X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=0297fce80bce03399354c8e01e159eb08bcd6ccb;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=1339988e925ce4cbe2149e130bfcc6e4ff4f79a3;hpb=f59219438e94c6c782995d472b654fb2526cb293;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 1339988..0297fce 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,360 +1,948 @@ -package jalview.gui; - -import java.awt.*; -import javax.swing.*; -import java.util.*; -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.analysis.*; - - -public class SeqCanvas extends JPanel -{ - 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(); - - public SeqCanvas(AlignViewport av) - { - this.av = av; - setLayout(new BorderLayout()); - } - - 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(); - - if (img == null || - imgWidth != getWidth() || - imgHeight != getHeight() || - paintFlag == true) { - - imgWidth = (getWidth() > 0 ? getWidth() : 1); - imgHeight = (getHeight() > 0 ? getHeight() : 1); - - img = createImage(imgWidth,imgHeight); - gg = img.getGraphics(); - - // 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()); - - paintFlag = false; - - oldstartx = -1; - oldendx = -1; - oldstarty = -1; - oldendy = -1; - } - - int startx = av.getStartRes(); - int starty = av.getStartSeq(); - - int endx = av.getEndRes(); - int endy = av.getEndSeq(); - - double charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - - chunkWidth = (int)(getWidth()/charWidth); - chunkHeight = (da.getHeight() + 2)*charHeight; - - av.setChunkHeight(chunkHeight); - av.setChunkWidth(chunkWidth); - - int offy = av.getStartSeq(); - - if (oldendx == -1) { - fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight); - - /* if (av.getWrapAlignment() == true) { - startx = (int)(offy/chunkWidth)*chunkWidth; - endx = startx + chunkWidth; - starty = offy%chunkHeight; - endy = starty + da.getHeight(); - - int ypos = 0; - int rowstart = starty; - - if (starty == 0) { - ypos = 2*charHeight; - } else if (starty == 1) { - starty = 0; - ypos = charHeight; - } - - if (endy > da.getHeight()) { - endy = da.getHeight(); - } - - if (endx > da.getWidth()) { - endx = da.getWidth(); - } - - if (rowstart < 2) { - drawScale(startx,endx,charWidth,charHeight,ypos); - } - - 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; - } - - startx += chunkWidth; - endx = startx + chunkWidth; - starty = 0; - - if (endx > da.getWidth()) { - endx = da.getWidth(); - } - // Draw the rest of the panels - - while (ypos <= getHeight()) { - drawScale(startx,endx,charWidth,charHeight,ypos); - drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos); - - ypos += chunkHeight; - startx += chunkWidth; - endx = startx + chunkWidth; - - if (endy > da.getHeight()) { - endy = da.getHeight(); - } - - if (endx > da.getWidth()) { - endx = da.getWidth(); - } - - } - } else*/ { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - - oldstartx = startx; - oldendx = endx; - oldstarty = starty; - oldendy = endy; - - } - } - - else if (oldstartx < startx) - { - // This is dragging horizontal scrollbar to the right - - int delx = (int)((startx - oldstartx) * charWidth); - int delx2 = (int)((oldendx - startx + 1) * charWidth); - - gg.copyArea(delx,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),-delx,0); - - if (startx > oldendx) - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - else - drawPanel(gg,oldendx+1,endx,starty,endy,startx,starty,0); - - - oldstartx = startx; - oldendx = endx; - - } else if (oldstartx > startx) - { - // Horizontal scrollbar pulled to the left - - int delx = (int)((oldstartx - startx) * charWidth); - int delx2 = (int)((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,(int)((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,(int)((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); - } - - oldstarty = starty; - oldendy = endy; - } - - 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()); - } - - - g.drawImage(img,0,0,this); - - } - - - - - 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); - - else if (sr instanceof GraphRenderer) - pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0), - av.getAlignment().getSequences(), - av.getPIDWindow(),x1,x2); - -*/ - - if (y2 > starty && y1 < av.getEndSeq()) { - - 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())); - } - - for (int i = y1 ; i < y2 ;i++) { - - 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"); - } -*/ - - r.drawSequence(g,cs,av.getAlignment().getSequenceAt(i), - x1, - x2, - (int)((x1-startx)*charWidth), - offset + AlignmentUtil.getPixelHeight(starty,i,av.getCharHeight()), - charWidth, - charHeight,showScores,av.getShowBoxes(),av.getShowText(),null,i,av); - - } - } - - - - public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) { - g.setColor(c); - g.fillRect(x1,y1,width,height); - } - - public int getChunkWidth() { - return chunkWidth; - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview 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 3 of the License, or (at your option) any later version. + * + * Jalview 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 Jalview. If not, see . + */ +package jalview.gui; + +import java.awt.*; +import java.awt.image.*; +import javax.swing.*; + +import jalview.datamodel.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class SeqCanvas extends JComponent +{ + final FeatureRenderer fr; + + final SequenceRenderer sr; + + BufferedImage img; + + Graphics2D gg; + + int imgWidth; + + int imgHeight; + + AlignViewport av; + + SearchResults searchResults = null; + + boolean fastPaint = false; + + int LABEL_WEST; + + int LABEL_EAST; + + int cursorX = 0; + + int cursorY = 0; + + /** + * Creates a new SeqCanvas object. + * + * @param av + * DOCUMENT ME! + */ + public SeqCanvas(AlignmentPanel ap) + { + this.av = ap.av; + fr = new FeatureRenderer(ap); + sr = new SequenceRenderer(av); + setLayout(new BorderLayout()); + PaintRefresher.Register(this, av.getSequenceSetId()); + setBackground(Color.white); + } + + public SequenceRenderer getSequenceRenderer() + { + return sr; + } + + public FeatureRenderer getFeatureRenderer() + { + return fr; + } + + /** + * 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) + { + int value = i; + if (av.hasHiddenColumns) + { + value = av.getColumnSelection().adjustForHiddenColumns(value); + } + + g.drawString(String.valueOf(value), (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); + } + } + + /** + * 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; + + if (av.hasHiddenColumns) + { + startx = av.getColumnSelection().adjustForHiddenColumns(startx); + endx = av.getColumnSelection().adjustForHiddenColumns(endx); + } + + int maxwidth = av.alignment.getWidth(); + if (av.hasHiddenColumns) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + } + + // WEST 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)); + } + } + } + + /** + * 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; + + if (av.hasHiddenColumns) + { + endx = av.getColumnSelection().adjustForHiddenColumns(endx); + } + + SequenceI seq; + // EAST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) + { + 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 = seq.findPosition(index); + + break; + } + + if (value != -1) + { + g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight)) + - (av.charHeight / 5)); + } + } + } + + boolean fastpainting = false; + + /** + * need to make this thread safe move alignment rendering in response to + * slider adjustment + * + * @param horizontal + * shift along + * @param vertical + * shift up or down in repaint + */ + public void fastPaint(int horizontal, int vertical) + { + if (fastpainting) + { + return; + } + fastpainting = true; + if (gg == null) + { + return; + } + + fastPaint = true; + + 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, 0); + gg.translate(-transX, -transY); + + repaint(); + fastpainting = false; + } + + /** + * 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) + { + BufferedImage lcimg = img; // take reference since other threads may null + // img and call later. + super.paintComponent(g); + + if (lcimg != null + && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g + .getClipBounds().height))) + { + g.drawImage(lcimg, 0, 0, this); + fastPaint = false; + return; + } + + // this draws the whole of the alignment + imgWidth = getWidth(); + imgHeight = getHeight(); + + imgWidth -= (imgWidth % av.charWidth); + imgHeight -= (imgHeight % av.charHeight); + + if ((imgWidth < 1) || (imgHeight < 1)) + { + return; + } + + if (lcimg == null || imgWidth != lcimg.getWidth() + || imgHeight != lcimg.getHeight()) + { + try + { + lcimg = img = new BufferedImage(imgWidth, imgHeight, + BufferedImage.TYPE_INT_RGB); + gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + } catch (OutOfMemoryError