X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=b7d74de8f033508fd72ef3a948865777d03533c1;hb=99bfb1a08e5ceb3a3c990bb49dcd7433a0880558;hp=6f63dd661e0b6ce21addddeedd6c793444103ae2;hpb=b836aae53d015cbbac0da38920299d075c874a95;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 6f63dd6..d15cdcf 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -20,75 +20,94 @@ */ package jalview.gui; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.HiddenColumns; -import jalview.datamodel.SearchResultsI; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.renderer.ScaleRenderer; -import jalview.renderer.ScaleRenderer.ScaleMark; -import jalview.viewmodel.ViewportListenerI; -import jalview.viewmodel.ViewportRanges; - -import java.awt.AlphaComposite; 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.Shape; import java.awt.image.BufferedImage; import java.beans.PropertyChangeEvent; +import java.util.Iterator; import java.util.List; -import javax.swing.JComponent; +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; /** - * DOCUMENT ME! + * 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. * - * @author $author$ - * @version $Revision$ */ -public class SeqCanvas extends JComponent implements ViewportListenerI +@SuppressWarnings("serial") +public class SeqCanvas extends JPanel implements ViewportListenerI { - final FeatureRenderer fr; + /** + * 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 SequenceRenderer sr; + final FeatureRenderer fr; BufferedImage img; - Graphics2D gg; + AlignViewport av; - int imgWidth; + int cursorX = 0; - int imgHeight; + int cursorY = 0; - AlignViewport av; + private final SequenceRenderer seqRdr; boolean fastPaint = false; - int LABEL_WEST; + private boolean fastpainting = false; - int LABEL_EAST; + private AnnotationPanel annotations; - int cursorX = 0; + /* + * measurements for drawing a wrapped alignment + */ + private int labelWidthEast; // label right width in pixels if shown - int cursorY = 0; + 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 av - * DOCUMENT ME! + * @param ap */ public SeqCanvas(AlignmentPanel ap) { this.av = ap.av; - updateViewport(); fr = new FeatureRenderer(ap); - sr = new SequenceRenderer(av); + seqRdr = new SequenceRenderer(av); setLayout(new BorderLayout()); PaintRefresher.Register(this, av.getSequenceSetId()); setBackground(Color.white); @@ -98,7 +117,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public SequenceRenderer getSequenceRenderer() { - return sr; + return seqRdr; } public FeatureRenderer getFeatureRenderer() @@ -106,31 +125,36 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return fr; } - int charHeight = 0, charWidth = 0; - - private void updateViewport() - { - charHeight = av.getCharHeight(); - charWidth = av.getCharWidth(); - } - /** - * DOCUMENT ME! + * Draws the scale above a region of a wrapped alignment, consisting of a + * column number every major interval (10 columns). * * @param g - * DOCUMENT ME! + * the graphics context to draw on, positioned at the start (bottom + * left) of the line on which to draw any scale marks * @param startx - * DOCUMENT ME! + * start alignment column (0..) * @param endx - * DOCUMENT ME! + * end alignment column (0..) * @param ypos - * DOCUMENT ME! + * y offset to draw at */ private void drawNorthScale(Graphics g, int startx, int endx, int ypos) { - updateViewport(); - for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx, - endx)) + 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) @@ -145,233 +169,213 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2)); } - g.drawLine((mpos * charWidth) + (charWidth / 2), (ypos + 2) - - (charHeight / 2), (mpos * charWidth) + (charWidth / 2), - ypos - 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); } } } /** - * DOCUMENT ME! + * Draw the scale to the left or right of a wrapped alignment * * @param g - * DOCUMENT ME! + * graphics context, positioned at the start of the scale to be drawn * @param startx - * DOCUMENT ME! + * first column of wrapped width (0.. excluding any hidden columns) * @param endx - * DOCUMENT ME! + * last column of wrapped width (0.. excluding any hidden columns) * @param ypos - * DOCUMENT ME! + * vertical offset at which to begin the scale + * @param left + * if true, scale is left of residues, if false, scale is right */ - void drawWestScale(Graphics g, int startx, int endx, int ypos) + void drawVerticalScale(Graphics g, final int startx, final int endx, + final int ypos, final boolean left) { - FontMetrics fm = getFontMetrics(av.getFont()); - ypos += charHeight; + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); - if (av.hasHiddenColumns()) - { - startx = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(startx); - endx = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(endx); - } + int yPos = ypos + charHeight; + int startX = startx; + int endX = endx; - int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth) - 1; + HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); + startX = hiddenColumns.visibleToAbsoluteColumn(startx); + endX = hiddenColumns.visibleToAbsoluteColumn(endx); } + FontMetrics fm = getFontMetrics(av.getFont()); - // WEST SCALE for (int i = 0; i < av.getAlignment().getHeight(); i++) { SequenceI seq = av.getAlignment().getSequenceAt(i); - int index = startx; - int value = -1; - while (index < endx) + /* + * 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 (jalview.util.Comparison.isGap(seq.getCharAt(index))) + if (!Comparison.isGap(seq.getCharAt(index))) + { + value = seq.findPosition(index); + break; + } + if (left) { index++; - - continue; } - - value = av.getAlignment().getSequenceAt(i).findPosition(index); - - break; - } - - if (value != -1) - { - int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) - - charWidth / 2; - g.drawString(value + "", x, (ypos + (i * charHeight)) - - (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 += charHeight; - - if (av.hasHiddenColumns()) - { - endx = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(endx); - } - - SequenceI seq; - // EAST SCALE - for (int i = 0; i < av.getAlignment().getHeight(); i++) - { - seq = av.getAlignment().getSequenceAt(i); - int index = endx; - int value = -1; - - while (index > startx) - { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + else { index--; - - continue; } - - value = seq.findPosition(index); - - break; } + /* + * 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) { - g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight)) - - (charHeight / 5)); + /* + * 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); } } - } - boolean fastpainting = false; + } /** - * need to make this thread safe move alignment rendering in response to - * slider adjustment + * 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 - * shift along + * columns to shift right (positive) or left (negative) * @param vertical - * shift up or down in repaint + * rows to shift down (positive) or up (negative) */ public void fastPaint(int horizontal, int vertical) { - if (fastpainting || gg == null) + + // effectively: + // if (horizontal != 0 && vertical != 0) + // throw new InvalidArgumentException(); + if (fastpainting || img == null) { return; } fastpainting = true; fastPaint = true; - updateViewport(); - - ViewportRanges ranges = av.getRanges(); - int sr = ranges.getStartRes(); - int er = ranges.getEndRes(); - int ss = ranges.getStartSeq(); - int es = ranges.getEndSeq(); - int transX = 0; - int transY = 0; - - gg.copyArea(horizontal * charWidth, vertical * charHeight, - img.getWidth(), img.getHeight(), -horizontal * charWidth, - -vertical * charHeight); - - if (horizontal > 0) // scrollbar pulled right, image to the left - { - transX = (er - sr - horizontal) * charWidth; - sr = er - horizontal; - } - else if (horizontal < 0) - { - er = sr - horizontal; - } - else if (vertical > 0) // scroll down + try { - ss = es - vertical; - - if (ss < ranges.getStartSeq()) - { // ie scrolling too fast, more than a page at a time - ss = ranges.getStartSeq(); - } - else + 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 { - transY = img.getHeight() - ((vertical + 1) * charHeight); + transX = (endRes - startRes - horizontal) * charWidth; + startRes = endRes - horizontal; } - } - else if (vertical < 0) - { - es = ss - vertical; - - if (es > ranges.getEndSeq()) + else if (horizontal < 0) { - es = ranges.getEndSeq(); + endRes = startRes - horizontal; } - } - gg.translate(transX, transY); - drawPanel(gg, sr, er, ss, es, 0); - gg.translate(-transX, -transY); + if (vertical > 0) // scroll down + { + startSeq = endSeq - vertical; - repaint(); - fastpainting = false; - } + 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; - /** - * 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. - */ + if (endSeq > ranges.getEndSeq()) + { + endSeq = ranges.getEndSeq(); + } + } - // Set this to false to force a full panel paint - @Override - public void paintComponent(Graphics g) - { - super.paintComponent(g); + // System.err.println(">>> FastPaint to " + transX + " " + transY + " " + // + horizontal + " " + vertical + " " + startRes + " " + endRes + // + " " + startSeq + " " + endSeq); - updateViewport(); + Graphics gg = img.getGraphics(); + gg.copyArea(horizontal * charWidth, vertical * charHeight, + img.getWidth(), img.getHeight(), -horizontal * charWidth, + -vertical * charHeight); - // img is a cached version of the last view we drew - // selectImage