/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.awt.BasicStroke; import java.awt.BorderLayout; import java.awt.Color; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.Rectangle; import java.awt.RenderingHints; import java.awt.image.BufferedImage; import java.beans.PropertyChangeEvent; import java.util.Iterator; import java.util.List; import javax.swing.JPanel; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.datamodel.VisibleContigsIterator; import jalview.renderer.ScaleRenderer; import jalview.renderer.ScaleRenderer.ScaleMark; import jalview.util.Comparison; import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; /** * The Swing component on which the alignment sequences, and annotations (if * shown), are drawn. This includes scales above, left and right (if shown) in * Wrapped mode, but not the scale above in Unwrapped mode. * */ @SuppressWarnings("serial") public class SeqCanvas extends JPanel implements ViewportListenerI { /** * vertical gap in pixels between sequences and annotations when in wrapped * mode */ static final int SEQS_ANNOTATION_GAP = 3; private static final String ZEROS = "0000000000"; final FeatureRenderer fr; BufferedImage img; AlignViewport av; int cursorX = 0; int cursorY = 0; private final SequenceRenderer seqRdr; boolean fastPaint = false; private boolean fastpainting = false; private AnnotationPanel annotations; /* * measurements for drawing a wrapped alignment */ private int labelWidthEast; // label right width in pixels if shown private int labelWidthWest; // label left width in pixels if shown int wrappedSpaceAboveAlignment; // gap between widths int wrappedRepeatHeightPx; // height in pixels of wrapped width private int wrappedVisibleWidths; // number of wrapped widths displayed // Don't do this! Graphics handles are supposed to be transient // private Graphics2D gg; /** * Creates a new SeqCanvas object. * * @param ap */ public SeqCanvas(AlignmentPanel ap) { this.av = ap.av; fr = new FeatureRenderer(ap); seqRdr = new SequenceRenderer(av); setLayout(new BorderLayout()); PaintRefresher.Register(this, av.getSequenceSetId()); setBackground(Color.white); av.getRanges().addPropertyChangeListener(this); } public SequenceRenderer getSequenceRenderer() { return seqRdr; } public FeatureRenderer getFeatureRenderer() { return fr; } /** * Draws the scale above a region of a wrapped alignment, consisting of a * column number every major interval (10 columns). * * @param g * the graphics context to draw on, positioned at the start (bottom * left) of the line on which to draw any scale marks * @param startx * start alignment column (0..) * @param endx * end alignment column (0..) * @param ypos * y offset to draw at */ private void drawNorthScale(Graphics g, int startx, int endx, int ypos) { int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); /* * white fill the scale space (for the fastPaint case) */ g.setColor(Color.white); g.fillRect(0, ypos - charHeight - charHeight / 2, getWidth(), charHeight * 3 / 2 + 2); g.setColor(Color.black); List marks = new ScaleRenderer().calculateMarks(av, startx, endx); for (ScaleMark mark : marks) { int mpos = mark.column; // (i - startx - 1) if (mpos < 0) { continue; } String mstring = mark.text; if (mark.major) { if (mstring != null) { g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2)); } /* * draw a tick mark below the column number, centred on the column; * height of tick mark is 4 pixels less than half a character */ int xpos = (mpos * charWidth) + (charWidth / 2); g.drawLine(xpos, (ypos + 2) - (charHeight / 2), xpos, ypos - 2); } } } /** * Draw the scale to the left or right of a wrapped alignment * * @param g * graphics context, positioned at the start of the scale to be drawn * @param startx * first column of wrapped width (0.. excluding any hidden columns) * @param endx * last column of wrapped width (0.. excluding any hidden columns) * @param ypos * vertical offset at which to begin the scale * @param left * if true, scale is left of residues, if false, scale is right */ void drawVerticalScale(Graphics g, final int startx, final int endx, final int ypos, final boolean left) { int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); int yPos = ypos + charHeight; int startX = startx; int endX = endx; if (av.hasHiddenColumns()) { HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); startX = hiddenColumns.visibleToAbsoluteColumn(startx); endX = hiddenColumns.visibleToAbsoluteColumn(endx); } FontMetrics fm = getFontMetrics(av.getFont()); for (int i = 0; i < av.getAlignment().getHeight(); i++) { SequenceI seq = av.getAlignment().getSequenceAt(i); /* * find sequence position of first non-gapped position - * to the right if scale left, to the left if scale right */ int index = left ? startX : endX; int value = -1; while (index >= startX && index <= endX) { if (!Comparison.isGap(seq.getCharAt(index))) { value = seq.findPosition(index); break; } if (left) { index++; } else { index--; } } /* * white fill the space for the scale */ g.setColor(Color.white); int y = (yPos + (i * charHeight)) - (charHeight / 5); // fillRect origin is top left of rectangle g.fillRect(0, y - charHeight, left ? labelWidthWest : labelWidthEast, charHeight + 1); if (value != -1) { /* * draw scale value, right justified within its width less half a * character width padding on the right */ int labelSpace = left ? labelWidthWest : labelWidthEast; labelSpace -= charWidth / 2; // leave space to the right String valueAsString = String.valueOf(value); int labelLength = fm.stringWidth(valueAsString); int xOffset = labelSpace - labelLength; g.setColor(Color.black); g.drawString(valueAsString, xOffset, y); } } } /** * Does a fast paint of an alignment in response to a scroll. Most of the * visible region is simply copied and shifted, and then any newly visible * columns or rows are drawn. The scroll may be horizontal or vertical, but * not both at once. Scrolling may be the result of * * * @param horizontal * columns to shift right (positive) or left (negative) * @param vertical * rows to shift down (positive) or up (negative) */ public void fastPaint(int horizontal, int vertical) { // effectively: // if (horizontal != 0 && vertical != 0) // throw new InvalidArgumentException(); if (fastpainting || img == null) { return; } fastpainting = true; fastPaint = true; try { int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); ViewportRanges ranges = av.getRanges(); int startRes = ranges.getStartRes(); int endRes = ranges.getEndRes(); int startSeq = ranges.getStartSeq(); int endSeq = ranges.getEndSeq(); int transX = 0; int transY = 0; if (horizontal > 0) // scrollbar pulled right, image to the left { transX = (endRes - startRes - horizontal) * charWidth; startRes = endRes - horizontal; } else if (horizontal < 0) { endRes = startRes - horizontal; } if (vertical > 0) // scroll down { startSeq = endSeq - vertical; if (startSeq < ranges.getStartSeq()) { // ie scrolling too fast, more than a page at a time startSeq = ranges.getStartSeq(); } else { transY = img.getHeight() - ((vertical + 1) * charHeight); } } else if (vertical < 0) { endSeq = startSeq - vertical; if (endSeq > ranges.getEndSeq()) { endSeq = ranges.getEndSeq(); } } // jalview.bin.Console.errPrintln(">>> FastPaint to " + transX + " " + transY + " " // + horizontal + " " + vertical + " " + startRes + " " + endRes // + " " + startSeq + " " + endSeq); Graphics gg = img.getGraphics(); gg.copyArea(horizontal * charWidth, vertical * charHeight, img.getWidth(), img.getHeight(), -horizontal * charWidth, -vertical * charHeight); /** @j2sNative xxi = this.img */ gg.translate(transX, transY); drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); gg.translate(-transX, -transY); gg.dispose(); // Call repaint on alignment panel so that repaints from other alignment // panel components can be aggregated. Otherwise performance of the // overview window and others may be adversely affected. // jalview.bin.Console.outPrintln("SeqCanvas fastPaint() repaint() request..."); av.getAlignPanel().repaint(); } finally { fastpainting = false; } } @Override public void paintComponent(Graphics g) { int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); int width = getWidth(); int height = getHeight(); width -= (width % charWidth); height -= (height % charHeight); // BH 2019 can't possibly fastPaint if either width or height is 0 if (width == 0 || height == 0) { return; } ViewportRanges ranges = av.getRanges(); int startRes = ranges.getStartRes(); int startSeq = ranges.getStartSeq(); int endRes = ranges.getEndRes(); int endSeq = ranges.getEndSeq(); // [JAL-3226] problem that JavaScript (or Java) may consolidate multiple // repaint() requests in unpredictable ways. In this case, the issue was // that in response to a CTRL-C/CTRL-V paste request, in Java a fast // repaint request preceded two full requests, thus resulting // in a full request for paint. In constrast, in JavaScript, the three // requests were bundled together into one, so the fastPaint flag was // still present for the second and third request. // // This resulted in incomplete painting. // // The solution was to set seqCanvas.fastPaint and idCanvas.fastPaint false // in PaintRefresher when the target to be painted is one of those two // components. // // BH 2019.04.22 // // An initial idea; can be removed once we determine this issue is closed: // if (av.isFastPaintDisabled()) // { // fastPaint = false; // } Rectangle vis, clip; if (img != null && (fastPaint || (vis = getVisibleRect()).width != (clip = g .getClipBounds()).width || vis.height != clip.height)) { g.drawImage(img, 0, 0, this); drawSelectionGroup((Graphics2D) g, startRes, endRes, startSeq, endSeq); fastPaint = false; } else { // img is a cached version of the last view we drew. // If we have no img or the size has changed, make a new one. // if (img == null || width != img.getWidth() || height != img.getHeight()) { img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); } Graphics2D gg = (Graphics2D) img.getGraphics(); gg.setFont(av.getFont()); if (av.antiAlias) { gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); } gg.setColor(Color.white); gg.fillRect(0, 0, img.getWidth(), img.getHeight()); if (av.getWrapAlignment()) { drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); } else { drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); } drawSelectionGroup(gg, startRes, endRes, startSeq, endSeq); g.drawImage(img, 0, 0, this); gg.dispose(); } if (av.cursorMode) { drawCursor(g, startRes, endRes, startSeq, endSeq); } } /** * Draw an alignment panel for printing * * @param g1 * Graphics object to draw with * @param startRes * start residue of print area * @param endRes * end residue of print area * @param startSeq * start sequence of print area * @param endSeq * end sequence of print area */ public void drawPanelForPrinting(Graphics g1, int startRes, int endRes, int startSeq, int endSeq) { drawPanel(g1, startRes, endRes, startSeq, endSeq, 0); drawSelectionGroup((Graphics2D) g1, startRes, endRes, startSeq, endSeq); } /** * Draw a wrapped alignment panel for printing * * @param g * Graphics object to draw with * @param canvasWidth * width of drawing area * @param canvasHeight * height of drawing area * @param startRes * start residue of print area */ public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth, int canvasHeight, int startRes) { drawWrappedPanel(g, canvasWidth, canvasHeight, startRes); SequenceGroup group = av.getSelectionGroup(); if (group != null) { drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight, startRes); } } /** * Returns the visible width of the canvas in residues, after allowing for * East or West scales (if shown) * * @param canvasWidth * the width in pixels (possibly including scales) * * @return */ public int getWrappedCanvasWidth(int canvasWidth) { int charWidth = av.getCharWidth(); FontMetrics fm = getFontMetrics(av.getFont()); int labelWidth = 0; if (av.getScaleRightWrapped() || av.getScaleLeftWrapped()) { labelWidth = getLabelWidth(fm); } labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0; labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; } public int getMinimumWrappedCanvasWidth() { int charWidth = av.getCharWidth(); FontMetrics fm = getFontMetrics(av.getFont()); int labelWidth = 0; if (av.getScaleRightWrapped() || av.getScaleLeftWrapped()) { labelWidth = getLabelWidth(fm); } labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0; labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; return labelWidthEast + labelWidthWest + charWidth; } /** * Returns a pixel width sufficient to show the largest sequence coordinate * (end position) in