/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1) * 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(); } }