X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=45bcf66d4c7bbb62c62229db86ad53007fe25719;hb=3e6b14950a06bb87c147493e4dfff0c4491ea25b;hp=507b7b04b94c391f789434ce4e589c70f5294a8c;hpb=00386d5511d779b555e93dbf71f33675937e1570;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 507b7b0..45bcf66 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,315 +1,909 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2006 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 { - FeatureRenderer fr; - Image img; - Graphics gg; - int imgWidth; - int imgHeight; + 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(AlignViewport av) + { + this.av = av; + fr = new FeatureRenderer(av); + sr = new SequenceRenderer(av); + setLayout(new BorderLayout()); + PaintRefresher.Register(this, av.getSequenceSetId()); + setBackground(Color.white); + } - AlignViewport av; + MCview.PDBCanvas pdbCanvas; + public SequenceRenderer getSequenceRenderer() + { + return sr; + } - public boolean paintFlag = false; + public FeatureRenderer getFeatureRenderer() + { + return fr; + } - boolean showScores = false; - boolean displaySearch = false; - int [] searchResults = null; + public void setPDBCanvas(MCview.PDBCanvas pc) + { + pdbCanvas = pc; + } - int chunkHeight; - int chunkWidth; + public AlignViewport getViewport() + { + return av; + } - public SeqCanvas(AlignViewport av) + /** + * 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) { - this.av = av; - fr = new FeatureRenderer(av); - setLayout(new BorderLayout()); - PaintRefresher.Register(this); + 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); + } } - public void drawScale(Graphics g, int startx, int endx,int ypos) { - int scalestartx = startx - startx%10 + 10; + /** + * 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; - g.setColor(Color.black); + if(av.hasHiddenColumns) + { + startx = av.getColumnSelection().adjustForHiddenColumns(startx); + endx = av.getColumnSelection().adjustForHiddenColumns(endx); + } - 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); + int maxwidth = av.alignment.getWidth(); + if (av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; - 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 ); + // 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; -/** - * 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. - */ + while (index > startx) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + { + index--; - public void paintComponent(Graphics g) - { + continue; + } - if (img==null || imgWidth!=getWidth() || imgHeight!=getHeight() || paintFlag) - { - imgWidth = getWidth(); - imgHeight = getHeight(); - img = createImage(imgWidth,imgHeight); - gg = img.getGraphics(); - gg.setFont(av.getFont()); - paintFlag = false; + value = seq.findPosition(index); + + break; + } + + if (value != -1) + { + g.drawString(String.valueOf(value), 0, + (ypos + (i * av.charHeight)) - (av.charHeight / 5)); + } + } } + /** + * DOCUMENT ME! + * + * @param horizontal DOCUMENT ME! + * @param vertical DOCUMENT ME! + */ + public void fastPaint(int horizontal, int vertical) + { + if (gg == null) + { + return; + } - chunkWidth = getWidth()/av.charWidth; - chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; - av.setChunkHeight(chunkHeight); - av.setChunkWidth(chunkWidth); + fastPaint = true; - fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight); + gg.copyArea(horizontal * av.charWidth, + vertical * av.charHeight, + imgWidth, + imgHeight, + -horizontal * av.charWidth, + -vertical * av.charHeight); - 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 sr = av.startRes; + int er = av.endRes; + int ss = av.startSeq; + int es = av.endSeq; + int transX = 0; + int transY = 0; - g.drawImage(img,0,0,this); + 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; + } + } - public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) - { - AlignmentI da = av.getAlignment(); + gg.translate(transX, transY); + drawPanel(gg, sr, er, ss, es, 0); + gg.translate(-transX, -transY); - int cWidth = canvasWidth/av.charWidth; - int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; + repaint(); + } - int endx = startRes+cWidth-1; - int ypos = 2*av.charHeight; + /** + * 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); - while (ypos <= canvasHeight) - { - drawScale(g, startRes, endx, ypos); - drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos); - ypos += cHeight; - startRes += cWidth; - endx = startRes + cWidth - 1; - if (endx > da.getWidth()) - endx = da.getWidth(); - } + if ( img != null && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) + || (getVisibleRect().height != g.getClipBounds().height))) + { + g.drawImage(img, 0, 0, this); + fastPaint = false; + return; + } - } + // this draws the whole of the alignment + imgWidth = getWidth(); + imgHeight = getHeight(); - public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { + imgWidth -= (imgWidth % av.charWidth); + imgHeight -= (imgHeight % av.charHeight); + if ((imgWidth < 1) || (imgHeight < 1)) + { + return; + } - g.setFont(av.getFont()); - RendererI sr = av.getRenderer(); + if (img == null || imgWidth != img.getWidth() || imgHeight != img.getHeight()) + { + try{ + img = new BufferedImage(imgWidth, imgHeight, + BufferedImage.TYPE_INT_RGB); + gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + }catch(OutOfMemoryError er) + { + System.gc(); + System.out.println(er +" making image, SeqCanvas"); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + javax.swing.JOptionPane.showInternalMessageDialog(Desktop. + desktop, + "Out of memory creating alignment image!!" + + + "\nSee help files for increasing Java Virtual Machine memory." + , "Out of memory", + javax.swing.JOptionPane.WARNING_MESSAGE); + } + }); + + return; + } + } - /*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.antiAlias) + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); - if (sr instanceof SequenceRenderer) - pid = AAFrequency.calculate(tmpseq,x1,x2); + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, imgHeight); - else if (sr instanceof GraphRenderer) - pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0), - av.getAlignment().getSequences(), - av.getPIDWindow(),x1,x2); -*/ + if (av.getWrapAlignment()) + { + drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes); + } + else + { + drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0); + } + + g.drawImage(img, 0, 0, this); + + if (pdbCanvas != null) + { + pdbCanvas.updateSeqColours(); + } + + } + + /** + * 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()); + } - /* if (y2 > starty && y1 < av.getEndSeq()) + return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + } + + + /** + * Generates a string of zeroes. + * @return String + */ + String getMask() { - 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++) + String mask = "00"; + int maxWidth = 0; + int tmp; + for(int i=0; imaxWidth) + 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) { - nextSeq = av.getAlignment().getSequenceAt(i); + AlignmentI al = av.getAlignment(); + + FontMetrics fm = getFontMetrics(av.getFont()); + - group = av.alignment.findGroup( nextSeq ); - groups = av.alignment.findAllGroups( nextSeq ); + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } - sr.drawSequence(g, nextSeq, groups,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, groups, x1, x2, - (x1 - startx) * av.charWidth, - offset + - AlignmentUtil.getPixelHeight(starty, i, av.charHeight), - av.charWidth, av.charHeight, null, i); - } + 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); - if( group!=null ) - { + av.endRes = av.startRes + cWidth; - g.setColor(Color.lightGray); - sx = (group.getStartRes()-startx)*av.charWidth; - sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); - ex = (group.getEndRes()+1-startx)*av.charWidth; - ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.charHeight); + int endx; + int ypos = hgap; + int maxwidth = av.alignment.getWidth()-1; + if(av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1; - if (!inGroup) + while ((ypos <= canvasHeight) && (startRes < maxwidth)) { - g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box - inGroup=true; + 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; - 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) * av.charWidth; - sy = offset + - AlignmentUtil.getPixelHeight(starty, i, av.charHeight); - ex = (group.getEndRes() + 1 - startx) * av.charWidth; - ey = offset + - AlignmentUtil.getPixelHeight(starty, i + 1, av.charHeight); - - 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; + if(annotations==null) + annotations = new AnnotationPanel(av); + return annotations.adjustPanelHeight(); } - /// Highlight search Results once all sequences have been drawn - if(displaySearch) + /** + * 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) { - for(int r=0; r= y1 && searchSeq < y2) + for (int i = 0; i < regions.size(); i++) { - SequenceRenderer ssr = (SequenceRenderer) sr; - ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq), - searchStart, - searchEnd, - (searchStart - startx) * av.charWidth, - offset + - AlignmentUtil.getPixelHeight(starty, searchSeq, - av.charHeight), - av.charWidth, - av.charHeight); + 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); } } + } - } - 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; - } - public void highlightSearchResults(int [] results) - { - // results are in the order sequence, startRes, endRes - if(results==null) - displaySearch = false; - else - displaySearch = true; + //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); - searchResults = results; + SequenceI nextSeq; + + /// First draw the sequences + ///////////////////////////// + for (int i = startSeq; i < endSeq; i++) + { + nextSeq = av.alignment.getSequenceAt(i); + + 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; + } - paintFlag = true; - repaint(); - } + 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(); + } }