X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=42424d9dc8a4a30b95cd7f93905ec5d9e0385ec5;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=38825c5cb21e16206e54b400aaf5c7de9f558593;hpb=dde60115cd1cee37c087bf73e43b53ab42d47932;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 38825c5..42424d9 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,504 +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 java.awt.*; -import javax.swing.*; import jalview.datamodel.*; -import jalview.analysis.*; +import java.awt.*; +import java.awt.image.*; -public class SeqCanvas extends JPanel -{ - FeatureRenderer fr; - Image img; - Graphics2D gg; - int imgWidth; - int imgHeight; +import javax.swing.*; +import jalview.schemes.*; - AlignViewport av; - 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 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; - fr = new FeatureRenderer(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); + } + MCview.PDBCanvas pdbCanvas; + public SequenceRenderer getSequenceRenderer() + { + return sr; } - void drawNorthScale(Graphics g, int startx, int endx,int ypos) { - int scalestartx = startx - startx % 10 + 10; + public FeatureRenderer getFeatureRenderer() + { + return fr; + } - g.setColor(Color.black); + public void setPDBCanvas(MCview.PDBCanvas pc) + { + pdbCanvas = pc; + } - // NORTH SCALE - for (int i = scalestartx; i < endx; i += 10) + public AlignViewport getViewport() { - String string = String.valueOf(i); - g.drawString(string, (i - startx - 1) * av.charWidth, - ypos - av.charHeight / 2); + return av; + } - 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++) + /** + * 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) { - SequenceI seq = av.alignment.getSequenceAt(i); - int index = startx; - int value = -1; - while (index < endx) - { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + int scalestartx = startx - (startx % 10) + 10; + + g.setColor(Color.black); + + // NORTH SCALE + for (int i = scalestartx; i < endx; i += 10) { - index++; - continue; + 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); } - - value = av.alignment.getSequenceAt(i).findPosition(index); - break; - } - if(value!=-1) - { - int x = fm.stringWidth("000") - 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) + /** + * 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) { - 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); - } - -} - + 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; + } -public void fastPaint(int horizontal, int vertical) -{ - if (horizontal == 0 && vertical == 0) - return; + value = av.alignment.getSequenceAt(i).findPosition(index); - gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth, - -vertical * av.charHeight); + break; + } - int sr = av.startRes, er = av.endRes + 1, 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; + 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)); + } + } } - else if (horizontal < 0) - er = sr - horizontal; - else if (vertical > 0) // scroll down + /** + * 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) { - transY = imgHeight - vertical * av.charHeight; - ss = es - vertical; - } - else if (vertical < 0) - es = ss - vertical; + ypos += av.charHeight; - gg.translate(transX, transY); + // EAST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) + { + SequenceI seq = av.alignment.getSequenceAt(i); + int index = endx; + int value = -1; - gg.setColor(Color.white); - gg.fillRect(0,0, (er-sr)*av.charWidth, (es-ss)*av.charHeight); - drawPanel(gg, sr, er, ss, es, sr, ss, 0); - gg.translate( -transX, -transY); + while (index > startx) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + { + index--; - fastPaint = true; - repaint(); + continue; + } -} + value = av.alignment.getSequenceAt(i).findPosition(index); -/** - * 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. - */ + break; + } - public void paintComponent(Graphics g) - { - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); + if (value != -1) + { + g.drawString(String.valueOf(value), av.charWidth/2, + (ypos + (i * av.charHeight)) - (av.charHeight / 5)); + } + } + } - if (fastPaint) + /** + * DOCUMENT ME! + * + * @param horizontal DOCUMENT ME! + * @param vertical DOCUMENT ME! + */ + public void fastPaint(int horizontal, int vertical) { - g.drawImage(img, 0, 0, this); - fastPaint = false; - return; - } + if (gg == null) + { + return; + } - // this draws the whole of the alignment - imgWidth = getWidth(); - imgHeight = getHeight(); + 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; - imgWidth -= imgWidth%av.charWidth; - imgHeight-= imgHeight%av.charHeight; + 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; - img = createImage(imgWidth,imgHeight); - gg = (Graphics2D)img.getGraphics(); - gg.setFont(av.getFont()); - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON); + if (es > av.endSeq) + { + es = av.endSeq; + } + } - gg.setColor(Color.white); - gg.fillRect(0,0,imgWidth,imgHeight); + gg.translate(transX, transY); + drawPanel(gg, sr, er, ss, es, sr, ss, 0); + gg.translate(-transX, -transY); - chunkWidth = getWrappedCanvasWidth( getWidth() ); - chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; + fastPaint = true; + repaint(); + } - av.setChunkHeight(chunkHeight); - av.setChunkWidth(chunkWidth); + /** + * 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); + sr.renderGaps(av.renderGaps); - 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 ( img != null && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) + || (getVisibleRect().height != g.getClipBounds().height))) + { + g.drawImage(img, 0, 0, this); + fastPaint = false; + return; + } - g.drawImage(img, 0, 0, this); - } + // this draws the whole of the alignment + imgWidth = getWidth(); + imgHeight = getHeight(); - public int getWrappedCanvasWidth(int cwidth) - { - FontMetrics fm = getFontMetrics(av.getFont()); + imgWidth -= (imgWidth % av.charWidth); + imgHeight -= (imgHeight % av.charHeight); - int LABEL_EAST = 0; - if(av.scaleRightWrapped) - LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" ); - int LABEL_WEST = 0; - if(av.scaleLeftWrapped) - LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"0" ); + if ((imgWidth < 1) || (imgHeight < 