will hold any selection we have - // lcimg is a local *copy* of img which we'll draw selectImage on top of + /** @j2sNative xxi = this.img */ - BufferedImage selectImage = drawSelectionGroup(); + gg.translate(transX, transY); + drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); + gg.translate(-transX, -transY); + gg.dispose(); - if (fastPaint || (getVisibleRect().width != g.getClipBounds().width) - || (getVisibleRect().height != g.getClipBounds().height)) + // 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. + // System.out.println("SeqCanvas fastPaint() repaint() request..."); + av.getAlignPanel().repaint(); + } finally { - BufferedImage lcimg = buildLocalImage(selectImage); - g.drawImage(lcimg, 0, 0, this); - - fastPaint = false; - return; + fastpainting = false; } + } + + @Override + public void paintComponent(Graphics g) + { + + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); int width = getWidth(); int height = getHeight(); @@ -379,345 +383,552 @@ public class SeqCanvas extends JComponent implements ViewportListenerI width -= (width % charWidth); height -= (height % charHeight); - if ((width < 1) || (height < 1)) - { - return; - } + // BH 2019 can't possibly fastPaint if either width or height is 0 - if (img == null || width != img.getWidth() || height != img.getHeight()) - { - img = setupImage(); - gg = (Graphics2D) img.getGraphics(); - gg.setFont(av.getFont()); - } - if (img == null) + if (width == 0 || height == 0) { return; } - - if (av.antiAlias) - { - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); - } - - gg.setColor(Color.white); - gg.fillRect(0, 0, img.getWidth(), img.getHeight()); - ViewportRanges ranges = av.getRanges(); - if (av.getWrapAlignment()) + 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)) { - drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); + g.drawImage(img, 0, 0, this); + drawSelectionGroup((Graphics2D) g, startRes, endRes, startSeq, + endSeq); + fastPaint = false; } else { - drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), - ranges.getStartSeq(), ranges.getEndSeq(), 0); - } - - BufferedImage lcimg = buildLocalImage(selectImage); - g.drawImage(lcimg, 0, 0, this); - } - - /* - * Make a local image by combining the cached image img - * with any selection - */ - private BufferedImage buildLocalImage(BufferedImage selectImage) - { - // clone the cached image - BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), - img.getType()); - Graphics2D g2d = lcimg.createGraphics(); - g2d.drawImage(img, 0, 0, null); + // 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); + } - // overlay selection group on lcimg - if (selectImage != null) - { - g2d.setComposite( - AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); - g2d.drawImage(selectImage, 0, 0, this); - } - g2d.dispose(); + Graphics2D gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); - return lcimg; - } + if (av.antiAlias) + { + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } - private void paintSeqGroup() - { - fastPaint = true; - repaint(); - } + gg.setColor(Color.white); + gg.fillRect(0, 0, img.getWidth(), img.getHeight()); - /*private void setupImage() - { - // this draws the whole of the alignment - imgWidth = getWidth(); - imgHeight = getHeight(); - - imgWidth -= (imgWidth % charWidth); - imgHeight -= (imgHeight % charHeight); - - if ((imgWidth < 1) || (imgHeight < 1)) - { - return; - } - - try + if (av.getWrapAlignment()) { - img = new BufferedImage(imgWidth, imgHeight, - BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works - gg = (Graphics2D) img.getGraphics(); - gg.setFont(av.getFont()); - } catch (OutOfMemoryError er) + drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); + } + else { - System.gc(); - System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er); - new OOMWarning("Creating alignment image for display", er); - - return; + drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); } - - }*/ - - private BufferedImage setupImage() - { - BufferedImage lcimg = null; - int width = getWidth(); - int height = getHeight(); + drawSelectionGroup(gg, startRes, endRes, startSeq, endSeq); - width -= (width % charWidth); - height -= (height % charHeight); + g.drawImage(img, 0, 0, this); + gg.dispose(); + } - if ((width < 1) || (height < 1)) + if (av.cursorMode) { - return null; + drawCursor(g, startRes, endRes, startSeq, endSeq); } + } - try - { - lcimg = new BufferedImage(width, height, - BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works - } catch (OutOfMemoryError er) - { - System.gc(); - System.err.println( - "Selection Group image OutOfMemory Redraw Error.