X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=59a6cb1072b4128b4445c47840a6cbb148c35c67;hb=d3bf4ae12b72df02dee34c95da750ab38a3816b9;hp=2eb8c4d401c99adcfa5a493e4349bf968d84cc38;hpb=79d9f7d16d1a5fe58ad2b91a0ee1a0bbe6938373;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 2eb8c4d..59a6cb1 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -25,85 +25,95 @@ 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; -import java.awt.AlphaComposite; // ok 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; /** - * 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 { - private static String ZEROS = "0000000000"; + /** + * vertical gap in pixels between sequences and annotations when in wrapped + * mode + */ + static final int SEQS_ANNOTATION_GAP = 3; - final FeatureRenderer fr; + private static final String ZEROS = "0000000000"; - final SequenceRenderer seqRdr; //ok + final FeatureRenderer fr; BufferedImage img; - Graphics2D gg; - - int imgWidth; - - int imgHeight; - AlignViewport av; - boolean fastPaint = false; - - boolean fastpainting = false; - int cursorX = 0; int cursorY = 0; + private final SequenceRenderer seqRdr; + + private boolean fastPaint = false; + + private boolean fastpainting = false; + private AnnotationPanel annotations; /* * measurements for drawing a wrapped alignment */ - int labelWidthWest; // label left width in pixels if shown - private int labelWidthEast; // label right width in pixels if shown - private int wrappedSpaceAboveAlignment; // gap between widths + private int labelWidthWest; // label left width in pixels if shown + + int wrappedSpaceAboveAlignment; // gap between widths - private int wrappedRepeatHeightPx; // height in pixels of wrapped width + int wrappedRepeatHeightPx; // height in pixels of wrapped width private int wrappedVisibleWidths; // number of wrapped widths displayed + private int availWidth; + + private int availHeight; + + private boolean allowFastPaint; + + // 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; fr = new FeatureRenderer(ap); - seqRdr = new SequenceRenderer(av); //ok + seqRdr = new SequenceRenderer(av); setLayout(new BorderLayout()); PaintRefresher.Register(this, av.getSequenceSetId()); setBackground(Color.white); @@ -113,7 +123,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public SequenceRenderer getSequenceRenderer() { - return seqRdr; //ok + return seqRdr; } public FeatureRenderer getFeatureRenderer() @@ -190,19 +200,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * @param left * if true, scale is left of residues, if false, scale is right */ - void drawVerticalScale(Graphics g, int startx, int endx, int ypos, - boolean left) + void drawVerticalScale(Graphics g, final int startx, final int endx, + final int ypos, final boolean left) { int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); - ypos += charHeight; + int yPos = ypos + charHeight; + int startX = startx; + int endX = endx; if (av.hasHiddenColumns()) { HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); - startx = hiddenColumns.adjustForHiddenColumns(startx); - endx = hiddenColumns.adjustForHiddenColumns(endx); + startX = hiddenColumns.visibleToAbsoluteColumn(startx); + endX = hiddenColumns.visibleToAbsoluteColumn(endx); } FontMetrics fm = getFontMetrics(av.getFont()); @@ -214,9 +226,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * 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 index = left ? startX : endX; int value = -1; - while (index >= startx && index <= endx) + while (index >= startX && index <= endX) { if (!Comparison.isGap(seq.getCharAt(index))) { @@ -237,29 +249,29 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * white fill the space for the scale */ g.setColor(Color.white); - int y = (ypos + (i * charHeight)) - (charHeight / 5); + 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, with half a character width - * separation from the sequence data + * 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 justify = fm.stringWidth(valueAsString) + charWidth; - int xpos = left ? labelWidthWest - justify + charWidth / 2 - : labelWidthEast - justify + charWidth / 2; + int labelLength = fm.stringWidth(valueAsString); + int xOffset = labelSpace - labelLength; g.setColor(Color.black); - g.drawString(valueAsString, xpos, y); + g.drawString(valueAsString, xOffset, y); } } + } - //ok /** * 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 @@ -271,6 +283,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI *
  • scrolling by trackpad, middle mouse button, or other device
    • *
  • by moving the box in the Overview window
    • *
  • programmatically to make a highlighted position visible
    • + *
  • pasting a block of sequences
    • * * * @param horizontal @@ -280,18 +293,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ public void fastPaint(int horizontal, int vertical) { - if (fastpainting || gg == null || img == null) //ok + + // 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(); @@ -300,100 +316,130 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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 = (endRes - startRes - horizontal) * charWidth; - startRes = endRes - horizontal; - } - else if (horizontal < 0) - { - endRes = startRes - horizontal; - } - else 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(); + if (horizontal > 0) // scrollbar pulled right, image to the left + { + transX = (endRes - startRes - horizontal) * charWidth; + startRes = endRes - horizontal; } - else + else if (horizontal < 0) { - transY = img.getHeight() - ((vertical + 1) * charHeight); + endRes = startRes - horizontal; } - } - else if (vertical < 0) - { - endSeq = startSeq - vertical; - if (endSeq > ranges.getEndSeq()) + if (vertical > 0) // scroll down { - endSeq = ranges.getEndSeq(); + 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; - gg.translate(transX, transY); - drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); - gg.translate(-transX, -transY); + if (endSeq > ranges.getEndSeq()) + { + endSeq = ranges.getEndSeq(); + } + } - repaint(); + // System.err.println(">>> 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); + 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. + av.getAlignPanel().repaint(); } finally { fastpainting = false; } } - //ok - //ok @Override public void paintComponent(Graphics g) { - super.paintComponent(g); - - int charHeight = av.getCharHeight(); - int charWidth = av.getCharWidth(); - - ViewportRanges ranges = av.getRanges(); - - int width = getWidth(); - int height = getHeight(); - - width -= (width % charWidth); - height -= (height % charHeight); + if (av.getAlignPanel().getHoldRepaint()) + { + return; + } - // selectImage is the selection group outline image - BufferedImage selectImage = drawSelectionGroup( - ranges.getStartRes(), ranges.getEndRes(), - ranges.getStartSeq(), ranges.getEndSeq()); + getAvailSizes(); - if ((img != null) && (fastPaint - || (getVisibleRect().width != g.getClipBounds().width) - || (getVisibleRect().height != g.getClipBounds().height))) + if (availWidth == 0 || availHeight == 0) { - BufferedImage lcimg = buildLocalImage(selectImage); - g.drawImage(lcimg, 0, 0, this); + 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 (allowFastPaint && 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 if ((width > 0) && (height > 0)) + else { - // img is a cached version of the last view we drew, if any - // if we have no img or the size has changed, make a new one - if (img == null || width != img.getWidth() - || height != img.getHeight()) + allowFastPaint = true; + // 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 || availWidth != img.getWidth() + || availHeight != img.getHeight()) { - img = setupImage(); - if (img == null) - { - return; - } - gg = (Graphics2D) img.getGraphics(); - gg.setFont(av.getFont()); + img = new BufferedImage(availWidth, availHeight, + BufferedImage.TYPE_INT_RGB); } + Graphics2D gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + if (av.antiAlias) { gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, @@ -401,25 +447,29 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } gg.setColor(Color.white); - gg.fillRect(0, 0, img.getWidth(), img.getHeight()); + gg.fillRect(0, 0, availWidth, availHeight); if (av.getWrapAlignment()) { - drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); + drawWrappedPanel(gg, availWidth, availHeight, ranges.getStartRes()); } else { - drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), - ranges.getStartSeq(), ranges.getEndSeq(), 0); + drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); } - // lcimg is a local *copy* of img which we'll draw selectImage on top of - BufferedImage lcimg = buildLocalImage(selectImage); - g.drawImage(lcimg, 0, 0, this); + drawSelectionGroup(gg, startRes, endRes, startSeq, endSeq); + + g.drawImage(img, 0, 0, this); + gg.dispose(); + } + + if (av.cursorMode) + { + drawCursor(g, startRes, endRes, startSeq, endSeq); } } -//ok - + /** * Draw an alignment panel for printing * @@ -439,14 +489,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { drawPanel(g1, startRes, endRes, startSeq, endSeq, 0); - BufferedImage selectImage = drawSelectionGroup(startRes, endRes, - startSeq, endSeq); - if (selectImage != null) - { - ((Graphics2D) g1).setComposite(AlphaComposite - .getInstance(AlphaComposite.SRC_OVER)); - g1.drawImage(selectImage, 0, 0, this); - } + drawSelectionGroup((Graphics2D) g1, startRes, endRes, startSeq, endSeq); } /** @@ -464,136 +507,50 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth, int canvasHeight, int startRes) { - SequenceGroup group = av.getSelectionGroup(); - drawWrappedPanel(g, canvasWidth, canvasHeight, startRes); + SequenceGroup group = av.getSelectionGroup(); if (group != null) { - BufferedImage selectImage = null; - try - { - selectImage = new BufferedImage(canvasWidth, canvasHeight, - BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works - } catch (OutOfMemoryError er) - { - System.gc(); - System.err.println("Print image OutOfMemory Error.\n" + er); - new OOMWarning("Creating wrapped alignment image for printing", er); - } - if (selectImage != null) - { - Graphics2D g2 = selectImage.createGraphics(); - setupSelectionGroup(g2, selectImage); - drawWrappedSelection(g2, group, canvasWidth, canvasHeight, - startRes); - - g2.setComposite( - AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); - g.drawImage(selectImage, 0, 0, this); - g2.dispose(); - } - } - } - - /* - * 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); - - // overlay selection group on lcimg - if (selectImage != null) - { - g2d.setComposite( - AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); - g2d.drawImage(selectImage, 0, 0, this); + drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight, + startRes); } - g2d.dispose(); - - return lcimg; - } - - /* - * Set up a buffered image of the correct height and size for the sequence canvas - */ - private BufferedImage setupImage() - { - BufferedImage lcimg = null; - - int charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - - int width = getWidth(); - int height = getHeight(); - - width -= (width % charWidth); - height -= (height % charHeight); - - if ((width < 1) || (height < 1)) - { - return null; - } - - try - { - lcimg = new BufferedImage(width, height, - BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works - } catch (OutOfMemoryError er) - { - System.gc(); - System.err.println( - "Group image OutOfMemory Redraw Error.