X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=f6ef5779f0e3433e508c8d38b14370e3301c15e9;hb=b437b816507d2acc59e34f70a9cf8c7f81921681;hp=6855468016e5c448132459efd9a19a9b6ad84c68;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index 6855468..f6ef577 100755 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@ -1,60 +1,81 @@ /* -* 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 -*/ + * 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.appletgui; import java.awt.*; -import jalview.datamodel.*; -import jalview.analysis.*; +import jalview.datamodel.*; -public class SeqCanvas extends Panel +public class SeqCanvas + extends Panel { - FeatureRenderer fr; - SequenceRenderer sr; - Image img; - Graphics gg; - int imgWidth; - int imgHeight; + FeatureRenderer fr; + SequenceRenderer sr; + Image img; + Graphics gg; + int imgWidth; + int imgHeight; - AlignViewport av; + AlignViewport av; - boolean showScores = false; - boolean displaySearch = false; - int [] searchResults = null; + SearchResults searchResults = null; - int chunkHeight; - int chunkWidth; + boolean fastPaint = false; - boolean fastPaint = false; + int cursorX = 0; + int cursorY = 0; - public SeqCanvas(AlignViewport av) - { - this.av = av; - fr = new FeatureRenderer(av); - sr = new SequenceRenderer(av); - PaintRefresher.Register(this); - } + public SeqCanvas(AlignViewport av) + { + this.av = av; + fr = new FeatureRenderer(av); + sr = new SequenceRenderer(av); + PaintRefresher.Register(this, av.alignment); + } + + public AlignViewport getViewport() + { + return av; + } - void drawNorthScale(Graphics g, int startx, int endx,int ypos) { + public FeatureRenderer getFeatureRenderer() + { + return fr; + } + + MCview.AppletPDBCanvas pdbCanvas; + public SequenceRenderer getSequenceRenderer() + { + return sr; + } + + public void setPDBCanvas(MCview.AppletPDBCanvas pc) + { + pdbCanvas = pc; + } + + + void drawNorthScale(Graphics g, int startx, int endx, int ypos) + { int scalestartx = startx - startx % 10 + 10; g.setColor(Color.black); @@ -76,8 +97,8 @@ public class SeqCanvas extends Panel void drawWestScale(Graphics g, int startx, int endx, int ypos) { FontMetrics fm = getFontMetrics(av.getFont()); - ypos+= av.charHeight; - // EAST SCALE + ypos += av.charHeight; + // EAST SCALE for (int i = 0; i < av.alignment.getHeight(); i++) { SequenceI seq = av.alignment.getSequenceAt(i); @@ -94,98 +115,126 @@ public class SeqCanvas extends Panel value = av.alignment.getSequenceAt(i).findPosition(index); break; } - if(value!=-1) + if (value != -1) { - int x = LABEL_WEST - fm.stringWidth(value+""); - g.drawString(value + "", x, ypos + i*av.charHeight - av.charHeight/5); + int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2; + 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) + ypos += av.charHeight; + // EAST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + SequenceI seq = av.alignment.getSequenceAt(i); + int index = endx; + int value = -1; + while (index > startx) { - index--; - continue; - } + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + { + index--; + continue; + } - value = av.alignment.getSequenceAt(i).findPosition(index); - break; + value = av.alignment.getSequenceAt(i).findPosition(index); + break; + } + if (value != -1) + { + g.drawString(value + "", av.charWidth/2, + ypos + i * av.charHeight - av.charHeight / 5); + } } - if(value!=-1) - g.drawString(value + "", 0, ypos + i*av.charHeight - av.charHeight/5); + } -} + int lastsr=0; + void fastPaint(int horizontal, int vertical) + { + if ( fastPaint || gg == null) + { + return; + } + // Its possible on certain browsers that the call to fastpaint + // is faster than it can paint, so this check here catches + // this possibility + if(lastsr + horizontal != av.startRes) + { + horizontal = av.startRes - lastsr; + } -public void fastPaint(int horizontal, int vertical) -{ - if (horizontal == 0 && vertical == 0 || gg==null) - return; + lastsr = av.startRes; - gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth, + fastPaint = true; + gg.copyArea(horizontal * av.charWidth, + vertical * av.charHeight, + imgWidth - horizontal * av.charWidth, + imgHeight - vertical * av.charHeight, + -horizontal * av.charWidth, -vertical * av.charHeight); + + int sr = av.startRes, er = av.endRes, 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; } else if (horizontal < 0) + { er = sr - horizontal; + } else if (vertical > 0) // scroll down { ss = es - vertical; - if(ss av.endSeq) + if (es > av.endSeq) + { es = av.endSeq; + } } - gg.translate(transX, transY); - gg.setColor(Color.white); - gg.fillRect(0,0, (er-sr+1)*av.charWidth, (es-ss)*av.charHeight); - drawPanel(gg, sr, er, ss, es, sr, ss, 0); + drawPanel(gg, sr, er, ss, es, 0); gg.translate( -transX, -transY); - fastPaint = true; repaint(); -} + } -/** - * 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. - */ + /** + * 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 update(Graphics g) { paint(g); @@ -193,6 +242,7 @@ public void fastPaint(int horizontal, int vertical) public void paint(Graphics g) { + if (fastPaint) { g.drawImage(img, 0, 0, this); @@ -201,312 +251,399 @@ public void fastPaint(int horizontal, int vertical) } // this draws the whole of the alignment - imgWidth = this.getSize().width; - imgHeight = this.getSize().height; + imgWidth = this.getSize().width; + imgHeight = this.getSize().height; - imgWidth -= imgWidth%av.charWidth; - imgHeight-= imgHeight%av.charHeight; + imgWidth -= imgWidth % av.charWidth; + imgHeight -= imgHeight % av.charHeight; - if(imgWidth<1 || imgHeight<1) - return; - - if(img==null || imgWidth!