\n" + er); - new OOMWarning("Creating alignment image for display", er); + /** + * 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); - return null; - } + 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); - return lcimg; + SequenceGroup group = av.getSelectionGroup(); + if (group != null) + { + drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight, + startRes); + } } /** - * DOCUMENT ME! + * Returns the visible width of the canvas in residues, after allowing for + * East or West scales (if shown) * - * @param cwidth - * DOCUMENT ME! + * @param canvasWidth + * the width in pixels (possibly including scales) * - * @return DOCUMENT ME! + * @return */ - public int getWrappedCanvasWidth(int cwidth) + public int getWrappedCanvasWidth(int canvasWidth) { + int charWidth = av.getCharWidth(); + FontMetrics fm = getFontMetrics(av.getFont()); - LABEL_EAST = 0; - LABEL_WEST = 0; + int labelWidth = 0; - if (av.getScaleRightWrapped()) + if (av.getScaleRightWrapped() || av.getScaleLeftWrapped()) { - LABEL_EAST = fm.stringWidth(getMask()); + labelWidth = getLabelWidth(fm); } - if (av.getScaleLeftWrapped()) - { - LABEL_WEST = fm.stringWidth(getMask()); - } + labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0; + + labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; - return (cwidth - LABEL_EAST - LABEL_WEST) / charWidth; + return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; } /** - * Generates a string of zeroes. + * 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. * - * @return String + * @param fm + * @return */ - String getMask() + protected int getLabelWidth(FontMetrics fm) { - String mask = "00"; + /* + * find the biggest sequence end position we need to show + * (note this is not necessarily the sequence length) + */ int maxWidth = 0; - int tmp; - for (int i = 0; i < av.getAlignment().getHeight(); i++) + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) { - tmp = av.getAlignment().getSequenceAt(i).getEnd(); - if (tmp > maxWidth) - { - maxWidth = tmp; - } + maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd()); } + int length = 0; for (int i = maxWidth; i > 0; i /= 10) { - mask += "0"; + length++; } - return mask; + + return fm.stringWidth(ZEROS.substring(0, length)) + av.getCharWidth(); } /** - * DOCUMENT ME! + * Draws as many widths of a wrapped alignment as can fit in the visible + * window * * @param g - * DOCUMENT ME! * @param canvasWidth - * DOCUMENT ME! + * available width in pixels * @param canvasHeight - * DOCUMENT ME! - * @param startRes - * DOCUMENT ME! + * available height in pixels + * @param startColumn + * the first column (0...) of the alignment to draw */ public void drawWrappedPanel(Graphics g, int canvasWidth, - int canvasHeight, int startRes) + int canvasHeight, final int startColumn) { - updateViewport(); - AlignmentI al = av.getAlignment(); - - FontMetrics fm = getFontMetrics(av.getFont()); + int wrappedWidthInResidues = calculateWrappedGeometry(canvasWidth, + canvasHeight); - LABEL_EAST = 0; - LABEL_WEST = 0; + av.setWrappedWidth(wrappedWidthInResidues); - if (av.getScaleRightWrapped()) + 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)) { - LABEL_EAST = fm.stringWidth(getMask()); + int endColumn = Math.min(maxWidth, + start + wrappedWidthInResidues - 1); + drawWrappedWidth(g, ypos, start, endColumn, canvasHeight); + ypos += wrappedRepeatHeightPx; + start += wrappedWidthInResidues; + currentWidth++; } - if (av.getScaleLeftWrapped()) + 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()) { - LABEL_WEST = fm.stringWidth(getMask()); + wrappedRepeatHeightPx += getAnnotationHeight(); + wrappedRepeatHeightPx += SEQS_ANNOTATION_GAP; // 3px } - int hgap = charHeight; - if (av.getScaleAboveWrapped()) + /* + * 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)) { - hgap += charHeight; + wrappedVisibleWidths++; } - int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth; - int cHeight = av.getAlignment().getHeight() * charHeight; + /* + * 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); - av.setWrappedWidth(cWidth); + return wrappedWidthInResidues; + } - av.getRanges().setViewportStartAndWidth(startRes, cWidth); + /** + * 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; - int ypos = hgap; - int maxwidth = av.getAlignment().getWidth(); + int endx = Math.min(startColumn + viewportWidth - 1, endColumn); - if (av.hasHiddenColumns()) - { - maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth); - } + /* + * 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; - while ((ypos <= canvasHeight) && (startRes < maxwidth)) - { - endx = startRes + cWidth - 1; + g.translate(xOffset, 0); - if (endx > maxwidth) - { - endx = maxwidth; - } + /* + * 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); - g.setFont(av.getFont()); - g.setColor(Color.black); + drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1, + ypos); - if (av.getScaleLeftWrapped()) - { - drawWestScale(g, startRes, endx, ypos); - } + int cHeight = av.getAlignment().getHeight() * av.getCharHeight(); - if (av.getScaleRightWrapped()) + if (av.isShowAnnotation()) + { + final int yShift = cHeight + ypos + SEQS_ANNOTATION_GAP; + g.translate(0, yShift); + if (annotations == null) { - g.translate(canvasWidth - LABEL_EAST, 0); - drawEastScale(g, startRes, endx, ypos); - g.translate(-(canvasWidth - LABEL_EAST), 0); + annotations = new AnnotationPanel(av); } - g.translate(LABEL_WEST, 0); + annotations.renderer.drawComponent(annotations, av, g, -1, + startColumn, endx + 1); + g.translate(0, -yShift); + } + g.translate(-xOffset, 0); + } - if (av.getScaleAboveWrapped()) - { - drawNorthScale(g, startRes, endx, ypos); - } + /** + * 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(); - if (av.hasHiddenColumns() && av.getShowHiddenMarkers()) - { - g.setColor(Color.blue); - int res; - HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - List positions = hidden.findHiddenRegionPositions(); - for (int pos : positions) - { - res = pos - startRes; + g.setFont(av.getFont()); - if (res < 0 || res > endx - startRes) - { - continue; - } + 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; - gg.fillPolygon( - new int[] { res * charWidth - charHeight / 4, - res * charWidth + charHeight / 4, res * charWidth }, - new int[] { ypos - (charHeight / 2), - ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 }, - 3); + 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); } - // When printing we have an extra clipped region, - // the Printable page which we need to account for here - Shape clip = g.getClip(); + /* + * 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 (clip == null) + if (av.getScaleAboveWrapped()) { - g.setClip(0, 0, cWidth * charWidth, canvasHeight); + drawNorthScale(g, startCol, endColumn, ypos); } - else + + if (av.hasHiddenColumns() && av.getShowHiddenMarkers()) { - g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth, - (int) clip.getBounds().getHeight()); + drawHiddenColumnMarkers(g, ypos, startCol, endColumn); } - drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos); + 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 (av.isShowAnnotation()) + if (res < 0 || res > endColumn - startColumn + 1) { - g.translate(0, cHeight + ypos + 3); - if (annotations == null) - { - annotations = new AnnotationPanel(av); - } + 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); + } + } - annotations.renderer.drawComponent(annotations, av, g, -1, - startRes, endx + 1); - g.translate(0, -cHeight - ypos - 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.setClip(clip); - g.translate(-LABEL_WEST, 0); - ypos += cHeight + getAnnotationHeight() + hgap; + g.translate(labelWidthWest, 0); + drawUnwrappedSelection(g, group, startx, endx, 0, + av.getAlignment().getHeight() - 1, ypos); + g.translate(-labelWidthWest, 0); + + ypos += wrappedRepeatHeightPx; - startRes += cWidth; + startx += cWidth; } + g.setStroke(new BasicStroke()); } - AnnotationPanel annotations; - + /** + * 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()) @@ -734,93 +945,102 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } /** - * DOCUMENT ME! + * 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 - * DOCUMENT ME! + * the graphics context, positioned at the first residue to be drawn * @param startRes - * DOCUMENT ME! + * offset of the first column to draw (0..) * @param endRes - * DOCUMENT ME! + * offset of the last column to draw (0..) * @param startSeq - * DOCUMENT ME! + * offset of the first sequence to draw (0..) * @param endSeq - * DOCUMENT ME! - * @param offset - * DOCUMENT ME! + * offset of the last sequence to draw (0..) + * @param yOffset + * vertical offset at which to draw (for wrapped alignments) */ - public void drawPanel(Graphics g1, int startRes, int endRes, - int startSeq, int endSeq, int offset) + public void drawPanel(Graphics g1, final int startRes, final int endRes, + final int startSeq, final int endSeq, final int yOffset) { - updateViewport(); + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + if (!av.hasHiddenColumns()) { - draw(g1, startRes, endRes, startSeq, endSeq, offset); + draw(g1, startRes, endRes, startSeq, endSeq, yOffset); } else { int screenY = 0; - int blockStart = startRes; - int blockEnd = endRes; - - for (int[] region : av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy()) - { - int hideStart = region[0]; - int hideEnd = region[1]; - - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } + int blockStart; + int blockEnd; - blockEnd = hideStart - 1; + 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, offset); + draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); - if (av.getShowHiddenMarkers()) + /* + * 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 + offset, (blockEnd - blockStart + 1) * charWidth - 1, - (endSeq - startSeq + 1) * charHeight + offset); + 0 + yOffset, (blockEnd - blockStart + 1) * charWidth - 1, + (endSeq - startSeq + 1) * charHeight + yOffset); } g1.