er) + { + System.gc(); + System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er); + new OOMWarning("Creating alignment image for display", er); + + return; + } + } + + if (av.antiAlias) + { + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } + + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, imgHeight); + + if (av.getWrapAlignment()) + { + drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes); + } + else + { + drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0); + } + + g.drawImage(lcimg, 0, 0, this); + + } + + /** + * DOCUMENT ME! + * + * @param cwidth + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getWrappedCanvasWidth(int cwidth) + { + FontMetrics fm = getFontMetrics(av.getFont()); + + LABEL_EAST = 0; + LABEL_WEST = 0; + + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } + + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } + + return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + } + + /** + * Generates a string of zeroes. + * + * @return String + */ + String getMask() + { + String mask = "00"; + int maxWidth = 0; + int tmp; + for (int i = 0; i < av.alignment.getHeight(); i++) + { + tmp = av.alignment.getSequenceAt(i).getEnd(); + if (tmp > maxWidth) + { + maxWidth = tmp; + } + } + + for (int i = maxWidth; 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(); + + FontMetrics fm = getFontMetrics(av.getFont()); + + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } + + 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; + + av.setWrappedWidth(cWidth); + + av.endRes = av.startRes + cWidth; + + int endx; + int ypos = hgap; + int maxwidth = av.alignment.getWidth() - 1; + + if (av.hasHiddenColumns) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + } + + while ((ypos <= canvasHeight) && (startRes < maxwidth)) + { + endx = startRes + cWidth - 1; + + if (endx > maxwidth) + { + endx = maxwidth; + } + + 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); + } + + if (av.hasHiddenColumns && av.showHiddenMarkers) + { + g.setColor(Color.blue); + int res; + for (int i = 0; i < av.getColumnSelection().getHiddenColumns() + .size(); i++) + { + res = av.getColumnSelection().findHiddenRegionPosition(i) + - startRes; + + if (res < 0 || res > endx - startRes) + { + continue; + } + + gg.fillPolygon(new int[] + { res * av.charWidth - av.charHeight / 4, + res * av.charWidth + av.charHeight / 4, res * av.charWidth }, + new int[] + { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2), + ypos - (av.charHeight / 2) + 8 }, 3); + + } + } + + // 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(), 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 - 3); + } + g.setClip(clip); + g.translate(-LABEL_WEST, 0); + + ypos += cHeight + getAnnotationHeight() + hgap; + + startRes += cWidth; + } + } + + AnnotationPanel annotations; + + int getAnnotationHeight() + { + if (!av.showAnnotation) + { + return 0; + } + + if (annotations == null) + { + annotations = new AnnotationPanel(av); + } + + return annotations.adjustPanelHeight(); + } + + /** + * DOCUMENT ME! + * + * @param g1 + * DOCUMENT ME! + * @param startRes + * DOCUMENT ME! + * @param endRes + * DOCUMENT ME! + * @param startSeq + * DOCUMENT ME! + * @param endSeq + * DOCUMENT ME! + * @param offset + * DOCUMENT ME! + */ + void drawPanel(Graphics g1, int startRes, int endRes, int startSeq, + int endSeq, int offset) + { + if (!av.hasHiddenColumns) + { + draw(g1, startRes, endRes, startSeq, endSeq, offset); + } + else + { + java.util.Vector regions = av.getColumnSelection().getHiddenColumns(); + + int screenY = 0; + int blockStart = startRes; + int blockEnd = endRes; + + for (int i = 0; regions != null && i < regions.size(); i++) + { + int[] region = (int[]) regions.elementAt(i); + int hideStart = region[0]; + int hideEnd = region[1]; + + if (hideStart <= blockStart) + { + blockStart += (hideEnd - hideStart) + 1; + continue; + } + + blockEnd = hideStart - 1; + + g1.translate(screenY * av.charWidth, 0); + + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + + if (av.getShowHiddenMarkers()) + { + g1.setColor(Color.blue); + + g1 + .drawLine((blockEnd - blockStart + 1) * av.charWidth - 1, + 0 + offset, (blockEnd - blockStart + 1) + * av.charWidth - 1, (endSeq - startSeq) + * av.charHeight + offset); + } + + g1.translate(-screenY * av.charWidth, 0); + screenY += blockEnd - blockStart + 1; + blockStart = hideEnd + 1; + } + + if (screenY <= (endRes - startRes)) + { + blockEnd = blockStart + (endRes - startRes) - screenY; + g1.translate(screenY * av.charWidth, 0); + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + + g1.translate(-screenY * av.charWidth, 0); + } + } + + } + + // int startRes, int endRes, int startSeq, int endSeq, int x, int y, + // int x1, int x2, int y1, int y2, int startx, int starty, + void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq, + int offset) + { + g.setFont(av.getFont()); + sr.prepare(g, av.renderGaps); + + SequenceI nextSeq; + + // / First draw the sequences + // /////////////////////////// + for (int i = startSeq; i < endSeq; i++) + { + nextSeq = av.alignment.getSequenceAt(i); + if (nextSeq == null) + { + // occasionally, a race condition occurs such that the alignment row is + // empty + continue; + } + sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq), + startRes, endRes, offset + ((i - startSeq) * av.charHeight)); + + if (av.showSequenceFeatures) + { + fr.drawSequence(g, nextSeq, startRes, endRes, offset + + ((i - startSeq) * av.charHeight)); + } + + // / Highlight search Results once all sequences have been drawn + // //////////////////////////////////////////////////////// + if (searchResults != null) + { + int[] visibleResults = searchResults.getResults(nextSeq, startRes, + endRes); + if (visibleResults != null) + { + for (int r = 0; r < visibleResults.length; r += 2) + { + sr.drawHighlightedText(nextSeq, visibleResults[r], + visibleResults[r + 1], (visibleResults[r] - startRes) + * av.charWidth, offset + + ((i - startSeq) * av.charHeight)); + } + } + } + + if (av.cursorMode && cursorY == i && cursorX >= startRes + && cursorX <= endRes) + { + sr.drawCursor(nextSeq, cursorX, + (cursorX - startRes) * av.charWidth, offset + + ((i - startSeq) * av.charHeight)); + } + } + + if (av.getSelectionGroup() != null + || av.alignment.getGroups().size() > 0) + { + drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); + } + + } + + void drawGroupsBoundaries(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq, int offset) + { + Graphics2D g = (Graphics2D) g1; + // + // /////////////////////////////////// + // Now outline any areas if necessary + // /////////////////////////////////// + SequenceGroup group = av.getSelectionGroup(); + + int sx = -1; + int sy = -1; + int ex = -1; + int groupIndex = -1; + int visWidth = (endRes - startRes + 1) * av.charWidth; + + if ((group == null) && (av.alignment.getGroups().size() > 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 = startSeq; i < endSeq; i++) + { + sx = (group.getStartRes() - startRes) * av.charWidth; + sy = offset + ((i - startSeq) * av.charHeight); + ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1; + + if (sx + ex < 0 || sx > visWidth) + { + continue; + } + + if ((sx <= (endRes - startRes) * av.charWidth) + && group.getSequences(null).contains( + av.alignment.getSequenceAt(i))) + { + if ((bottom == -1) + && !group.getSequences(null).contains( + av.alignment.getSequenceAt(i + 1))) + { + bottom = sy + av.charHeight; + } + + if (!inGroup) + { + if (((top == -1) && (i == 0)) + || !group.getSequences(null).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 < visWidth) + { + g.drawLine(sx, oldY, sx, sy); + } + + if (sx + ex < visWidth) + { + g.drawLine(sx + ex, oldY, sx + ex, sy); + } + + if (sx < 0) + { + ex += sx; + sx = 0; + } + + if (sx + ex > visWidth) + { + ex = visWidth; + } + + else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) + { + ex = (endRes - startRes + 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 - startSeq) * av.charHeight); + if (sx >= 0 && sx < visWidth) + { + g.drawLine(sx, oldY, sx, sy); + } + + if (sx + ex < visWidth) + { + g.drawLine(sx + ex, oldY, sx + ex, sy); + } + + if (sx < 0) + { + ex += sx; + sx = 0; + } + + if (sx + ex > visWidth) + { + ex = visWidth; + } + else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) + { + ex = (endRes - startRes + 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++; + + g.setStroke(new BasicStroke()); + + if (groupIndex >= av.alignment.getGroups().size()) + { + break; + } + + group = (SequenceGroup) av.alignment.getGroups().elementAt( + groupIndex); + + } while (groupIndex < av.alignment.getGroups().size()); + + } + + } + + /** + * DOCUMENT ME! + * + * @param results + * DOCUMENT ME! + */ + public void highlightSearchResults(SearchResults results) + { + img = null; + + searchResults = results; + + repaint(); + } +}