\n" + er); - new OOMWarning("Creating alignment image for display", er); - - return null; - } - - return lcimg; } /** - * Returns the visible width of the canvas in residues, after allowing for - * East or West scales (if shown) + * Using the current font, determine fields labelWidthEast and labelWidthWest, + * and return the number of residues that can fill the remaining width * - * @param canvasWidth + * @param w * the width in pixels (possibly including scales) * - * @return + * @return the visible width in residues, after allowing for East or West + * scales (if shown) + * */ - public int getWrappedCanvasWidth(int canvasWidth) + public int getWrappedCanvasWidth(int w) { int charWidth = av.getCharWidth(); FontMetrics fm = getFontMetrics(av.getFont()); - labelWidthEast = 0; - labelWidthWest = 0; + int labelWidth = (av.getScaleRightWrapped() || av.getScaleLeftWrapped() + ? getLabelWidth(fm) + : 0); - if (av.getScaleRightWrapped()) - { - labelWidthEast = getLabelWidth(fm); - } + labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0; - if (av.getScaleLeftWrapped()) - { - labelWidthWest = labelWidthEast > 0 ? labelWidthEast - : getLabelWidth(fm); - } + labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; - return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; + return (w - labelWidthEast - labelWidthWest) / charWidth; } /** - * Returns a pixel width suitable for showing the largest sequence coordinate - * (end position) in the alignment. Returns 2 plus the number of decimal - * digits to be shown (3 for 1-10, 4 for 11-99 etc). + * 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 @@ -611,13 +568,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd()); } - int length = 2; + // quick int log10 + int length = 0; for (int i = maxWidth; i > 0; i /= 10) { length++; } - return fm.stringWidth(ZEROS.substring(0, length)); + return fm.stringWidth(ZEROS.substring(0, length)) + av.getCharWidth(); } /** @@ -625,26 +583,28 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * window * * @param g - * @param canvasWidth + * @param availWidth * available width in pixels - * @param canvasHeight + * @param availHeight * 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) + public void drawWrappedPanel(Graphics g, int availWidth, int availHeight, + final int startColumn) { - int wrappedWidthInResidues = calculateWrappedGeometry(canvasWidth, - canvasHeight); - + int wrappedWidthInResidues = calculateWrappedGeometry(); 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(); + /* - * draw one width at a time (including any scales or annotation shown), + * 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; @@ -654,9 +614,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int currentWidth = 0; while ((currentWidth < wrappedVisibleWidths) && (start < maxWidth)) { - int endColumn = Math - .min(maxWidth, start + wrappedWidthInResidues - 1); - drawWrappedWidth(g, ypos, start, endColumn, canvasHeight); + int endColumn = Math.min(maxWidth, + start + wrappedWidthInResidues - 1); + drawWrappedWidth(g, ypos, start, endColumn, availHeight); ypos += wrappedRepeatHeightPx; start += wrappedWidthInResidues; currentWidth++; @@ -665,6 +625,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawWrappedDecorators(g, startColumn); } + private void getAvailSizes() + { + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + availWidth = getWidth(); + availHeight = getHeight(); + availWidth -= (availWidth % charWidth); + availHeight -= (availHeight % charHeight); + } + /** * Calculates and saves values needed when rendering a wrapped alignment. * These depend on many factors, including @@ -675,26 +645,27 @@ public class SeqCanvas extends JComponent implements ViewportListenerI *
  • whether scales are shown left, right or above the alignment
    • * * + * @param availWidth + * @param availHeight + * @return the number of residue columns in each width + */ + protected int calculateWrappedGeometry() + { + getAvailSizes(); + return calculateWrappedGeometry(availWidth, availHeight); + + } + + /** + * for test only * @param canvasWidth * @param canvasHeight - * @return the number of residue columns in each width + * @return */ - protected int calculateWrappedGeometry(int canvasWidth, int canvasHeight) + public int calculateWrappedGeometry(int canvasWidth, int canvasHeight) { - int charHeight = av.getCharHeight(); - int charWidth = av.getCharWidth(); - /* - * width of labels in pixels left and right (if shown) - */ - int labelWidth = 0; - if (av.getScaleRightWrapped() || av.getScaleLeftWrapped()) - { - FontMetrics fm = getFontMetrics(av.getFont()); - labelWidth = getLabelWidth(fm); - } - labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0; - labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; + int charHeight = av.getCharHeight(); /* * vertical space in pixels between wrapped widths of alignment @@ -704,29 +675,27 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * (av.getScaleAboveWrapped() ? 