the alignment, calculated as the FontMetrics width of * zeroes "0000000" limited to the number of decimal digits to be shown (3 for * 1-10, 4 for 11-99 etc). One character width is added to this, to allow for * half a character width space on either side. * * @param fm * @return */ protected int getLabelWidth(FontMetrics fm) { /* * find the biggest sequence end position we need to show * (note this is not necessarily the sequence length) */ int maxWidth = 0; AlignmentI alignment = av.getAlignment(); for (int i = 0; i < alignment.getHeight(); i++) { maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd()); } int length = 0; for (int i = maxWidth; i > 0; i /= 10) { length++; } return fm.stringWidth(ZEROS.substring(0, length)) + av.getCharWidth(); } /** * Draws as many widths of a wrapped alignment as can fit in the visible * window * * @param g * @param canvasWidth * available width in pixels * @param canvasHeight * available height in pixels * @param startColumn * the first column (0...) of the alignment to draw */ public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, final int startColumn) { int wrappedWidthInResidues = calculateWrappedGeometry(canvasWidth, canvasHeight); av.setWrappedWidth(wrappedWidthInResidues); ViewportRanges ranges = av.getRanges(); ranges.setViewportStartAndWidth(startColumn, wrappedWidthInResidues); // we need to call this again to make sure the startColumn + // wrappedWidthInResidues values are used to calculate wrappedVisibleWidths // correctly. calculateWrappedGeometry(canvasWidth, canvasHeight); /* * draw one width at a time (excluding any scales shown), * until we have run out of either alignment or vertical space available */ int ypos = wrappedSpaceAboveAlignment; int maxWidth = ranges.getVisibleAlignmentWidth(); int start = startColumn; int currentWidth = 0; while ((currentWidth < wrappedVisibleWidths) && (start < maxWidth)) { int endColumn = Math.min(maxWidth, start + wrappedWidthInResidues - 1); drawWrappedWidth(g, ypos, start, endColumn, canvasHeight); ypos += wrappedRepeatHeightPx; start += wrappedWidthInResidues; currentWidth++; } drawWrappedDecorators(g, startColumn); } /** * Calculates and saves values needed when rendering a wrapped alignment. * These depend on many factors, including * * * @param canvasWidth * @param canvasHeight * @return the number of residue columns in each width */ protected int calculateWrappedGeometry(int canvasWidth, int canvasHeight) { int charHeight = av.getCharHeight(); /* * vertical space in pixels between wrapped widths of alignment * - one character height, or two if scale above is drawn */ wrappedSpaceAboveAlignment = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); /* * compute height in pixels of the wrapped widths * - start with space above plus sequences */ wrappedRepeatHeightPx = wrappedSpaceAboveAlignment; wrappedRepeatHeightPx += av.getAlignment().getHeight() * charHeight; /* * add annotations panel height if shown * also gap between sequences and annotations */ if (av.isShowAnnotation()) { wrappedRepeatHeightPx += getAnnotationHeight(); wrappedRepeatHeightPx += SEQS_ANNOTATION_GAP; // 3px } /* * number of visible widths (the last one may be part height), * ensuring a part height includes at least one sequence */ ViewportRanges ranges = av.getRanges(); wrappedVisibleWidths = canvasHeight / wrappedRepeatHeightPx; int remainder = canvasHeight % wrappedRepeatHeightPx; if (remainder >= (wrappedSpaceAboveAlignment + charHeight)) { wrappedVisibleWidths++; } /* * compute width in residues; this also sets East and West label widths */ int wrappedWidthInResidues = getWrappedCanvasWidth(canvasWidth); av.setWrappedWidth(wrappedWidthInResidues); // update model accordingly /* * limit visibleWidths to not exceed width of alignment */ int xMax = ranges.getVisibleAlignmentWidth(); int startToEnd = xMax - ranges.getStartRes(); int maxWidths = startToEnd / wrappedWidthInResidues; if (startToEnd % wrappedWidthInResidues > 0) { maxWidths++; } wrappedVisibleWidths = Math.min(wrappedVisibleWidths, maxWidths); return wrappedWidthInResidues; } /** * Draws one width of a wrapped alignment, including sequences and * annnotations, if shown, but not scales or hidden column markers * * @param g * @param ypos * @param startColumn * @param endColumn * @param canvasHeight */ protected void drawWrappedWidth(Graphics g, final int ypos, final int startColumn, final int endColumn, final int canvasHeight) { ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); int endx = Math.min(startColumn + viewportWidth - 1, endColumn); /* * move right before drawing by the width of the scale left (if any) * plus column offset from left margin (usually zero, but may be non-zero * when fast painting is drawing just a few columns) */ int charWidth = av.getCharWidth(); int xOffset = labelWidthWest + ((startColumn - ranges.getStartRes()) % viewportWidth) * charWidth; g.translate(xOffset, 0); /* * white fill the region to be drawn (so incremental fast paint doesn't * scribble over an existing image) */ g.setColor(Color.white); g.fillRect(0, ypos, (endx - startColumn + 1) * charWidth, wrappedRepeatHeightPx); drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1, ypos); int cHeight = av.getAlignment().getHeight() * av.getCharHeight(); if (av.isShowAnnotation()) { final int yShift = cHeight + ypos + SEQS_ANNOTATION_GAP; g.translate(0, yShift); if (annotations == null) { annotations = new AnnotationPanel(av); } annotations.renderer.drawComponent(annotations, av, g, -1, startColumn, endx + 1); g.translate(0, -yShift); } g.translate(-xOffset, 0); } /** * Draws scales left, right and above (if shown), and any hidden column * markers, on all widths of the wrapped alignment * * @param g * @param startColumn */ protected void drawWrappedDecorators(Graphics g, final int startColumn) { int charWidth = av.getCharWidth(); g.setFont(av.getFont()); g.setColor(Color.black); int ypos = wrappedSpaceAboveAlignment; ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); int maxWidth = ranges.getVisibleAlignmentWidth(); int widthsDrawn = 0; int startCol = startColumn; while (widthsDrawn < wrappedVisibleWidths) { int endColumn = Math.min(maxWidth, startCol + viewportWidth - 1); if (av.getScaleLeftWrapped()) { drawVerticalScale(g, startCol, endColumn - 1, ypos, true); } if (av.getScaleRightWrapped()) { int