X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=3cf7f9af60209e18c38d938e94c062cf1cbb618b;hb=246746e55bd02c66746d5cd872f49890cbae206a;hp=27a8a9ccae9fdb52e32414a8ca3d3b8e4116ae2a;hpb=193558cf2b5905e77fd402cf2fc204adcaa74b69;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 27a8a9c..3cf7f9a 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,355 +1,707 @@ +/* + * 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 javax.swing.*; -import java.awt.event.*; import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.analysis.*; +import java.awt.*; +import java.awt.image.*; -public class SeqCanvas extends JPanel -{ - Image img; - Graphics gg; - int imgWidth; - int imgHeight; - - AlignViewport av; +import javax.swing.*; - public boolean paintFlag = false; - boolean showScores = false; +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class SeqCanvas extends JComponent +{ + FeatureRenderer fr; + SequenceRenderer sr; + BufferedImage img; + Graphics2D gg; + int imgWidth; + int imgHeight; + AlignViewport av; boolean displaySearch = false; - int [] searchResults = null; - + int[] searchResults = null; int chunkHeight; int chunkWidth; + boolean fastPaint = false; + int LABEL_WEST; + int LABEL_EAST; + boolean isOverview = false; + /** + * Creates a new SeqCanvas object. + * + * @param av DOCUMENT ME! + */ public SeqCanvas(AlignViewport av) { - this.av = av; - setLayout(new BorderLayout()); - PaintRefresher.Register(this); - + 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,int 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) { - - AlignmentI da = av.getAlignment(); - - 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 drawNorthScale(Graphics g, int startx, int endx, int ypos) { + int scalestartx = startx - (startx % 10) + 10; - imgWidth = getWidth(); - imgHeight = getHeight(); + g.setColor(Color.black); - img = createImage(imgWidth,imgHeight); - gg = img.getGraphics(); + // 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); + } + } - gg.setFont(av.getFont()); + /** + * 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; - paintFlag = false; + // 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)); + } + } } - chunkWidth = getWidth()/av.charWidth; - chunkHeight = (da.getHeight() + 2)*av.charHeight; - - av.setChunkHeight(chunkHeight); - av.setChunkWidth(chunkWidth); + /** + * 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--; - fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight); + continue; + } - /* if (av.getWrapAlignment()) { - int offy = av.getStartSeq(); - startx = (int)(offy/chunkWidth)*chunkWidth; - endx = startx + chunkWidth; - starty = offy%chunkHeight; - endy = starty + da.getHeight(); + value = av.alignment.getSequenceAt(i).findPosition(index); - int ypos = 0; - int rowstart = starty; + break; + } - if (starty == 0) { - ypos = 2*charHeight; - } else if (starty == 1) { - starty = 0; - ypos = charHeight; - } + if (value != -1) + { + g.drawString(String.valueOf(value), av.charWidth/2, + (ypos + (i * av.charHeight)) - (av.charHeight / 5)); + } + } + } - if (endy > da.getHeight()) { - endy = da.getHeight(); - } + /** + * DOCUMENT ME! + * + * @param horizontal DOCUMENT ME! + * @param vertical DOCUMENT ME! + */ + public void fastPaint(int horizontal, int vertical) + { + if (gg == null) + { + return; + } - if (endx > da.getWidth()) { - endx = da.getWidth(); - } + gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth, + -vertical * av.charHeight); - if (rowstart < 2) { - drawScale(startx,endx,charWidth,charHeight,ypos); - } + int sr = av.startRes; + int er = av.endRes; + int ss = av.startSeq; + int es = av.endSeq; + int transX = 0; + int transY = 0; - drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos); + 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 (rowstart == 0) { - ypos = ypos + chunkHeight; - } else if (rowstart == 1) { - ypos = ypos + chunkHeight; - } else { - ypos = ypos + chunkHeight - rowstart*charHeight; - } + if (es > av.endSeq) + { + es = av.endSeq; + } + } - startx += chunkWidth; - endx = startx + chunkWidth; - starty = 0; + gg.translate(transX, transY); + drawPanel(gg, sr, er, ss, es, sr, ss, 0); + gg.translate(-transX, -transY); - if (endx > da.getWidth()) { - endx = da.getWidth(); - } - // Draw the rest of the panels + fastPaint = true; + repaint(); + } - while (ypos <= getHeight()) { - drawScale(startx,endx,charWidth,charHeight,ypos); - drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos); + /** + * 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) + { + sr.renderGaps(av.renderGaps); - ypos += chunkHeight; - startx += chunkWidth; - endx = startx + chunkWidth; + if ((img != null) && + (fastPaint || (getWidth() != g.getClipBounds().width) || + (getHeight() != g.getClipBounds().height))) + { + g.drawImage(img, 0, 0, this); + fastPaint = false; - if (endy > da.getHeight()) { - endy = da.getHeight(); - } + return; + } - if (endx > da.getWidth()) { - endx = da.getWidth(); - } + // this draws the whole of the alignment + imgWidth = getWidth(); + imgHeight = getHeight(); - } - } - else*/ - { - drawPanel(gg,av.startRes,av.endRes,av.startSeq,av.endSeq,av.startRes,av.startSeq,0); - } + imgWidth -= (imgWidth % av.charWidth); + imgHeight -= (imgHeight % av.charHeight); + if ((imgWidth < 1) || (imgHeight < 1)) + { + return; + } - /* 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()); - }*/ - g.drawImage(img,0,0,this); + 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); + } - public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { + g.drawImage(img, 0, 0, this); + } + /** + * DOCUMENT ME! + * + * @param cwidth DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getWrappedCanvasWidth(int cwidth) + { + FontMetrics fm = getFontMetrics(av.getFont()); - g.setFont(av.getFont()); - int charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - RendererI sr = av.getRenderer(); + LABEL_EAST = 0; + LABEL_WEST = 0; - /*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) + { + LABEL_EAST = fm.stringWidth(getMask()+"0"); + } - if (sr instanceof SequenceRenderer) - pid = AAFrequency.calculate(tmpseq,x1,x2); + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } - else if (sr instanceof GraphRenderer) - pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0), - av.getAlignment().getSequences(), - av.getPIDWindow(),x1,x2); + return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + } -*/ - /* 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())); - }*/ - - SequenceI nextSeq; - SequenceGroup group=null; - SequenceGroup [] groups=null; - boolean inGroup=false; // are we in a defined group? - boolean inRB=false; //Are we in a rubberband group? - int sx=-1, sy=-1, ex=-1, ey=-1; - int oldStartX=0,oldEndX=0,oldY=0; - int oldRStartX=0,oldREndX=0,oldRY=0; - for (int i = y1 ; i < y2 ;i++) + /** + * Generates a string of zeroes. + * @return String + */ + String getMask() { - nextSeq = av.getAlignment().getSequenceAt(i); - - group = av.alignment.findGroup( nextSeq ); - groups = av.alignment.findAllGroups( nextSeq ); + String mask = "0"; + for (int i = av.alignment.getWidth(); i > 0; i /= 10) + { + mask += "0"; + } + return mask; + } - sr.drawSequence(g, nextSeq, groups,x1,x2, - (x1 - startx) * charWidth, - offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()), - charWidth,charHeight,null, i); + /** + * 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(); - if( group!=null ) - { + FontMetrics fm = getFontMetrics(av.getFont()); - g.setColor(Color.lightGray); + int LABEL_EAST = 0; - 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.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()+"0"); + } + int LABEL_WEST = 0; - if (!inGroup) + if (av.scaleLeftWrapped) { - g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box - inGroup=true; + LABEL_WEST = fm.stringWidth(getMask()); } - g.drawLine(sx, sy, sx, ey ); // vertical line, left hand side - g.drawLine( ex,sy,ex,ey); // vertical line, right hand side - if (i == y2 - 1)// last line of alignment, seal the box - g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box - - oldStartX = sx; - oldEndX = ex; - oldY = ey; - - } - else if(inGroup) - { - g.setColor(Color.lightGray); - g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box - } - else - inGroup = false; - - group = av.getRubberbandGroup(); - if( group != null && group.sequences.contains(nextSeq) ) - { - g.setColor(Color.RED.brighter()); - 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 (!inRB) - { - - g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box - inRB = true; - } - - g.drawLine(sx, sy, sx, ey); // vertical line, left hand side - g.drawLine(ex, sy, ex, ey); // vertical line, right hand side - if (i == y2 - 1) // last line of alignment, seal the box - g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box - - oldRStartX = sx; - oldREndX = ex; - oldRY = ey; - } - else if(inRB) - { - g.setColor(Color.RED.brighter()); - g.drawLine(oldRStartX, oldRY, oldREndX, oldRY); // Horizontal, bottom of old box - inRB = false; - } - else - inRB = false; + 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 < av.alignment.getWidth())) + { + 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()); + } + + 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(); + } + } } - /// Highlight search Results once all sequences have been drawn - if(displaySearch) + /** + * 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! + */ + synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1, + int y2, int startx, int starty, int offset) { - for(int r=0; r= y1 && searchSeq < y2) + SequenceI nextSeq; + + /// First draw the sequences + ///////////////////////////// + for (int i = y1; i < y2; i++) { - SequenceRenderer ssr = (SequenceRenderer) sr; - ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq), - searchStart, - searchEnd, - (searchStart - startx) * charWidth, - offset + - AlignmentUtil.getPixelHeight(starty, searchSeq, - charHeight), - charWidth, - charHeight); + nextSeq = av.alignment.getSequenceAt(i); + + sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), + x1, x2, (x1 - startx) * av.charWidth, + offset + ((i - starty) * av.charHeight), av.charWidth, + av.charHeight); + + if (av.showSequenceFeatures) + { + fr.drawSequence(g, nextSeq, + av.alignment.findAllGroups(nextSeq), x1, x2, + (x1 - startx) * av.charWidth, + offset + ((i - starty) * av.charHeight), av.charWidth, + av.charHeight); + } } - } - } - } + // + ///////////////////////////////////// + // Now outline any areas if necessary + ///////////////////////////////////// + SequenceGroup group = av.getSelectionGroup(); + java.util.Vector groups = av.alignment.getGroups(); - public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) { - g.setColor(c); - g.fillRect(x1,y1,width,height); - } + int sx = -1; + int sy = -1; + int ex = -1; + int groupIndex = -1; - public int getChunkWidth() { - return chunkWidth; - } + if ((group == null) && (groups.size() > 0)) + { + group = (SequenceGroup) groups.elementAt(0); + groupIndex = 0; + } - public void highlightSearchResults(int [] results) - { - // results are in the order sequence, startRes, endRes - if(results==null) - displaySearch = false; - else - displaySearch = true; - searchResults = results; + if (group != null && !isOverview) + { + 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 >= groups.size()) + { + break; + } + + group = (SequenceGroup) groups.elementAt(groupIndex); + } + while (groupIndex < groups.size()); + } - paintFlag = true; - repaint(); - } + /// 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(); + } }