2 : 1); /* - * height in pixels of the wrapped widths + * compute height in pixels of the wrapped widths + * - start with space above plus sequences */ - wrappedRepeatHeightPx = wrappedSpaceAboveAlignment; - // add sequences - wrappedRepeatHeightPx += av.getRanges().getViewportHeight() - * charHeight; - // add annotations panel height if shown - wrappedRepeatHeightPx += getAnnotationHeight(); + wrappedRepeatHeightPx = wrappedSpaceAboveAlignment + + av.getAlignment().getHeight() * charHeight; /* - * number of residue columns we can show in each row; - * this is just canvas width less scale left and right (if shown), - * as a whole multiple of character widths + * add annotations panel height if shown + * also gap between sequences and annotations */ - int wrappedWidthInResidues = (canvasWidth - labelWidthEast - - labelWidthWest) / charWidth; + 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(); - int xMax = ranges.getVisibleAlignmentWidth(); wrappedVisibleWidths = canvasHeight / wrappedRepeatHeightPx; int remainder = canvasHeight % wrappedRepeatHeightPx; if (remainder >= (wrappedSpaceAboveAlignment + charHeight)) @@ -735,10 +704,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } /* + * compute width in residues; this also sets East and West label widths + */ + int wrappedWidthInResidues = getWrappedCanvasWidth(canvasWidth); + + /* * limit visibleWidths to not exceed width of alignment */ - int maxWidths = (xMax - ranges.getStartRes()) / wrappedWidthInResidues; - if (xMax % wrappedWidthInResidues > 0) + int xMax = ranges.getVisibleAlignmentWidth(); + int startToEnd = xMax - ranges.getStartRes(); + int maxWidths = startToEnd / wrappedWidthInResidues; + if (startToEnd % wrappedWidthInResidues > 0) { maxWidths++; } @@ -757,12 +733,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * @param endColumn * @param canvasHeight */ - protected void drawWrappedWidth(Graphics g, int ypos, int startColumn, - int endColumn, int canvasHeight) + protected void drawWrappedWidth(Graphics g, final int ypos, + final int startColumn, final int endColumn, + final int canvasHeight) { - int charHeight = av.getCharHeight(); - int charWidth = av.getCharWidth(); - ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); @@ -773,41 +747,30 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * 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); - - // When printing we have an extra clipped region, - // the Printable page which we need to account for here - Shape clip = g.getClip(); + * charWidth; - if (clip == null) - { - g.setClip(0, 0, viewportWidth * charWidth, canvasHeight); - } - else - { - g.setClip(0, (int) clip.getBounds().getY(), - viewportWidth * charWidth, (int) clip.getBounds().getHeight()); - } + g.translate(xOffset, 0); /* * white fill the region to be drawn (so incremental fast paint doesn't * scribble over an existing image) */ - gg.setColor(Color.white); - gg.fillRect(0, ypos, (endx - startColumn + 1) * charWidth, + 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() * charHeight; + int cHeight = av.getAlignment().getHeight() * av.getCharHeight(); if (av.isShowAnnotation()) { - g.translate(0, cHeight + ypos + 3); + final int yShift = cHeight + ypos + SEQS_ANNOTATION_GAP; + g.translate(0, yShift); if (annotations == null) { annotations = new AnnotationPanel(av); @@ -815,9 +778,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI annotations.renderer.drawComponent(annotations, av, g, -1, startColumn, endx + 1); - g.translate(0, -cHeight - ypos - 3); + g.translate(0, -yShift); } - g.setClip(clip); g.translate(-xOffset, 0); } @@ -828,11 +790,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * @param g * @param startColumn */ - protected void drawWrappedDecorators(Graphics g, int startColumn) + protected void drawWrappedDecorators(Graphics g, final int startColumn) { int charWidth = av.getCharWidth(); g.setFont(av.getFont()); + g.setColor(Color.black); int ypos = wrappedSpaceAboveAlignment; @@ -840,20 +803,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int viewportWidth = ranges.getViewportWidth(); int maxWidth = ranges.getVisibleAlignmentWidth(); int widthsDrawn = 0; + int startCol = startColumn; + while (widthsDrawn < wrappedVisibleWidths) { - int endColumn = Math.min(maxWidth, startColumn + viewportWidth - 1); + int endColumn = Math.min(maxWidth, startCol + viewportWidth - 1); if (av.getScaleLeftWrapped()) { - drawVerticalScale(g, startColumn, endColumn - 1, ypos, true); + drawVerticalScale(g, startCol, endColumn - 1, ypos, true); } if (av.getScaleRightWrapped()) { int x = labelWidthWest + viewportWidth * charWidth; + g.translate(x, 0); - drawVerticalScale(g, startColumn, endColumn, ypos, false); + drawVerticalScale(g, startCol, endColumn, ypos, false); g.translate(-x, 0); } @@ -861,32 +827,38 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * 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.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, startColumn, endColumn, ypos); + drawNorthScale(g, startCol, endColumn, ypos); } if (av.hasHiddenColumns() && av.getShowHiddenMarkers()) { - drawHiddenColumnMarkers(g, ypos, startColumn, endColumn); + drawHiddenColumnMarkers(g, ypos, startCol, endColumn); } g.translate(-labelWidthWest, 0); ypos += wrappedRepeatHeightPx; - startColumn += viewportWidth; + startCol += viewportWidth; widthsDrawn++; } } /** + * Draws markers (triangles) above hidden column positions between startColumn + * and endColumn. + * * @param g * @param ypos * @param startColumn @@ -899,13 +871,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int charWidth = av.getCharWidth(); g.setColor(Color.blue); + int res; HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - List positions = hidden.findHiddenRegionPositions(); - for (int pos : positions) + + Iterator it = hidden.getStartRegionIterator(startColumn, + endColumn); + while (it.hasNext()) { - int res = pos - startColumn; + res = it.next() - startColumn; - if (res < 0 || res > endColumn - startColumn) + if (res < 0 || res > endColumn - startColumn + 1) { continue; } @@ -923,44 +898,49 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } + private final static BasicStroke dottedStroke = new BasicStroke(1, + BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f); + + private final static BasicStroke basicStroke = new BasicStroke(); + /* * Draw a selection group over a wrapped alignment */ private void drawWrappedSelection(Graphics2D g, SequenceGroup group, - int canvasWidth, - int canvasHeight, int startRes) + int canvasWidth, int canvasHeight, int startRes) { - int charHeight = av.getCharHeight(); - int charWidth = av.getCharWidth(); - - // height gap above each panel - int hgap = charHeight; - if (av.getScaleAboveWrapped()) - { - hgap += charHeight; - } + // 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(dottedStroke); + g.setColor(Color.RED); + int charWidth = av.getCharWidth(); int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; - int cHeight = av.getAlignment().getHeight() * charHeight; - int startx = startRes; - int endx; - int ypos = hgap; // vertical offset - int maxwidth = av.getAlignment().getWidth(); - - if (av.hasHiddenColumns()) - { - maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth); - } + int maxwidth = av.getAlignment().getVisibleWidth(); + + // JAL-3253-applet had this: + // // height gap above each panel + // int charHeight = av.getCharHeight(); + // int hgap = charHeight; + // if (av.getScaleAboveWrapped()) + // { + // hgap += charHeight; + // } + // int dy = getAnnotationHeight() + hgap + // + av.getAlignment().getHeight() * charHeight; + // int ypos = hgap; // vertical offset + + // this is from 0b573ed (gmungoc) + int dy = wrappedRepeatHeightPx; + int ypos = wrappedSpaceAboveAlignment; - // chop the wrapped alignment extent up into panel-sized blocks and treat - // each block as if it were a block from an unwrapped alignment while ((ypos <= canvasHeight) && (startx < maxwidth)) { // set end value to be start + width, or maxwidth, whichever is smaller - endx = startx + cWidth - 1; + int endx = startx + cWidth - 1; if (endx > maxwidth) { @@ -970,19 +950,25 @@ public class SeqCanvas extends JComponent implements ViewportListenerI g.translate(labelWidthWest, 0); drawUnwrappedSelection(g, group, startx, endx, 0, - av.getAlignment().getHeight() - 1, - ypos); + av.getAlignment().getHeight() - 1, ypos); g.translate(-labelWidthWest, 0); // update vertical offset - ypos += cHeight + getAnnotationHeight() + hgap; + ypos += dy; // update horizontal offset startx += cWidth; } + g.setStroke(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()) @@ -1030,29 +1016,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI else { int screenY = 0; - final int screenYMax = endRes - startRes; - int blockStart = startRes; - int blockEnd = endRes; + int blockStart; + int blockEnd; - for (int[] region : av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy()) - { - int hideStart = region[0]; - int hideEnd = region[1]; + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + VisibleContigsIterator regions = hidden + .getVisContigsIterator(startRes, endRes + 1, true); - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } + 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 */ - blockEnd = Math.min(hideStart - 1, blockStart + screenYMax - - screenY); - g1.translate(screenY * charWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); @@ -1061,7 +1041,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * draw the downline of the hidden column marker (ScalePanel draws the * triangle on top) if we reached it */ - if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1) + if (av.getShowHiddenMarkers() + && (regions.hasNext() || regions.endsAtHidden())) { g1.setColor(Color.blue); @@ -1072,23 +1053,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI g1.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - - if (screenY > screenYMax) - { - // already rendered last block - return; - } - } - - if (screenY <= screenYMax) - { - // remaining visible region to render - blockEnd = blockStart + screenYMax - screenY; - g1.translate(screenY * charWidth, 0); - draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); - - g1.translate(-screenY * charWidth, 0); } } @@ -1146,26 +1110,19 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasSearchResults()) { SearchResultsI searchResults = av.getSearchResults(); - int[] visibleResults = searchResults.getResults(nextSeq, - startRes, endRes); + 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)); + visibleResults[r + 1], + (visibleResults[r] - startRes) * charWidth, + offset + ((i - startSeq) * charHeight)); } } } - - if (av.cursorMode && cursorY == i && cursorX >= startRes - && cursorX <= endRes) - { - seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth, - offset + ((i - startSeq) * charHeight)); - } } if (av.getSelectionGroup() != null @@ -1176,14 +1133,21 @@ 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 groupIndex = -1; @@ -1196,58 +1160,44 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (group != null) { - g.setStroke(new BasicStroke()); - g.setColor(group.getOutlineColour()); - do { + g.setColor(group.getOutlineColour()); drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, offset); groupIndex++; - - g.setStroke(new BasicStroke()); - if (groupIndex >= av.getAlignment().getGroups().size()) { break; } - group = av.getAlignment().getGroups().get(groupIndex); - } while (groupIndex < av.getAlignment().getGroups().size()); - } - } - - /* - * Draw