x = labelWidthWest + viewportWidth * charWidth; g.translate(x, 0); drawVerticalScale(g, startCol, endColumn, ypos, false); g.translate(-x, 0); } /* * white fill region of scale above and hidden column markers * (to support incremental fast paint of image) */ g.translate(labelWidthWest, 0); g.setColor(Color.white); g.fillRect(0, ypos - wrappedSpaceAboveAlignment, viewportWidth * charWidth + labelWidthWest, wrappedSpaceAboveAlignment); g.setColor(Color.black); g.translate(-labelWidthWest, 0); g.translate(labelWidthWest, 0); if (av.getScaleAboveWrapped()) { drawNorthScale(g, startCol, endColumn, ypos); } if (av.hasHiddenColumns() && av.getShowHiddenMarkers()) { drawHiddenColumnMarkers(g, ypos, startCol, endColumn); } g.translate(-labelWidthWest, 0); ypos += wrappedRepeatHeightPx; startCol += viewportWidth; widthsDrawn++; } } /** * Draws markers (triangles) above hidden column positions between startColumn * and endColumn. * * @param g * @param ypos * @param startColumn * @param endColumn */ protected void drawHiddenColumnMarkers(Graphics g, int ypos, int startColumn, int endColumn) { int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); g.setColor(Color.blue); int res; HiddenColumns hidden = av.getAlignment().getHiddenColumns(); Iterator it = hidden.getStartRegionIterator(startColumn, endColumn); while (it.hasNext()) { res = it.next() - startColumn; if (res < 0 || res > endColumn - startColumn + 1) { continue; } /* * draw a downward-pointing triangle at the hidden columns location * (before the following visible column) */ int xMiddle = res * charWidth; int[] xPoints = new int[] { xMiddle - charHeight / 4, xMiddle + charHeight / 4, xMiddle }; int yTop = ypos - (charHeight / 2); int[] yPoints = new int[] { yTop, yTop, yTop + 8 }; g.fillPolygon(xPoints, yPoints, 3); } } /* * Draw a selection group over a wrapped alignment */ private void drawWrappedSelection(Graphics2D g, SequenceGroup group, int canvasWidth, int canvasHeight, int startRes) { // chop the wrapped alignment extent up into panel-sized blocks and treat // each block as if it were a block from an unwrapped alignment g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f)); g.setColor(Color.RED); int charWidth = av.getCharWidth(); int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; int startx = startRes; int maxwidth = av.getAlignment().getVisibleWidth(); int ypos = wrappedSpaceAboveAlignment; while ((ypos <= canvasHeight) && (startx < maxwidth)) { // set end value to be start + width, or maxwidth, whichever is smaller int endx = startx + cWidth - 1; if (endx > maxwidth) { endx = maxwidth; } g.translate(labelWidthWest, 0); drawUnwrappedSelection(g, group, startx, endx, 0, av.getAlignment().getHeight() - 1, ypos); g.translate(-labelWidthWest, 0); ypos += wrappedRepeatHeightPx; startx += cWidth; } g.setStroke(new BasicStroke()); } /** * Answers zero if annotations are not shown, otherwise recalculates and * answers the total height of all annotation rows in pixels * * @return */ int getAnnotationHeight() { if (!av.isShowAnnotation()) { return 0; } if (annotations == null) { annotations = new AnnotationPanel(av); } return annotations.adjustPanelHeight(); } /** * Draws the visible region of the alignment on the graphics context. If there * are hidden column markers in the visible region, then each sub-region * between the markers is drawn separately, followed by the hidden column * marker. * * @param g1 * the graphics context, positioned at the first residue to be drawn * @param startRes * offset of the first column to draw (0..) * @param endRes * offset of the last column to draw (0..) * @param startSeq * offset of the first sequence to draw (0..) * @param endSeq * offset of the last sequence to draw (0..) * @param yOffset * vertical offset at which to draw (for wrapped alignments) */ public void drawPanel(Graphics g1, final int startRes, final int endRes, final int startSeq, final int endSeq, final int yOffset) { int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); if (!av.hasHiddenColumns()) { draw(g1, startRes, endRes, startSeq, endSeq, yOffset); } else { int screenY = 0; int blockStart; int blockEnd; HiddenColumns hidden = av.getAlignment().getHiddenColumns(); VisibleContigsIterator regions = hidden .getVisContigsIterator(startRes, endRes + 1, true); while (regions.hasNext()) { int[] region = regions.next(); blockEnd = region[1]; blockStart = region[0]; /* * draw up to just before the next hidden region, or the end of * the visible region, whichever comes first */ g1.translate(screenY * charWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); /* * draw the downline of the hidden column marker (ScalePanel draws the * triangle on top) if we reached it */ if (av.getShowHiddenMarkers() && (regions.hasNext() || regions.endsAtHidden())) { g1.setColor(Color.blue); g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1, 0 + yOffset, (blockEnd - blockStart + 1) * charWidth - 1, (endSeq - startSeq + 1) * charHeight + yOffset); } g1.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; } } } /** * Draws a region of the visible alignment * * @param g1 * @param startRes * offset of the first column in the visible region (0..) * @param endRes * offset of the last column in the visible region (0..) * @param startSeq * offset of the first sequence in the visible region (0..) * @param endSeq * offset of the last sequence in the visible region (0..) * @param yOffset * vertical offset at which to draw (for wrapped alignments) */ private void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset) { int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); g.setFont(av.getFont()); seqRdr.prepare(g, av.isRenderGaps()); SequenceI nextSeq; // / First draw the sequences // /////////////////////////// for (int i = startSeq; i <= endSeq; i++) { nextSeq = av.getAlignment().getSequenceAt(i); if (nextSeq == null) { // occasionally, a race condition occurs such that the alignment row is // empty continue; } seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), startRes, endRes, offset + ((i - startSeq) * charHeight)); if (av.isShowSequenceFeatures()) { fr.drawSequence(g, nextSeq, startRes, endRes, offset + ((i - startSeq) * charHeight), false); } /* * highlight search Results once sequence has been drawn */ if (av.hasSearchResults()) { SearchResultsI