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - - if (screenY > (endRes - startRes)) - { - // already rendered last block - return; - } - } - - if (screenY <= (endRes - startRes)) - { - // remaining visible region to render - blockEnd = blockStart + (endRes - startRes) - screenY; - g1.translate(screenY * charWidth, 0); - draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - - g1.translate(-screenY * 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, + /** + * 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()); - sr.prepare(g, av.isRenderGaps()); + seqRdr.prepare(g, av.isRenderGaps()); SequenceI nextSeq; @@ -835,39 +1055,34 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // empty continue; } - sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), + 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); + fr.drawSequence(g, nextSeq, startRes, endRes, + offset + ((i - startSeq) * charHeight), false); } - // / Highlight search Results once all sequences have been drawn - // //////////////////////////////////////////////////////// + /* + * highlight search Results once sequence has been drawn + */ if (av.hasSearchResults()) { - int[] visibleResults = av.getSearchResults().getResults(nextSeq, - startRes, endRes); + SearchResultsI searchResults = av.getSearchResults(); + 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) - * charWidth, offset - + ((i - startSeq) * charHeight)); + seqRdr.drawHighlightedText(nextSeq, visibleResults[r], + visibleResults[r + 1], + (visibleResults[r] - startRes) * charWidth, + offset + ((i - startSeq) * charHeight)); } } } - - if (av.cursorMode && cursorY == i && cursorX >= startRes - && cursorX <= endRes) - { - sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth, - offset + ((i - startSeq) * charHeight)); - } } if (av.getSelectionGroup() != null @@ -878,22 +1093,24 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } + /** + * 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; - // - // /////////////////////////////////// - // Now outline any areas if necessary - // /////////////////////////////////// SequenceGroup group = null; - - int sx = -1; - int sy = -1; - int ex = -1; int groupIndex = -1; - int visWidth = (endRes - startRes + 1) * charWidth; if (av.getAlignment().getGroups().size() > 0) { @@ -905,381 +1122,1040 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { do { - int oldY = -1; - int i = 0; - boolean inGroup = false; - int top = -1; - int bottom = -1; + g.setColor(group.getOutlineColour()); + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, + endSeq, offset); - for (i = startSeq; i <= endSeq; i++) + groupIndex++; + if (groupIndex >= av.getAlignment().getGroups().size()) { - // position of start residue of group relative to startRes, in pixels - sx = (group.getStartRes() - startRes) * charWidth; - sy = offset + ((i - startSeq) * charHeight); - // width of group in pixels - ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - 1; - - if (sx + ex < 0 || sx > visWidth) - { - continue; - } - - if ((sx <= (endRes - startRes) * charWidth) - && group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i))) - { - if ((bottom == -1) - && !group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i + 1))) - { - bottom = sy + charHeight; - } - - if (!inGroup) - { - if (((top == -1) && (i == 0)) - || !group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i - 1))) - { - top = sy; - } - - oldY = sy; - inGroup = true; - - g.setStroke(new BasicStroke()); - g.setColor(group.getOutlineColour()); - } - } - else - { - if (inGroup) - { - // 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 + ex < visWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } + break; + } + group = av.getAlignment().getGroups().get(groupIndex); + } while (groupIndex < av.getAlignment().getGroups().size()); + } + } - if (sx < 0) - { - // ex += sx; - // sx = 0; - } + /** + * 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; + } - if (sx + ex > visWidth) - { - ex = visWidth; - } + 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()); + } - else if (sx + ex >= (endRes - startRes + 1) * charWidth) - { - ex = (endRes - startRes + 1) * charWidth; - } + /** + * 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; - // draw horizontal line at top of group - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } + // 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; - // draw horizontal line at bottom of group - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } + // convert the cursorX into a position on the visible alignment + int cursor_xpos = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(cursorX); - inGroup = false; - } - } - } + if (av.getAlignment().getHiddenColumns().isVisible(cursorX)) + { - if (inGroup) + if (av.getWrapAlignment()) { - sy = offset + ((i - startSeq) * charHeight); - if (sx >= 0 && sx < visWidth) - { - g.drawLine(sx, oldY, sx, sy); - } - - if (sx + ex < visWidth) + // 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()) { - g.drawLine(sx + ex, oldY, sx + ex, sy); + hgap += charHeight; } - if (sx < 0) - { - ex += sx; - sx = 0; - } + int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) + / charWidth; + int cHeight = av.getAlignment().getHeight() * charHeight; - if (sx + ex > visWidth) - { - ex = visWidth; - } - else if (sx + ex >= (endRes - startRes + 1) * charWidth) - { - ex = (endRes - startRes + 1) * charWidth; - } + endx = startx + cWidth - 1; + int ypos = hgap; // vertical offset - if (top != -1) + // iterate down the wrapped panels + while ((ypos <= canvasHeight) && (endx < cursor_xpos)) { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } + // update vertical offset + ypos += cHeight + getAnnotationHeight() + hgap; - if (bottom != -1) - { - g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); - bottom = -1; + // update horizontal offset + startx += cWidth; + endx = startx + cWidth - 1; } - - inGroup = false; + yoffset = ypos; + xoffset = labelWidthWest; } - groupIndex++; - - g.setStroke(new BasicStroke()); - - if (groupIndex >= av.getAlignment().getGroups().size()) + // now check if cursor is within range for x values + if (cursor_xpos >= startx && cursor_xpos <= endx) { - break; - } - - group = av.getAlignment().getGroups().get(groupIndex); - - } while (groupIndex < av.getAlignment().getGroups().size()); + // 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 the selection group as a separate image and overlay + /** + * 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 BufferedImage drawSelectionGroup() + private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group, + int startRes, int endRes, int startSeq, int endSeq, int offset) { - // get a new image of the correct size - BufferedImage selectionImage = setupImage(); + int charWidth = av.getCharWidth(); - if (selectionImage == null) + if (!av.hasHiddenColumns()) { - return null; + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, + offset); } - - SequenceGroup group = av.getSelectionGroup(); - if (group == null) + else { - // nothing to draw - return null; - } - - // set up drawing colour - Graphics2D g = (Graphics2D) selectionImage.getGraphics(); - // set background to transparent - g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); - g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight()); + // package into blocks of visible columns + int screenY = 0; + int blockStart; + int blockEnd; - g.setComposite(AlphaComposite.Src); - g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, - BasicStroke.JOIN_ROUND, 3f, new float[] - { 5f, 3f }, 0f)); - g.setColor(Color.RED); + 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]; - int visWidth = av.getRanges().getViewportWidth() * charWidth; + g.translate(screenY * charWidth, 0); + drawPartialGroupOutline(g, group, blockStart, blockEnd, startSeq, + endSeq, offset); - int startRes = av.getRanges().getStartRes(); + g.translate(-screenY * charWidth, 0); + screenY += blockEnd - blockStart + 1; + } + } + } - // set x start and end positions of group - int startx = (group.getStartRes() - startRes) * charWidth; - int endx = (group.getEndRes() - startRes + 1) * charWidth; + /** + * 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; - // get sequences to determine y positions of group - int startSeq = av.getRanges().getStartSeq(); - for (i = startSeq; i <= av.getRanges().getEndSeq(); ++i) - { - int sy = (i - startSeq) * charHeight; + List seqs = group.getSequences(null); - if (group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i))) + // 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++) { - if ((bottom == -1) && !group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i + 1))) - { - bottom = sy + charHeight; - } + sy = verticalOffset + (i - startSeq) * charHeight; - if (!inGroup) + if ((sx <= (endRes - startRes) * charWidth) + && seqs.contains(av.getAlignment().getSequenceAt(i))) { - if (((top == -1) && (i == 0)) || !group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i - 1))) + if ((bottom == -1) + && !seqs.contains(av.getAlignment().getSequenceAt(i + 1))) { - top = sy; + bottom = sy + charHeight; } - oldY = sy; - inGroup = true; - } - } - else - { - if (inGroup) - { - // if start position is visible, draw vertical line to left of - // group - if (startx >= 0 && startx < visWidth * charWidth) - { - g.drawLine(startx, oldY, startx, sy); - } - - // if end position is visible, draw vertical line to right of - // group - if (endx <= visWidth * charWidth) + if (!inGroup) { - g.drawLine(endx, oldY, endx, sy); - } - - if (endx > visWidth * charWidth) - { - endx = visWidth * charWidth; - } - - // draw horizontal line at top of group - if (top != -1) - { - g.drawLine(startx, top, endx, top); - top = -1; - } + if (((top == -1) && (i == 0)) || !seqs + .contains(av.getAlignment().getSequenceAt(i - 1))) + { + top = sy; + } - // draw horizontal line at bottom of group - if (bottom != -1) - { - g.drawLine(startx, bottom, endx, bottom); - bottom = -1; + oldY = sy; + inGroup = true; } + } + else if (inGroup) + { + drawVerticals(g, sx, xwidth, visWidth, oldY, sy); + drawHorizontals(g, sx, xwidth, visWidth, top, bottom); + // reset top and bottom + top = -1; + bottom = -1; inGroup = false; } } - } - if (inGroup) - { - int sy = (i - startSeq) * charHeight; - if (startx >= 0 && startx < visWidth) + if (inGroup) { - g.drawLine(startx, oldY, startx, sy); + sy = verticalOffset + ((i - startSeq) * charHeight); + drawVerticals(g, sx, xwidth, visWidth, oldY, sy); + drawHorizontals(g, sx, xwidth, visWidth, top, bottom); } + } + } - if (endx < visWidth) - { - g.drawLine(endx, oldY, endx, sy); - } + /** + * 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); + + } - if (endx > visWidth) + /** + * 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) { - endx = visWidth; + redrawn = drawMappedPositionsWrapped(previous); + drawn = drawMappedPositionsWrapped(results); + redrawn |= drawn; } - - if (top != -1) + else { - g.drawLine(startx, top, endx, top); - top = -1; + redrawn = drawMappedPositions(previous); + drawn = drawMappedPositions(results); + redrawn |= drawn; } - if (bottom != -1) + /* + * if highlights were either removed or added, repaint + */ + if (redrawn) { - g.drawLine(startx, bottom - 1, endx, bottom - 1); - bottom = -1; + repaint(); } - inGroup = false; - } + /* + * return true only if highlights were added + */ + return drawn; - return selectionImage; + } finally + { + fastpainting = false; + } } /** - * DOCUMENT ME! + * 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 - * DOCUMENT ME! + * @return */ - public void highlightSearchResults(SearchResultsI results) + protected boolean drawMappedPositions(SearchResultsI results) { - img = null; + 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); - av.setSearchResults(results); + 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); + } + } + } + } - repaint(); + 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(); - + // System.err.println(">>SeqCanvas propertyChange " + eventName); if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED)) { - paintSeqGroup(); + fastPaint = true; + repaint(); + return; } - else if (av.getWrapAlignment()) + else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT)) { + fastPaint = false; + // System.err.println("!!!! 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)) { - repaint(); + 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; } } - else + // 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)) { - int scrollX = 0; - if (eventName.equals(ViewportRanges.STARTRES)) + if (av.getWrapAlignment()) { - // Make sure we're not trying to draw a panel - // larger than the visible window - ViewportRanges vpRanges = av.getRanges(); - scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); - int range = vpRanges.getEndRes() - vpRanges.getStartRes(); - if (scrollX > range) + 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) { - scrollX = range; + /* + * 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); } - else if (scrollX < -range) + + 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)) { - scrollX = -range; + gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx, + -positions * charWidth, heightToCopy, widthToCopy, + -wrappedRepeatHeightPx); } + y += wrappedRepeatHeightPx; + xpos += viewportWidth; } + } + gg.dispose(); + } - // 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)) - { - // scroll - startres and endres both change - fastPaint(scrollX, 0); - } - else if (eventName.equals(ViewportRanges.STARTSEQ)) + /** + * 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) { - // scroll - fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + 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; } + }