=img.getWidth(this) || imgHeight!=img.getHeight(this)) - { - img = createImage(imgWidth, imgHeight); - gg = img.getGraphics(); - gg.setFont(av.getFont()); - } - - gg.setColor(Color.white); - gg.fillRect(0,0,imgWidth,imgHeight); + if (imgWidth < 1 || imgHeight < 1) + { + return; + } - chunkWidth = getWrappedCanvasWidth( getSize().width ); - chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; + if (img == null || imgWidth != img.getWidth(this) || + imgHeight != img.getHeight(this)) + { + img = createImage(imgWidth, imgHeight); + gg = img.getGraphics(); + gg.setFont(av.getFont()); + } - av.setChunkHeight(chunkHeight); - av.setChunkWidth(chunkWidth); + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, imgHeight); if (av.getWrapAlignment()) - drawWrappedPanel(gg, getSize().width, getSize().height, av.startRes); + { + drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes); + } else - drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0); + { + drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0); + } g.drawImage(img, 0, 0, this); + if (pdbCanvas != null) + { + pdbCanvas.updateSeqColours(); + } } int LABEL_WEST, LABEL_EAST; public int getWrappedCanvasWidth(int cwidth) { - FontMetrics fm = getFontMetrics(av.getFont()); + FontMetrics fm = getFontMetrics(av.getFont()); - LABEL_EAST = 0; - LABEL_WEST = 0; + LABEL_EAST = 0; + LABEL_WEST = 0; - if(av.scaleRightWrapped) - LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" ); + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } - if(av.scaleLeftWrapped) - LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" ); + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } - return (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth; + return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; } - public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) + + /** + * Generates a string of zeroes. + * @return String + */ + String getMask() + { + String mask = "00"; + for (int i = av.alignment.getWidth(); i > 0; i /= 10) + { + mask += "0"; + } + return mask; + } + + public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, + int startRes) { - AlignmentI al = av.getAlignment(); + AlignmentI al = av.getAlignment(); - FontMetrics fm = getFontMetrics(av.getFont()); + 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"); + int LABEL_EAST = 0; + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } + + int LABEL_WEST = 0; + + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } - int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth; - int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; + int hgap = av.charHeight; + if(av.scaleAboveWrapped) + hgap += av.charHeight; - av.endRes = av.startRes + cWidth; + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + int cHeight = av.getAlignment().getHeight() * av.charHeight; - int endx = startRes+cWidth-1; - int ypos = 2*av.charHeight; + av.setWrappedWidth(cWidth); - while (ypos <= canvasHeight && startRes al.getWidth()) { + endx = al.getWidth(); + } + g.setColor(Color.black); - if(av.scaleLeftWrapped) - drawWestScale(g, startRes, endx, ypos); + 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.scaleRightWrapped) + if (av.scaleAboveWrapped) { - g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0); - drawEastScale(g, startRes, endx, ypos); - g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0); + drawNorthScale(g, startRes, endx, ypos); } - g.translate(LABEL_WEST,0); - if(av.scaleAboveWrapped) - drawNorthScale(g, startRes, endx, ypos); + if(g.getClip()==null) + g.setClip(0, 0, cWidth * av.charWidth, canvasHeight); + drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); + g.setClip(null); - // 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().y, - cWidth*av.charWidth, - (int)clip.getBounds().height - ); - drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos); - g.setClip(clip); - g.translate(-LABEL_WEST,0); + if(av.showAnnotation) + { + g.translate(0, cHeight + ypos+4); + if(annotations==null) + annotations = new AnnotationPanel(av); - ypos += cHeight; - startRes += cWidth; - endx = startRes + cWidth - 1; + annotations.drawComponent( g, startRes, endx ); + g.translate(0, -cHeight - ypos-4); + } + g.translate(-LABEL_WEST, 0); - if (endx > al.getWidth()) - endx = al.getWidth(); - } + ypos += cHeight+getAnnotationHeight()+hgap; + + + startRes += cWidth; + } } + AnnotationPanel annotations; + int getAnnotationHeight() + { + if(!av.showAnnotation) + return 0; - synchronized public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { + if(annotations==null) + annotations = new AnnotationPanel(av); + + return annotations.adjustPanelHeight(); + } + + void drawPanel(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset) + { g.setFont(av.getFont()); sr.renderGaps(av.renderGaps); SequenceI nextSeq; - /// First draw the sequences - ///////////////////////////// - for (int i = y1 ; i < y2 ;i++) + ///////////////////////////// + for (int i = startSeq; i < endSeq; i++) + { + nextSeq = av.alignment.getSequenceAt(i); + + sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), startRes, endRes, + offset + ( (i - startSeq) * av.charHeight)); + + if (av.showSequenceFeatures) { - 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); - - 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); - } + fr.drawSequence(g, nextSeq, startRes, endRes, + offset + ((i - startSeq) * av.charHeight), + av.charWidth, 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), + av.charWidth, av.charHeight); + } + } + + if (av.cursorMode && cursorY == i + && cursorX >= startRes && cursorX <= endRes) + { + sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth, + offset + ( (i - startSeq) * av.charHeight)); + } - // Now outline any areas if necessary - ///////////////////////////////////// - SequenceGroup group = av.getSelectionGroup(); - java.util.Vector groups = av.alignment.getGroups(); + } - int sx = -1, sy = -1, ex = -1; - int groupIndex = -1; - if (group == null && groups.size() > 0) - { - group = (SequenceGroup) groups.elementAt(0); + // + ///////////////////////////////////// + // Now outline any areas if necessary + ///////////////////////////////////// + SequenceGroup group = av.getSelectionGroup(); + + int sx = -1; + int sy = -1; + int ex = -1; + int groupIndex = -1; + + if ((group == null) && (av.alignment.getGroups().size() > 0)) + { + group = (SequenceGroup) av.alignment.getGroups().elementAt(0); groupIndex = 0; - } + } - if (group != null) + if ( group != null) + { do { - int oldY = -1; - int i = 0; - boolean inGroup = false; - int top=-1, bottom =-1; - for (i = y1; i < y2; i++) - { - sx = (group.getStartRes() - startx) * av.charWidth; - sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); - ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1; + int oldY = -1; + int i = 0; + boolean inGroup = false; + int top = -1; + int bottom = -1; - if (sx < getSize().width - && ex > 0 - && group.sequences.contains(av.alignment.getSequenceAt(i))) + for (i = startSeq; i < endSeq; i++) { - if (bottom == -1 && (i==av.alignment.getHeight()-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; + 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>imgWidth) + { + continue; + } - oldY = sy; - inGroup = true; - if (group == av.getSelectionGroup()) + if ( (sx <= (endRes-startRes)*av.charWidth) && + group.sequences.contains(av.alignment.getSequenceAt( + i))) { - g.setColor(new Color(255,0,0)); + if (bottom == -1) + { + if(i == endSeq-1 || // Dont check for i+1 if on the bottom row + !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.setColor(Color.red); + } + else + { + g.setColor(group.getOutlineColour()); + } + } } else { - g.setColor(group.getOutlineColour()); + 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 >= (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; + } } - } } - else + + if (inGroup) { - if (inGroup) + sy = offset + ( (i - startSeq) * 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) { - g.drawLine(sx, oldY, sx, sy ); - g.drawLine(sx+ex, oldY, sx+ex, sy ); + ex += sx; + sx = 0; + } - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top =-1; - } - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } + if (sx + ex > imgWidth) + ex = imgWidth; + 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; + } - inGroup = false; + if (bottom != -1) + { + g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); + bottom = -1; } + + inGroup = false; } - } - if (inGroup) - { + groupIndex++; - if(top!=-1) + if (groupIndex >= av.alignment.getGroups().size()) { - g.drawLine(sx, top, sx + ex, top); - top =-1; + break; } - 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; - - group = (SequenceGroup) groups.elementAt(groupIndex); - - } - while (groupIndex < groups.size()); - - - /// Highlight search Results once all sequences have been drawn - ////////////////////////////////////////////////////////// - if(displaySearch) - { - for(int r=0; r= 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 x2) - searchEnd = x2; - - ssr.drawHighlightedText(seq, - searchStart, - searchEnd, - (searchStart - startx) * av.charWidth, - offset + - AlignmentUtil.getPixelHeight(starty, searchSeq, - av.charHeight), - av.charWidth, - av.charHeight); - } + group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex); } + while (groupIndex < av.alignment.getGroups().size()); } - } - - - public void highlightSearchResults(int [] results) + public void highlightSearchResults(SearchResults results) { - // results are in the order sequence, startRes, endRes - if(results==null) - displaySearch = false; - else - displaySearch = true; - searchResults = results; repaint(); } - }