searchResults = av.getSearchResults(); int[] visibleResults = searchResults.getResults(nextSeq, startRes, endRes); if (visibleResults != null) { for (int r = 0; r < visibleResults.length; r += 2) { seqRdr.drawHighlightedText(nextSeq, visibleResults[r], visibleResults[r + 1], (visibleResults[r] - startRes) * charWidth, offset + ((i - startSeq) * charHeight)); } } } } if (av.getSelectionGroup() != null || av.getAlignment().getGroups().size() > 0) { drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); } } /** * Draws the outlines of any groups defined on the alignment (excluding the * current selection group, if any) * * @param g1 * @param startRes * @param endRes * @param startSeq * @param endSeq * @param offset */ void drawGroupsBoundaries(Graphics g1, int startRes, int endRes, int startSeq, int endSeq, int offset) { Graphics2D g = (Graphics2D) g1; SequenceGroup group = null; int groupIndex = -1; if (av.getAlignment().getGroups().size() > 0) { group = av.getAlignment().getGroups().get(0); groupIndex = 0; } if (group != null) { do { g.setColor(group.getOutlineColour()); drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, offset); groupIndex++; if (groupIndex >= av.getAlignment().getGroups().size()) { break; } group = av.getAlignment().getGroups().get(groupIndex); } while (groupIndex < av.getAlignment().getGroups().size()); } } /** * Draws the outline of the current selection group (if any) * * @param g * @param startRes * @param endRes * @param startSeq * @param endSeq */ private void drawSelectionGroup(Graphics2D g, int startRes, int endRes, int startSeq, int endSeq) { SequenceGroup group = av.getSelectionGroup(); if (group == null) { return; } g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f)); g.setColor(Color.RED); if (!av.getWrapAlignment()) { drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq, 0); } else { drawWrappedSelection(g, group, getWidth(), getHeight(), av.getRanges().getStartRes()); } g.setStroke(new BasicStroke()); } /** * Draw the cursor as a separate image and overlay * * @param startRes * start residue of area to draw cursor in * @param endRes * end residue of area to draw cursor in * @param startSeq * start sequence of area to draw cursor in * @param endSeq * end sequence of are to draw cursor in * @return a transparent image of the same size as the sequence canvas, with * the cursor drawn on it, if any */ private void drawCursor(Graphics g, int startRes, int endRes, int startSeq, int endSeq) { // convert the cursorY into a position on the visible alignment int cursor_ypos = cursorY; // don't do work unless we have to if (cursor_ypos >= startSeq && cursor_ypos <= endSeq) { int yoffset = 0; int xoffset = 0; int startx = startRes; int endx = endRes; // convert the cursorX into a position on the visible alignment int cursor_xpos = av.getAlignment().getHiddenColumns() .absoluteToVisibleColumn(cursorX); if (av.getAlignment().getHiddenColumns().isVisible(cursorX)) { if (av.getWrapAlignment()) { // work out the correct offsets for the cursor int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); int canvasWidth = getWidth(); int canvasHeight = getHeight(); // height gap above each panel int hgap = charHeight; if (av.getScaleAboveWrapped()) { hgap += charHeight; } int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; int cHeight = av.getAlignment().getHeight() * charHeight; endx = startx + cWidth - 1; int ypos = hgap; // vertical offset // iterate down the wrapped panels while ((ypos <= canvasHeight) && (endx < cursor_xpos)) { // update vertical offset ypos += cHeight + getAnnotationHeight() + hgap; // update horizontal offset startx += cWidth; endx = startx + cWidth - 1; } yoffset = ypos; xoffset = labelWidthWest; } // now check if cursor is within range for x values if (cursor_xpos >= startx && cursor_xpos <= endx) { // get the character the cursor is drawn at SequenceI seq = av.getAlignment().getSequenceAt(cursorY); char s = seq.getCharAt(cursorX); seqRdr.drawCursor(g, s, xoffset + (cursor_xpos - startx) * av.getCharWidth(), yoffset + (cursor_ypos - startSeq) * av.getCharHeight()); } } } } /** * Draw a selection group over an unwrapped alignment * * @param g * graphics object to draw with * @param group * selection group * @param startRes * start residue of area to draw * @param endRes * end residue of area to draw * @param startSeq * start sequence of area to draw * @param endSeq * end sequence of area to draw * @param offset * vertical offset (used when called from wrapped alignment code) */ private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group, int startRes, int endRes, int startSeq, int endSeq, int offset) { int charWidth = av.getCharWidth(); if (!av.hasHiddenColumns()) { drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, offset); } else { // package into blocks of visible columns int screenY = 0; int blockStart; int blockEnd; HiddenColumns hidden = av.getAlignment().getHiddenColumns(); VisibleContigsIterator regions = hidden .getVisContigsIterator(startRes, endRes + 1, true); while (regions.hasNext()) { int[] region = regions.next(); blockEnd = region[1]; blockStart = region[0]; g.translate(screenY * charWidth, 0); drawPartialGroupOutline(g, group, blockStart, blockEnd, startSeq, endSeq, offset); g.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; } } } /** * Draws part of a selection group outline * * @param g * @param group * @param startRes * @param endRes * @param startSeq * @param endSeq * @param verticalOffset */ private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group, int startRes, int endRes, int startSeq, int endSeq, int verticalOffset) { int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); int visWidth = (endRes - startRes + 1) * charWidth; int oldY = -1; int i = 0; boolean inGroup = false; int top = -1; int bottom = -1; int sy = -1; List seqs = group.getSequences(null); // position of start residue of group relative to startRes, in pixels int sx = (group.getStartRes() - startRes) * charWidth; // width of group in pixels int xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - 1; if (!