.getHeight()) { - endy = da.getHeight(); - } + /** + * 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); - if (endx > da.getWidth()) { - endx = da.getWidth(); - } + sr.renderGaps(av.renderGaps); - if (rowstart < 2) { - drawScale(startx,endx,charWidth,charHeight,ypos); - } + if ( img != null && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) + || (getVisibleRect().height != g.getClipBounds().height))) + { + g.drawImage(img, 0, 0, this); + fastPaint = false; + return; + } - 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; - } + // this draws the whole of the alignment + imgWidth = getWidth(); + imgHeight = getHeight(); - startx += chunkWidth; - endx = startx + chunkWidth; - starty = 0; + imgWidth -= (imgWidth % av.charWidth); + imgHeight -= (imgHeight % av.charHeight); - if (endx > da.getWidth()) { - endx = da.getWidth(); - } - // Draw the rest of the panels + if ((imgWidth < 1) || (imgHeight < 1)) + { + return; + } - while (ypos <= getHeight()) { - drawScale(startx,endx,charWidth,charHeight,ypos); - drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos); + 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); - ypos += chunkHeight; - startx += chunkWidth; - endx = startx + chunkWidth; + 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); + } - } - } - else - { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); + g.drawImage(img, 0, 0, this); - oldstartx = startx; - oldendx = endx; - oldstarty = starty; - oldendy = endy; + if (pdbCanvas != null) + { + pdbCanvas.updateSeqColours(); + } - } } - else if (oldstartx < startx) + /** + * DOCUMENT ME! + * + * @param cwidth DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getWrappedCanvasWidth(int cwidth) { - // This is dragging horizontal scrollbar to the right + FontMetrics fm = getFontMetrics(av.getFont()); - int delx = (startx - oldstartx) * charWidth; - int delx2 = (oldendx - startx + 1) * charWidth; + LABEL_EAST = 0; + LABEL_WEST = 0; - gg.copyArea(delx,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),-delx,0); + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()+"0"); + } - if (startx > oldendx) - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - else - drawPanel(gg,oldendx+1,endx,starty,endy,startx,starty,0); + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } + return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + } - oldstartx = startx; - oldendx = endx; - } else if (oldstartx > startx) + /** + * Generates a string of zeroes. + * @return String + */ + String getMask() { - // Horizontal scrollbar pulled to the left - - int delx = (oldstartx - startx) * charWidth; - int delx2 = (endx - oldstartx +1) * charWidth; - - gg.copyArea(0,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),delx,0); - - if (oldstartx > endx) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - } else { - drawPanel(gg,startx,oldstartx-1,starty,endy,startx,starty,0); - } - - oldstartx = startx; - oldendx = endx; - - } 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,(endx-startx+1)*charWidth,dely2,0,-dely); - - 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; - - } else if (oldstarty > starty) { - - // Vertical scrollbar up - int dely = AlignmentUtil.getPixelHeight(endy,oldendy,charHeight); - int dely2 = AlignmentUtil.getPixelHeight(oldstarty,endy,charHeight); - - gg.copyArea(0,0,(endx-startx+1)*charWidth,dely2,0,dely); - - if (oldstarty > endy) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - } else { - drawPanel(gg,startx,endx,starty,oldstarty,startx,starty,0); + String mask = "0"; + for (int i = av.alignment.getWidth(); i > 0; i /= 10) + { + mask += "0"; } - - oldstarty = starty; - oldendy = endy; + return mask; } - if ((oldendy -oldstarty) > (getWidth() / av.getCharWidth())) { - System.out.println("LIMITS ERROR LIMITS ERROR"); - System.out.println("Corrds " + (oldendy-oldstarty) + " " + (getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth()); - } + /** + * 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) + { + AlignmentI al = av.getAlignment(); - // gg.setColor(Color.red); - // gg.drawRect( groupX, groupY, groupendX-groupX, groupendY-groupY ); - // gg.drawRect( groupX+1, groupY+1, groupendX-groupX-2, groupendY-groupY-2 ); + FontMetrics fm = getFontMetrics(av.getFont()); + int LABEL_EAST = 0; - g.drawImage(img,0,0,this); + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()+"0"); + } - } + int