/* * 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.*; public class SeqCanvas extends Panel { FeatureRenderer fr; SequenceRenderer sr; Image img; Graphics gg; int imgWidth; int imgHeight; AlignViewport av; SearchResults searchResults = null; 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, av.alignment); } public AlignViewport getViewport() { return av; } 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); // NORTH SCALE for (int i = scalestartx; i < endx; i += 10) { String string = String.valueOf(i); g.drawString(string, (i - startx - 1) * av.charWidth, ypos - av.charHeight / 2); g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos + 2 - av.charHeight / 2, (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2); } } 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++) { 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); } } } void drawEastScale(Graphics g, int startx, int endx, int ypos) { ypos += av.charHeight; // EAST SCALE for (int i = 0; i < av.alignment.getHeight(); i++) { SequenceI seq = av.alignment.getSequenceAt(i); int index = endx; int value = -1; while (index > startx) { if (jalview.util.Comparison.isGap(seq.getCharAt(index))) { index--; continue; } value = seq.findPosition(index); break; } if (value != -1) { g.drawString(value + "", av.charWidth/2, 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; } lastsr = av.startRes; 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.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(); } /** * 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); } public void paint(Graphics g) { if (fastPaint) { g.drawImage(img, 0, 0, this); fastPaint = false; return; } // this draws the whole of the alignment imgWidth = this.getSize().width; imgHeight = this.getSize().height; 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 (av.getWrapAlignment()) { drawWrappedPanel(gg, imgWidth, imgHeight, 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(); } } int LABEL_WEST, LABEL_EAST; public int getWrappedCanvasWidth(int cwidth) { cwidth -= cwidth % av.charWidth; 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"; 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(); 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; while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth())) { endx = startRes + cWidth -1; if (endx > al.getWidth()) { endx = al.getWidth(); } g.setColor(Color.black); if (av.scaleLeftWrapped) { drawWestScale(g, startRes, endx, ypos); } if (av.scaleRightWrapped) { g.translate(canvasWidth - LABEL_EAST, 0); drawEastScale(g, startRes, endx, ypos); g.translate(-(canvasWidth - LABEL_EAST), 0); } g.translate(LABEL_WEST, 0); if (av.scaleAboveWrapped) { drawNorthScale(g, startRes, endx, ypos); } if(g.getClip()==null) g.setClip(0, 0, cWidth * av.charWidth, canvasHeight); drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); g.setClip(null); if(av.showAnnotation) { g.translate(0, cHeight + ypos+4); if(annotations==null) annotations = new AnnotationPanel(av); annotations.drawComponent( g, startRes, endx+1 ); g.translate(0, -cHeight - ypos-4); } 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(); } 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 = 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) { 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(); 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 ) { do { int oldY = -1; int i = 0; boolean inGroup = false; int top = -1; int bottom = -1; int alHeight = av.alignment.getHeight()-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>imgWidth) { continue; } if ( (sx <= (endRes-startRes)*av.charWidth) && group.getSequences(false).contains(av.alignment.getSequenceAt( i))) { if ( (bottom == -1) && (i >= alHeight || !group.getSequences(false).contains( av.alignment.getSequenceAt(i + 1)))) { bottom = sy + av.charHeight; } if (!inGroup) { if (((top == -1) && (i == 0)) || !group.getSequences(false).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 { 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; } } } 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) { 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 - 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()); } } public void highlightSearchResults(SearchResults results) { searchResults = results; repaint(); } }