the selection group as a separate image and overlay + /** + * Draws the outline of the current selection group (if any) + * + * @param g + * @param startRes + * @param endRes + * @param startSeq + * @param endSeq */ - private BufferedImage drawSelectionGroup(int startRes, int endRes, + private void drawSelectionGroup(Graphics2D g, int startRes, int endRes, int startSeq, int endSeq) { - // get a new image of the correct size - BufferedImage selectionImage = setupImage(); - - if (selectionImage == null) - { - return null; - } - SequenceGroup group = av.getSelectionGroup(); if (group == null) { - // nothing to draw - return null; + return; } - // set up drawing colour - Graphics2D g = (Graphics2D) selectionImage.getGraphics(); - - setupSelectionGroup(g, selectionImage); - + 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, @@ -1258,44 +1208,118 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawWrappedSelection(g, group, getWidth(), getHeight(), av.getRanges().getStartRes()); } - - g.dispose(); - return selectionImage; + g.setStroke(new BasicStroke()); } - /* - * Set up graphics for selection group + /** + * 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 setupSelectionGroup(Graphics2D g, - BufferedImage selectionImage) + private void drawCursor(Graphics g, int startRes, int endRes, + int startSeq, int endSeq) { - // set background to transparent - g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); - g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight()); + // convert the cursorY into a position on the visible alignment + int cursor_ypos = cursorY; - // set up foreground to draw red dashed line - 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); + // 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) + * + * @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(); - + int charWidth = av.getCharWidth(); + if (!av.hasHiddenColumns()) { drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, @@ -1305,61 +1329,45 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { // package into blocks of visible columns int screenY = 0; - int blockStart = startRes; - int blockEnd = endRes; + int blockStart; + int blockEnd; - for (int[] region : av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy()) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + VisibleContigsIterator regions = hidden + .getVisContigsIterator(startRes, endRes + 1, true); + while (regions.hasNext()) { - int hideStart = region[0]; - int hideEnd = region[1]; - - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } - - blockEnd = hideStart - 1; + int[] region = regions.next(); + blockEnd = region[1]; + blockStart = region[0]; g.translate(screenY * charWidth, 0); - drawPartialGroupOutline(g, group, - blockStart, blockEnd, startSeq, endSeq, offset); + drawPartialGroupOutline(g, group, blockStart, blockEnd, startSeq, + endSeq, offset); g.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - - if (screenY > (endRes - startRes)) - { - // already rendered last block - break; - } - } - - if (screenY <= (endRes - startRes)) - { - // remaining visible region to render - blockEnd = blockStart + (endRes - startRes) - screenY; - g.translate(screenY * charWidth, 0); - drawPartialGroupOutline(g, group, - blockStart, blockEnd, startSeq, endSeq, offset); - - g.translate(-screenY * charWidth, 0); } } } - /* - * Draw the selection group as a separate image and overlay + /** + * 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 charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); int visWidth = (endRes - startRes + 1) * charWidth; int oldY = -1; @@ -1367,161 +1375,184 @@ public class SeqCanvas extends JComponent implements ViewportListenerI boolean inGroup = false; int top = -1; int bottom = -1; - - int sx = -1; int sy = -1; - int xwidth = -1; - - for (i = startSeq; i <= endSeq; i++) - { - // position of start residue of group relative to startRes, in pixels - sx = (group.getStartRes() - startRes) * charWidth; - // width of group in pixels - xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - - 1; + List seqs = group.getSequences(null); - sy = verticalOffset + (i - startSeq) * charHeight; + // position of start residue of group relative to startRes, in pixels + int sx = (group.getStartRes() - startRes) * charWidth; - if (sx + xwidth < 0 || sx > visWidth) - { - continue; - } + // width of group in pixels + int xwidth = (((group.getEndRes() + 1) - group.getStartRes()) + * charWidth) - 1; - if ((sx <= (endRes - startRes) * charWidth) - && group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i))) + 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; - } - - if (!inGroup) - { - if (((top == -1) && (i == 0)) || !group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i - 1))) - { - top = sy; - } + sy = verticalOffset + (i - startSeq) * charHeight; - oldY = sy; - inGroup = true; - } - } - else - { - if (inGroup) + if ((sx <= (endRes - startRes) * charWidth) + && seqs.contains(av.getAlignment().getSequenceAt(i))) { - // 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) + if ((bottom == -1) + && !seqs.contains(av.getAlignment().getSequenceAt(i + 1))) { - g.drawLine(sx + xwidth, oldY, sx + xwidth, sy); + bottom = sy + charHeight; } - if (sx < 0) + if (!inGroup) { - xwidth += sx; - sx = 0; - } - - // don't let width extend beyond current block, or group extent - // fixes JAL-2672 - if (sx + xwidth >= (endRes - startRes + 1) * charWidth) - { - xwidth = (endRes - startRes + 1) * charWidth - sx; - } - - // draw horizontal line at top of group - if (top != -1) - { - g.drawLine(sx, top, sx + xwidth, 