LABEL_WEST = 0; + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } + int hgap = av.charHeight; + if(av.scaleAboveWrapped) + hgap += av.charHeight; + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + int cHeight = av.getAlignment().getHeight() * av.charHeight; - public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { + av.setWrappedWidth(cWidth); -/* - Startx and starty appear to be the same as x1, y1, unless you find different - x1 x2 - y1************************************************** - * * - * * - * * - * * - **************************************************y2 + av.endRes = av.startRes + cWidth; -/* - 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()); - int charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - RendererI sr = av.getRenderer(); + int endx = (startRes + cWidth) - 1; + int ypos = hgap; - /*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)); + while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth())) + { + g.setFont(av.getFont()); + g.setColor(Color.black); + + if (av.scaleLeftWrapped) + { + drawWestScale(g, startRes, endx, ypos); + } + + if (av.scaleRightWrapped) + { + g.translate(canvasWidth - LABEL_EAST, 0); + drawEastScale(g, startRes, endx, ypos); + g.translate(-(canvasWidth - LABEL_EAST), 0); + } + + g.translate(LABEL_WEST, 0); + + 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 (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; + } + + + drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos); + + 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(); + } + } + } - 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, - (x1-startx)*charWidth, - offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()), - (x2-x1+1)*charWidth, - offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight())); + aaRatio += .025; + if(aaRatio>1) + aaRatio = 1; + + repaint(); } - SequenceI nextSeq; - SequenceGroup group=null; - boolean newGroup=false; - int sx, sy, ex, ey; - int oldStartX=0,oldEndX=0,oldY=0; - for (int i = y1 ; i < y2 ;i++) + public void decreaseAARation() { - nextSeq = av.getAlignment().getSequenceAt(i); - if(group==null || group!=av.alignment.findGroup( nextSeq )) - newGroup = true; - else - newGroup = false; + aaRatio -= .025; + if(aaRatio<0) + aaRatio = 0; - group = av.alignment.findGroup( nextSeq ); - - sr.drawSequence(g, nextSeq, group,x1,x2, - (x1 - startx) * charWidth, - offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()), - charWidth,charHeight,null, i); + repaint(); + } - if( group!=null ) - { + 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()); - g.setColor(Color.GREEN); + SequenceI nextSeq, dna = null; + int aaHeight = av.charHeight, dnaHeight = av.charHeight; + Font dnafont = null, aafont = av.getFont(); - sx = (group.getStartRes()-startx)*charWidth; - sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()); - ex = (group.getEndRes()+1-startx)*charWidth; - ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.getCharHeight()); + /* 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); + } +*/ + ColourSchemeI cs = av.getGlobalColourScheme(); - if (newGroup) + /// First draw the sequences + ///////////////////////////// + for (int i = y1; i < y2; i++) { - g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box - g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box + 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; + } - /// Highlight search Results once all sequences have been drawn - if(displaySearch) - { - for(int r=0; rimgWidth) + { + 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()); + } - if (searchSeq >= y1 && searchSeq <= y2) + /// Highlight search Results once all sequences have been drawn + ////////////////////////////////////////////////////////// + if (displaySearch) { - SequenceRenderer ssr = (SequenceRenderer) sr; - ssr.drawHighlightedText(g, av.getAlignment().getSequenceAt(searchSeq), - searchStart, - searchEnd, - (searchStart - startx) * charWidth, - offset + - AlignmentUtil.getPixelHeight(starty, searchSeq, - charHeight), - charWidth, - charHeight); + 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); + } + } } - } } - - - - /*bg.drawImage(image,0,0,null); - int size=width*height; - int pixel, b, x,y; - if(value!=0 ) - { - if(painted!=null) - { - for(int i=0; i