(sx + xwidth < 0 || sx > visWidth)) { for (i = startSeq; i <= endSeq; i++) { sy = verticalOffset + (i - startSeq) * charHeight; if ((sx <= (endRes - startRes) * charWidth) && seqs.contains(av.getAlignment().getSequenceAt(i))) { if ((bottom == -1) && !seqs.contains(av.getAlignment().getSequenceAt(i + 1))) { bottom = sy + charHeight; } if (!inGroup) { if (((top == -1) && (i == 0)) || !seqs .contains(av.getAlignment().getSequenceAt(i - 1))) { top = sy; } oldY = sy; inGroup = true; } } else if (inGroup) { drawVerticals(g, sx, xwidth, visWidth, oldY, bottom); drawHorizontals(g, sx, xwidth, visWidth, top, bottom+1); // reset top and bottom top = -1; bottom = -1; inGroup = false; } } if (inGroup) { sy = verticalOffset + ((i - startSeq) * charHeight); drawVerticals(g, sx, xwidth, visWidth, oldY, bottom); drawHorizontals(g, sx, xwidth, visWidth, top, bottom+1); } } } /** * Draw horizontal selection group boundaries at top and bottom positions * * @param g * graphics object to draw on * @param sx * start x position * @param xwidth * width of gap * @param visWidth * visWidth maximum available width * @param top * position to draw top of group at * @param bottom * position to draw bottom of group at */ private void drawHorizontals(Graphics2D g, int sx, int xwidth, int visWidth, int top, int bottom) { int width = xwidth; int startx = sx; if (startx < 0) { width += startx; startx = 0; } // don't let width extend beyond current block, or group extent // fixes JAL-2672 if (startx + width >= visWidth) { width = visWidth - startx; } if (top != -1) { g.drawLine(startx, top, startx + width, top); } if (bottom != -1) { g.drawLine(startx, bottom - 1, startx + width, bottom - 1); } } /** * Draw vertical lines at sx and sx+xwidth providing they lie within * [0,visWidth) * * @param g * graphics object to draw on * @param sx * start x position * @param xwidth * width of gap * @param visWidth * visWidth maximum available width * @param oldY * top y value * @param sy * bottom y value */ private void drawVerticals(Graphics2D g, int sx, int xwidth, int visWidth, int oldY, int sy) { // if start position is visible, draw vertical line to left of // group if (sx >= 0 && sx < visWidth) { g.drawLine(sx, oldY, sx, sy); } // if end position is visible, draw vertical line to right of // group if (sx + xwidth < visWidth) { g.drawLine(sx + xwidth, oldY, sx + xwidth, sy); } } /** * Highlights search results in the visible region by rendering as white text * on a black background. Any previous highlighting is removed. Answers true * if any highlight was left on the visible alignment (so status bar should be * set to match), else false. This method does _not_ set the 'fastPaint' flag, * so allows the next repaint to update the whole display. * * @param results * @return */ public boolean highlightSearchResults(SearchResultsI results) { return highlightSearchResults(results, false); } /** * Highlights search results in the visible region by rendering as white text * on a black background. Any previous highlighting is removed. Answers true * if any highlight was left on the visible alignment (so status bar should be * set to match), else false. *

* Optionally, set the 'fastPaint' flag for a faster redraw if only the * highlighted regions are modified. This speeds up highlighting across linked * alignments. *

* Currently fastPaint is not implemented for scrolled wrapped alignments. If * a wrapped alignment had to be scrolled to show the highlighted region, then * it should be fully redrawn, otherwise a fast paint can be performed. This * argument could be removed if fast paint of scrolled wrapped alignment is * coded in future (JAL-2609). * * @param results * @param doFastPaint * if true, sets a flag so the next repaint only redraws the modified * image * @return */ public boolean highlightSearchResults(SearchResultsI results, boolean doFastPaint) { if (fastpainting) { return false; } boolean wrapped = av.getWrapAlignment(); try { fastPaint = doFastPaint; fastpainting = fastPaint; /* * to avoid redrawing the whole visible region, we instead * redraw just the minimal regions to remove previous highlights * and add new ones */ SearchResultsI previous = av.getSearchResults(); av.setSearchResults(results); boolean redrawn = false; boolean drawn = false; if (wrapped) { redrawn = drawMappedPositionsWrapped(previous); drawn = drawMappedPositionsWrapped(results); redrawn |= drawn; } else { redrawn = drawMappedPositions(previous); drawn = drawMappedPositions(results); redrawn |= drawn; } /* * if highlights were either removed or added, repaint */ if (redrawn) { repaint(); } /* * return true only if highlights were added */ return drawn; } finally { fastpainting = false; } } /** * Redraws the minimal rectangle in the visible region (if any) that includes * mapped positions of the given search results. Whether or not positions are * highlighted depends on the SearchResults set on the Viewport. This allows * this method to be called to either clear or set highlighting. Answers true * if any positions were drawn (in which case a repaint is still required), * else false. * * @param results * @return */ protected boolean drawMappedPositions(SearchResultsI results) { if ((results == null) || (img == null)) // JAL-2784 check gg is not null { return false; } /* * calculate the minimal rectangle to redraw that * includes both new and existing search results */ int firstSeq = Integer.MAX_VALUE; int lastSeq = -1; int firstCol = Integer.MAX_VALUE; int lastCol = -1; boolean matchFound = false; ViewportRanges ranges = av.getRanges(); int firstVisibleColumn = ranges.getStartRes(); int lastVisibleColumn = ranges.getEndRes(); AlignmentI alignment = av.getAlignment(); if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() .visibleToAbsoluteColumn(lastVisibleColumn); } for (int seqNo = ranges.getStartSeq(); seqNo <= ranges .getEndSeq(); seqNo++) { SequenceI seq = alignment.getSequenceAt(seqNo); int[] visibleResults = results.getResults(seq, firstVisibleColumn, lastVisibleColumn); if (visibleResults != null) { for (int i = 0; i < visibleResults.length - 1; i += 2) { int firstMatchedColumn = visibleResults[i]; int lastMatchedColumn = visibleResults[i + 1]; if (firstMatchedColumn <= lastVisibleColumn && lastMatchedColumn >= firstVisibleColumn) { /* * found a search results match in the visible region - * remember the first and last sequence matched, and the first * and last visible columns in the matched positions */ matchFound = true; firstSeq = Math.min(firstSeq, seqNo); lastSeq = Math.max(lastSeq, seqNo); firstMatchedColumn = Math.max(firstMatchedColumn, firstVisibleColumn); lastMatchedColumn = Math.min(lastMatchedColumn, lastVisibleColumn); firstCol = Math.min(firstCol, firstMatchedColumn); lastCol = Math.max(lastCol, lastMatchedColumn); } } } } if (matchFound) { if (av.hasHiddenColumns()) { firstCol = alignment.getHiddenColumns() .absoluteToVisibleColumn(firstCol); lastCol = alignment.getHiddenColumns() .absoluteToVisibleColumn(lastCol); } int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth(); int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight(); Graphics gg = img.getGraphics(); gg.translate(transX, transY); drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0); gg.translate(-transX, -transY); gg.dispose(); } return matchFound; } @Override public void propertyChange(PropertyChangeEvent evt) { String eventName = evt.getPropertyName(); // jalview.bin.Console.errPrintln(">>SeqCanvas propertyChange " + eventName); if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED)) { fastPaint = true; repaint(); return; } else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT)) { fastPaint = false; // jalview.bin.Console.errPrintln("!!!! fastPaint false from MOVE_VIEWPORT"); repaint(); return; } int scrollX = 0; if (eventName.equals(ViewportRanges.STARTRES) || eventName.equals(ViewportRanges.STARTRESANDSEQ)) { // Make sure we're not trying to draw a panel // larger than the visible window if (eventName.equals(ViewportRanges.STARTRES)) { scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); } else { scrollX = ((int[]) evt.getNewValue())[0] - ((int[]) evt.getOldValue())[0]; } ViewportRanges vpRanges = av.getRanges(); int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1; if (scrollX > range) { scrollX = range; } else if (scrollX < -range) { scrollX = -range; } } // Both scrolling and resizing change viewport ranges: scrolling changes // both start and end points, but resize only changes end values. // Here we only want to fastpaint on a scroll, with resize using a normal // paint, so scroll events are identified as changes to the horizontal or // vertical start value. if (eventName.equals(ViewportRanges.STARTRES)) { if (av.getWrapAlignment()) { fastPaintWrapped(scrollX); } else { fastPaint(scrollX, 0); } } else if (eventName.equals(ViewportRanges.STARTSEQ)) { // scroll fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); } else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) { if (av.getWrapAlignment()) { fastPaintWrapped(scrollX); } else { fastPaint(scrollX, 0); } } else if (eventName.equals(ViewportRanges.STARTSEQ)) { // scroll fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); } else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) { if (av.getWrapAlignment()) { fastPaintWrapped(scrollX); } } } /** * Does a minimal update of the image for a scroll movement. This method * handles scroll movements of up to one width of the wrapped alignment (one * click in the vertical scrollbar). Larger movements (for example after a * scroll to highlight a mapped position) trigger a full redraw instead. * * @param scrollX * number of positions scrolled (right if positive, left if negative) */ protected void fastPaintWrapped(int scrollX) { ViewportRanges ranges = av.getRanges(); if (Math.abs(scrollX) >= ranges.getViewportWidth()) { /* * shift of one view width or more is * overcomplicated to handle in this method */ fastPaint = false; repaint(); return; } if (fastpainting || img == null) { return; } fastPaint = true; fastpainting = true; try { Graphics gg = img.getGraphics(); calculateWrappedGeometry(getWidth(), getHeight()); /* * relocate the regions of the alignment that are still visible */ shiftWrappedAlignment(-scrollX); /* * add new columns (sequence, annotation) * - at top left if scrollX < 0 * - at right of last two widths if scrollX > 0 */ if (scrollX < 0) { int startRes = ranges.getStartRes(); drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes, startRes - scrollX - 1, getHeight()); } else { fastPaintWrappedAddRight(scrollX); } /* * draw all scales (if shown) and hidden column markers */ drawWrappedDecorators(gg, ranges.getStartRes()); gg.dispose(); repaint(); } finally { fastpainting = false; } } /** * Draws the specified number of columns at the 'end' (bottom right) of a * wrapped alignment view, including sequences and annotations if shown, but * not scales. Also draws the same number of columns at the right hand end of * the second last width shown, if the last width is not full height (so * cannot simply be copied from the graphics image). * * @param columns */ protected void fastPaintWrappedAddRight(int columns) { if (columns == 0) { return; } Graphics gg = img.getGraphics(); ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); int charWidth = av.getCharWidth(); /** * draw full height alignment in the second last row, last columns, if the * last row was not full height */ int visibleWidths = wrappedVisibleWidths; int canvasHeight = getHeight(); boolean lastWidthPartHeight = (wrappedVisibleWidths * wrappedRepeatHeightPx) > canvasHeight; if (lastWidthPartHeight) { int widthsAbove = Math.max(0, visibleWidths - 2); int ypos = wrappedRepeatHeightPx * widthsAbove + wrappedSpaceAboveAlignment; int endRes = ranges.getEndRes(); endRes += widthsAbove * viewportWidth; int startRes = endRes - columns; int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth) * charWidth; /* * white fill first to erase annotations */ gg.translate(xOffset, 0); gg.setColor(Color.white); gg.fillRect(labelWidthWest, ypos, (endRes - startRes + 1) * charWidth, wrappedRepeatHeightPx); gg.translate(-xOffset, 0); drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight); } /* * draw newly visible columns in last wrapped width (none if we * have reached the end of the alignment) * y-offset for drawing last width is height of widths above, * plus one gap row */ int widthsAbove = visibleWidths - 1; int ypos = wrappedRepeatHeightPx * widthsAbove + wrappedSpaceAboveAlignment; int endRes = ranges.getEndRes(); endRes += widthsAbove * viewportWidth; int startRes = endRes - columns + 1; /* * white fill first to erase annotations */ int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth) * charWidth; gg.translate(xOffset, 0); gg.setColor(Color.white); int width = viewportWidth * charWidth - xOffset; gg.fillRect(labelWidthWest, ypos, width, wrappedRepeatHeightPx); gg.translate(-xOffset, 0); gg.setFont(av.getFont()); gg.setColor(Color.black); if (startRes < ranges.getVisibleAlignmentWidth()) { drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight); } /* * and finally, white fill any space below the visible alignment */ int heightBelow = canvasHeight - visibleWidths * wrappedRepeatHeightPx; if (heightBelow > 0) { gg.setColor(Color.white); gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow); } gg.dispose(); } /** * Shifts the visible alignment by the specified number of columns - left if * negative, right if positive. Copies and moves sequences and annotations (if * shown). Scales, hidden column markers and any newly visible columns must be * drawn separately. * * @param positions */ protected void shiftWrappedAlignment(int positions) { if (positions == 0) { return; } Graphics gg = img.getGraphics(); int charWidth = av.getCharWidth(); int canvasHeight = getHeight(); ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); int widthToCopy = (ranges.getViewportWidth() - Math.abs(positions)) * charWidth; int heightToCopy = wrappedRepeatHeightPx - wrappedSpaceAboveAlignment; int xMax = ranges.getVisibleAlignmentWidth(); if (positions > 0) { /* * shift right (after scroll left) * for each wrapped width (starting with the last), copy (width-positions) * columns from the left margin to the right margin, and copy positions * columns from the right margin of the row above (if any) to the * left margin of the current row */ /* * get y-offset of last wrapped width, first row of sequences */ int y = canvasHeight / wrappedRepeatHeightPx * wrappedRepeatHeightPx; y += wrappedSpaceAboveAlignment; int copyFromLeftStart = labelWidthWest; int copyFromRightStart = copyFromLeftStart + widthToCopy; while (y >= 0) { /* * shift 'widthToCopy' residues by 'positions' places to the right */ gg.copyArea(copyFromLeftStart, y, widthToCopy, heightToCopy, positions * charWidth, 0); if (y > 0) { /* * copy 'positions' residue from the row above (right hand end) * to this row's left hand end */ gg.copyArea(copyFromRightStart, y - wrappedRepeatHeightPx, positions * charWidth, heightToCopy, -widthToCopy, wrappedRepeatHeightPx); } y -= wrappedRepeatHeightPx; } } else { /* * shift left (after scroll right) * for each wrapped width (starting with the first), copy (width-positions) * columns from the right margin to the left margin, and copy positions * columns from the left margin of the row below (if any) to the * right margin of the current row */ int xpos = av.getRanges().getStartRes(); int y = wrappedSpaceAboveAlignment; int copyFromRightStart = labelWidthWest - positions * charWidth; while (y < canvasHeight) { gg.copyArea(copyFromRightStart, y, widthToCopy, heightToCopy, positions * charWidth, 0); if (y + wrappedRepeatHeightPx < canvasHeight - wrappedRepeatHeightPx && (xpos + viewportWidth <= xMax)) { gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx, -positions * charWidth, heightToCopy, widthToCopy, -wrappedRepeatHeightPx); } y += wrappedRepeatHeightPx; xpos += viewportWidth; } } gg.dispose(); } /** * Redraws any positions in the search results in the visible region of a * wrapped alignment. Any highlights are drawn depending on the search results * set on the Viewport, not the results argument. This allows * this method to be called either to clear highlights (passing the previous * search results), or to draw new highlights. * * @param results * @return */ protected boolean drawMappedPositionsWrapped(SearchResultsI results) { if ((results == null) || (img == null)) // JAL-2784 check gg is not null { return false; } int charHeight = av.getCharHeight(); boolean matchFound = false; calculateWrappedGeometry(getWidth(), getHeight()); int wrappedWidth = av.getWrappedWidth(); int wrappedHeight = wrappedRepeatHeightPx; ViewportRanges ranges = av.getRanges(); int canvasHeight = getHeight(); int repeats = canvasHeight / wrappedHeight; if (canvasHeight / wrappedHeight > 0) { repeats++; } int firstVisibleColumn = ranges.getStartRes(); int lastVisibleColumn = ranges.getStartRes() + repeats * ranges.getViewportWidth() - 1; AlignmentI alignment = av.getAlignment(); if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() .visibleToAbsoluteColumn(lastVisibleColumn); } int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); Graphics gg = img.getGraphics(); for (int seqNo = ranges.getStartSeq(); seqNo <= ranges .getEndSeq(); seqNo++) { SequenceI seq = alignment.getSequenceAt(seqNo); int[] visibleResults = results.getResults(seq, firstVisibleColumn, lastVisibleColumn); if (visibleResults != null) { for (int i = 0; i < visibleResults.length - 1; i += 2) { int firstMatchedColumn = visibleResults[i]; int lastMatchedColumn = visibleResults[i + 1]; if (firstMatchedColumn <= lastVisibleColumn && lastMatchedColumn >= firstVisibleColumn) { /* * found a search results match in the visible region */ firstMatchedColumn = Math.max(firstMatchedColumn, firstVisibleColumn); lastMatchedColumn = Math.min(lastMatchedColumn, lastVisibleColumn); /* * draw each mapped position separately (as contiguous positions may * wrap across lines) */ for (int mappedPos = firstMatchedColumn; mappedPos <= lastMatchedColumn; mappedPos++) { int displayColumn = mappedPos; if (av.hasHiddenColumns()) { displayColumn = alignment.getHiddenColumns() .absoluteToVisibleColumn(displayColumn); } /* * transX: offset from left edge of canvas to residue position */ int transX = labelWidthWest + ((displayColumn - ranges.getStartRes()) % wrappedWidth) * av.getCharWidth(); /* * transY: offset from top edge of canvas to residue position */ int transY = gapHeight; transY += (displayColumn - ranges.getStartRes()) / wrappedWidth * wrappedHeight; transY += (seqNo - ranges.getStartSeq()) * av.getCharHeight(); /* * yOffset is from graphics origin to start of visible region */ int yOffset = 0;// (displayColumn / wrappedWidth) * wrappedHeight; if (transY < getHeight()) { matchFound = true; gg.translate(transX, transY); drawPanel(gg, displayColumn, displayColumn, seqNo, seqNo, yOffset); gg.translate(-transX, -transY); } } } } } } gg.dispose(); return matchFound; } /** * Answers the width in pixels of the left scale labels (0 if not shown) * * @return */ int getLabelWidthWest() { return labelWidthWest; } }