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(sx, bottom, sx + xwidth, 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) - { - sy = verticalOffset + ((i - startSeq) * charHeight); - if (sx >= 0 && sx < visWidth) + if (inGroup) { - g.drawLine(sx, oldY, sx, sy); + sy = verticalOffset + ((i - startSeq) * charHeight); + drawVerticals(g, sx, xwidth, visWidth, oldY, sy); + drawHorizontals(g, sx, xwidth, visWidth, top, bottom); } + } + } - if (sx + xwidth < visWidth) - { - g.drawLine(sx + xwidth, oldY, sx + xwidth, 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; + } - if (sx < 0) - { - xwidth += sx; - sx = 0; - } + // don't let width extend beyond current block, or group extent + // fixes JAL-2672 + if (startx + width >= visWidth) + { + width = visWidth - startx; + } - if (sx + xwidth > visWidth) - { - xwidth = visWidth; - } - else if (sx + xwidth >= (endRes - startRes + 1) * charWidth) - { - xwidth = (endRes - startRes + 1) * charWidth; - } + if (top != -1) + { + g.drawLine(startx, top, startx + width, top); + } - if (top != -1) - { - g.drawLine(sx, top, sx + xwidth, top); - top = -1; - } + if (bottom != -1) + { + g.drawLine(startx, bottom - 1, startx + width, bottom - 1); + } + } - if (bottom != -1) - { - g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1); - 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); + } - inGroup = false; + // 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. *

    - * Currently fastPaint is not implemented for 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). + * 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 noFastPaint + * @param doFastPaint + * if true, sets a flag so the next repaint only redraws the modified + * image * @return */ public boolean highlightSearchResults(SearchResultsI results, - boolean noFastPaint) + boolean doFastPaint) { if (fastpainting) { @@ -1530,7 +1561,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI boolean wrapped = av.getWrapAlignment(); try { - fastPaint = !noFastPaint; + fastPaint = doFastPaint; fastpainting = fastPaint; /* @@ -1587,7 +1618,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ protected boolean drawMappedPositions(SearchResultsI results) { - if (results == null) + if ((results == null) || (img == null)) // JAL-2784 check gg is not null { return false; } @@ -1609,9 +1640,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(firstVisibleColumn); + .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(lastVisibleColumn); + .visibleToAbsoluteColumn(lastVisibleColumn); } for (int seqNo = ranges.getStartSeq(); seqNo <= ranges @@ -1654,14 +1685,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { firstCol = alignment.getHiddenColumns() - .findColumnPosition(firstCol); - lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol); + .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; @@ -1672,52 +1706,157 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { String eventName = evt.getPropertyName(); - if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED)) + // BH 2019.07.27 removes dead code introduced in aad3650 and simplifies + // logic, emphasizing no check for ENDRES or ENDSEQ + + // 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. + + // Make sure we're not trying to draw a panel + // larger than the visible window + int scrollX = 0; + int scrollY = 0; + switch (eventName) { + case SequenceGroup.SEQ_GROUP_CHANGED: fastPaint = true; repaint(); - } - else if (eventName.equals(ViewportRanges.STARTRES)) - { - int scrollX = 0; - if (eventName.equals(ViewportRanges.STARTRES)) + return; + case ViewportRanges.MOVE_VIEWPORT: + fastPaint = false; + repaint(); + return; + case ViewportRanges.STARTSEQ: + // meaning STARTOREND + // typically scroll, but possibly just the end changed + fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + return; + case ViewportRanges.STARTRES: + // meaning STARTOREND + scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); + break; + case ViewportRanges.STARTRESANDSEQ: + scrollX = ((int[]) evt.getNewValue())[0] + - ((int[]) evt.getOldValue())[0]; + scrollY = ((int[]) evt.getNewValue())[1] + - ((int[]) evt.getOldValue())[1]; + if (scrollX != 0 && scrollY != 0) { - // 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) - { - scrollX = range; - } - else if (scrollX < -range) - { - scrollX = -range; - } + // all sorts of problems in JavaScript if this is commented out. + repaint(); + return; - // 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. - - // scroll - startres and endres both change - if (av.getWrapAlignment()) - { - fastPaintWrapped(scrollX); - } - else - { - fastPaint(scrollX, 0); - } - } - else if (eventName.equals(ViewportRanges.STARTSEQ)) - { - // scroll - fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); } + break; + default: + return; + } + + ViewportRanges vpRanges = av.getRanges(); + int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1; + scrollX = Math.max(Math.min(scrollX, range), -range); + // only STARTRES or STARTRESANDSEQ: + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); } + else + { + fastPaint(scrollX, scrollY); + } + + // BH 2019.07.27 was: + // if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED)) + // { + // fastPaint = true; + // repaint(); + // return; + // } + // else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT)) + // { + // fastPaint = false; + // // System.err.println("!!!! fastPaint false from MOVE_VIEWPORT"); + // repaint(); + // return; + // } + // + // 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. + // BH 2019.07.27 was: + // 