1)) + { + return; + } - return (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth; - } + 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); - public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) - { - AlignmentI al = av.getAlignment(); + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, imgHeight); - 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" ); + 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); + } - int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth; - int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; + g.drawImage(img, 0, 0, this); - int endx = startRes+cWidth-1; - int ypos = 2*av.charHeight; + if (pdbCanvas != null) + { + pdbCanvas.updateSeqColours(); + } + } - while (ypos <= canvasHeight && endx al.getWidth()) - endx = al.getWidth(); + /** + * Generates a string of zeroes. + * @return String + */ + String getMask() + { + String mask = "0"; + for (int i = av.alignment.getWidth(); i > 0; i /= 10) + { + mask += "0"; } + return mask; + } - } + /** + * 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(); - public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { + FontMetrics fm = getFontMetrics(av.getFont()); - Graphics2D g = (Graphics2D)g1; - g.setFont(av.getFont()); - RendererI sr = av.getRenderer(); + int LABEL_EAST = 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); + int LABEL_WEST = 0; - else if (sr instanceof GraphRenderer) - pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0), - av.getAlignment().getSequences(), - av.getPIDWindow(),x1,x2); + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } -*/ + int hgap = av.charHeight; + if(av.scaleAboveWrapped) + hgap += av.charHeight; - /* 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; - - /// 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,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); - } - } - // - ///////////////////////////////////// + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + int cHeight = av.getAlignment().getHeight() * av.charHeight; - // Now outline any areas if necessary - ///////////////////////////////////// - SequenceGroup group = av.getSelectionGroup(); - java.util.Vector groups = av.alignment.getGroups(); + av.setWrappedWidth(cWidth); - int sx = -1, sy = -1, ex = -1; - int groupIndex = -1; - if (group == null && groups.size() > 0) - { - group = (SequenceGroup) groups.elementAt(0); - groupIndex = 0; - } + av.endRes = av.startRes + cWidth; - if (group != null) - do - { - int oldY = -1; - int i = 0; - boolean inGroup = false; - int top=-1, bottom =-1; - for (i = y1; i < y2; i++) + + int endx = (startRes + cWidth) - 1; + int ypos = hgap; + + + while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth())) { - sx = (group.getStartRes() - startx) * av.charWidth; - sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); - ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth; + g.setFont(av.getFont()); + g.setColor(Color.black); - if (av.getWrapAlignment()) - { - if (sx < 0) - sx = 0; + if (av.scaleLeftWrapped) + { + drawWestScale(g, startRes, endx, ypos); + } - if (ex > getWidth()) + if (av.scaleRightWrapped) { - if (av.getWrapAlignment()) - ex = getWrappedCanvasWidth(getWidth()) * av.charWidth; + 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); } - } - else if(ex>getWidth()) - ex -= av.charWidth; + // When printing we have an extra clipped region, + // the Printable page which we need to account for here + Shape clip = g.getClip(); - 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 (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 (!inGroup) + if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size()) { - if (top == -1 && i==0 || - !group.sequences.contains(av.alignment.getSequenceAt(i - 1))) - top = sy; + endx = av.vconsensus.size() - 2; + } - 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) + drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos); + + if(av.showAnnotation) { - g.drawLine(sx, oldY, sx, sy ); - g.drawLine(sx+ex, oldY, sx+ex, sy ); + g.translate(0, cHeight + ypos + 3); + if(annotations==null) + annotations = new AnnotationPanel(av); - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top =-1; - } - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } + 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; - inGroup = false; + if (endx > al.getWidth()) + { + endx = al.getWidth(); } - } } + } - if (inGroup) - { + AnnotationPanel annotations; + int getAnnotationHeight() + { + if(!av.showAnnotation) + return 0; - 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; + if(annotations==null) + annotations = new AnnotationPanel(av); - group = (SequenceGroup) groups.elementAt(groupIndex); + return annotations.adjustPanelHeight(); + } - } - while (groupIndex < groups.size()); + /** + * 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() + { + aaRatio += .025; + if(aaRatio>1) + aaRatio = 1; + + repaint(); + } + + public void decreaseAARation() + { + aaRatio -= .025; + if(aaRatio<0) + aaRatio = 0; + + repaint(); + } - /// Highlight search Results once all sequences have been drawn - ////////////////////////////////////////////////////////// - if(displaySearch) + 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) + ColourSchemeI cs = av.getGlobalColourScheme(); + + /// First draw the sequences + ///////////////////////////// + for (int i = y1; i < y2; i++) { - SequenceRenderer ssr = (SequenceRenderer) sr; - if(searchStart x2) - searchEnd = x2; - ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq), - searchStart, - searchEnd, - (searchStart - startx) * av.charWidth, - offset + - AlignmentUtil.getPixelHeight(starty, searchSeq, - av.charHeight), - av.charWidth, - av.charHeight); + 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); - public void highlightSearchResults(int [] results) - { - // results are in the order sequence, startRes, endRes - if(results==null) - displaySearch = false; - else - displaySearch = true; + int searchStart = seq.findIndex(searchResults[r + 1]) - 1; + int searchEnd = seq.findIndex(searchResults[r + 2]) - 1; - searchResults = results; + SequenceRenderer ssr = (SequenceRenderer) sr; - repaint(); - } + 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(); + } }