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); + // } + // } + // + // BH oops! + // + // 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); + // } + // } } /** @@ -1733,10 +1872,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { ViewportRanges ranges = av.getRanges(); - if (Math.abs(scrollX) > ranges.getViewportWidth()) + if (Math.abs(scrollX) >= ranges.getViewportWidth()) { /* - * shift of more than one view width is + * shift of one view width or more is * overcomplicated to handle in this method */ fastPaint = false; @@ -1744,7 +1883,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return; } - if (fastpainting || gg == null) + if (fastpainting || img == null) { return; } @@ -1754,7 +1893,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI try { - calculateWrappedGeometry(getWidth(), getHeight()); + + Graphics gg = img.getGraphics(); + + calculateWrappedGeometry(); /* * relocate the regions of the alignment that are still visible @@ -1769,8 +1911,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (scrollX < 0) { int startRes = ranges.getStartRes(); - drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes, startRes - - scrollX - 1, getHeight()); + drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes, + startRes - scrollX - 1, getHeight()); } else { @@ -1782,6 +1924,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ drawWrappedDecorators(gg, ranges.getStartRes()); + gg.dispose(); + repaint(); } finally { @@ -1805,6 +1949,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return; } + Graphics gg = img.getGraphics(); + ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); int charWidth = av.getCharWidth(); @@ -1815,7 +1961,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ int visibleWidths = wrappedVisibleWidths; int canvasHeight = getHeight(); - boolean lastWidthPartHeight = (wrappedVisibleWidths * wrappedRepeatHeightPx) > canvasHeight; + boolean lastWidthPartHeight = (wrappedVisibleWidths + * wrappedRepeatHeightPx) > canvasHeight; if (lastWidthPartHeight) { @@ -1831,13 +1978,15 @@ public class SeqCanvas extends JComponent implements ViewportListenerI /* * white fill first to erase annotations */ + gg.translate(xOffset, 0); gg.setColor(Color.white); - gg.fillRect(labelWidthWest, ypos, - (endRes - startRes + 1) * charWidth, wrappedRepeatHeightPx); + gg.fillRect(labelWidthWest, ypos, (endRes - startRes + 1) * charWidth, + wrappedRepeatHeightPx); gg.translate(-xOffset, 0); drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight); + } /* @@ -1881,6 +2030,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI gg.setColor(Color.white); gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow); } + gg.dispose(); } /** @@ -1897,6 +2047,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { return; } + + Graphics gg = img.getGraphics(); + int charWidth = av.getCharWidth(); int canvasHeight = getHeight(); @@ -1927,10 +2080,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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); @@ -1959,18 +2119,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (y + wrappedRepeatHeightPx < canvasHeight - wrappedRepeatHeightPx && (xpos + viewportWidth <= xMax)) { - gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx, -positions - * charWidth, heightToCopy, widthToCopy, + 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 @@ -1983,7 +2142,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ protected boolean drawMappedPositionsWrapped(SearchResultsI results) { - if (results == null) + if ((results == null) || (img == null)) // JAL-2784 check gg is not null { return false; } @@ -1991,7 +2150,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI boolean matchFound = false; - calculateWrappedGeometry(getWidth(), getHeight()); + calculateWrappedGeometry(); int wrappedWidth = av.getWrappedWidth(); int wrappedHeight = wrappedRepeatHeightPx; @@ -2004,20 +2163,22 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } int firstVisibleColumn = ranges.getStartRes(); - int lastVisibleColumn = ranges.getStartRes() + repeats - * ranges.getViewportWidth() - 1; + int lastVisibleColumn = ranges.getStartRes() + + repeats * ranges.getViewportWidth() - 1; AlignmentI alignment = av.getAlignment(); if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(firstVisibleColumn); + .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(lastVisibleColumn); + .visibleToAbsoluteColumn(lastVisibleColumn); } int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); + Graphics gg = img.getGraphics(); + for (int seqNo = ranges.getStartSeq(); seqNo <= ranges .getEndSeq(); seqNo++) { @@ -2052,15 +2213,15 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { displayColumn = alignment.getHiddenColumns() - .findColumnPosition(displayColumn); + .absoluteToVisibleColumn(displayColumn); } /* * transX: offset from left edge of canvas to residue position */ int transX = labelWidthWest - + ((displayColumn - ranges.getStartRes()) % wrappedWidth) - * av.getCharWidth(); + + ((displayColumn - ranges.getStartRes()) + % wrappedWidth) * av.getCharWidth(); /* * transY: offset from top edge of canvas to residue position @@ -2087,7 +2248,29 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } } - + + gg.dispose(); + return matchFound; } + + /** + * Answers the width in pixels of the left scale labels (0 if not shown) + * + * @return + */ + int getLabelWidthWest() + { + return labelWidthWest; + } + + /** + * Clears the flag that allows a 'fast paint' on the next repaint, so + * requiring a full repaint + */ + public void setNoFastPaint() + { + allowFastPaint = false; + } + }