X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=b7d74de8f033508fd72ef3a948865777d03533c1;hb=99bfb1a08e5ceb3a3c990bb49dcd7433a0880558;hp=46f2d84517f35412eb3ffbea302b1f875147a3ba;hpb=919cef3e2b8c066ab9fe5cbfe7f76fa54601b788;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 46f2d84..d15cdcf 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -20,94 +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.util.Comparison; -import jalview.viewmodel.ViewportListenerI; -import jalview.viewmodel.ViewportRanges; - 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 { - 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 sr; + 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; - int charHeight = 0; + private final SequenceRenderer seqRdr; + + boolean fastPaint = false; - int charWidth = 0; + 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 - private int wrappedRepeatHeightPx; // height in pixels of wrapped width + 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); @@ -117,7 +117,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public SequenceRenderer getSequenceRenderer() { - return sr; + return seqRdr; } public FeatureRenderer getFeatureRenderer() @@ -125,12 +125,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return fr; } - private void updateViewport() - { - charHeight = av.getCharHeight(); - charWidth = av.getCharWidth(); - } - /** * Draws the scale above a region of a wrapped alignment, consisting of a * column number every major interval (10 columns). @@ -147,7 +141,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ private void drawNorthScale(Graphics g, int startx, int endx, int ypos) { - updateViewport(); + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); /* * white fill the scale space (for the fastPaint case) @@ -189,6 +184,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * Draw the scale to the left or right of a wrapped alignment * * @param g + * graphics context, positioned at the start of the scale to be drawn * @param startx * first column of wrapped width (0.. excluding any hidden columns) * @param endx @@ -198,16 +194,21 @@ 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) { - ypos += charHeight; + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + + int yPos = ypos + charHeight; + int startX = startx; + int endX = endx; if (av.hasHiddenColumns()) { HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); - startx = hiddenColumns.adjustForHiddenColumns(startx); - endx = hiddenColumns.adjustForHiddenColumns(endx); + startX = hiddenColumns.visibleToAbsoluteColumn(startx); + endX = hiddenColumns.visibleToAbsoluteColumn(endx); } FontMetrics fm = getFontMetrics(av.getFont()); @@ -219,9 +220,9 @@ 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))) { @@ -242,30 +243,27 @@ 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); - y -= charHeight; // fillRect: origin is top left of rectangle - int xpos = left ? 0 : labelWidthWest + charWidth - * av.getRanges().getViewportWidth(); - g.fillRect(xpos, y, left ? labelWidthWest : labelWidthEast, + int y = (yPos + (i * charHeight)) - (charHeight / 5); + // fillRect origin is top left of rectangle + g.fillRect(0, y - charHeight, left ? labelWidthWest : labelWidthEast, charHeight + 1); - y += charHeight; // drawString: origin is bottom left of text 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; - xpos = left ? labelWidthWest - justify + charWidth / 2 - : getWidth() - 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); } } + } /** @@ -279,6 +277,7 @@ 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 @@ -288,16 +287,20 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ 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; - try { - updateViewport(); + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); ViewportRanges ranges = av.getRanges(); int startRes = ranges.getStartRes(); @@ -307,9 +310,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int transX = 0; int transY = 0; - gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth, - imgHeight, -horizontal * charWidth, -vertical * charHeight); - if (horizontal > 0) // scrollbar pulled right, image to the left { transX = (endRes - startRes - horizontal) * charWidth; @@ -319,7 +319,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { endRes = startRes - horizontal; } - else if (vertical > 0) // scroll down + + if (vertical > 0) // scroll down { startSeq = endSeq - vertical; @@ -329,7 +330,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } else { - transY = imgHeight - ((vertical + 1) * charHeight); + transY = img.getHeight() - ((vertical + 1) * charHeight); } } else if (vertical < 0) @@ -342,11 +343,27 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } + // 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); + + /** @j2sNative xxi = this.img */ + gg.translate(transX, transY); drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); gg.translate(-transX, -transY); + gg.dispose(); - repaint(); + // 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 { fastpainting = false; @@ -356,73 +373,152 @@ public class SeqCanvas extends JComponent implements ViewportListenerI @Override public void paintComponent(Graphics g) { - updateViewport(); - BufferedImage lcimg = img; // take reference since other threads may null - // img and call later. - super.paintComponent(g); - if (lcimg != null && (fastPaint - || (getVisibleRect().width != g.getClipBounds().width) - || (getVisibleRect().height != g.getClipBounds().height))) - { - g.drawImage(lcimg, 0, 0, this); - fastPaint = false; - return; - } + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + + int width = getWidth(); + int height = getHeight(); - // this draws the whole of the alignment - imgWidth = getWidth(); - imgHeight = getHeight(); + width -= (width % charWidth); + height -= (height % charHeight); - imgWidth -= (imgWidth % charWidth); - imgHeight -= (imgHeight % charHeight); + // BH 2019 can't possibly fastPaint if either width or height is 0 - if ((imgWidth < 1) || (imgHeight < 1)) + if (width == 0 || height == 0) { return; } - if (lcimg == null || imgWidth != lcimg.getWidth() - || imgHeight != lcimg.getHeight()) + ViewportRanges ranges = av.getRanges(); + int startRes = ranges.getStartRes(); + int startSeq = ranges.getStartSeq(); + int endRes = ranges.getEndRes(); + int endSeq = ranges.getEndSeq(); + + // [JAL-3226] problem that JavaScript (or Java) may consolidate multiple + // repaint() requests in unpredictable ways. In this case, the issue was + // that in response to a CTRL-C/CTRL-V paste request, in Java a fast + // repaint request preceded two full requests, thus resulting + // in a full request for paint. In constrast, in JavaScript, the three + // requests were bundled together into one, so the fastPaint flag was + // still present for the second and third request. + // + // This resulted in incomplete painting. + // + // The solution was to set seqCanvas.fastPaint and idCanvas.fastPaint false + // in PaintRefresher when the target to be painted is one of those two + // components. + // + // BH 2019.04.22 + // + // An initial idea; can be removed once we determine this issue is closed: + // if (av.isFastPaintDisabled()) + // { + // fastPaint = false; + // } + + Rectangle vis, clip; + if (img != null + && (fastPaint + || (vis = getVisibleRect()).width != (clip = g + .getClipBounds()).width + || vis.height != clip.height)) { - try + g.drawImage(img, 0, 0, this); + drawSelectionGroup((Graphics2D) g, startRes, endRes, startSeq, + endSeq); + fastPaint = false; + } + else + { + // img is a cached version of the last view we drew. + // If we have no img or the size has changed, make a new one. + // + if (img == null || width != img.getWidth() + || height != img.getHeight()) { - lcimg = img = new BufferedImage(imgWidth, imgHeight, - BufferedImage.TYPE_INT_RGB); - gg = (Graphics2D) img.getGraphics(); - gg.setFont(av.getFont()); - } catch (OutOfMemoryError er) + img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); + } + + Graphics2D gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + + if (av.antiAlias) { - System.gc(); - System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er); - new OOMWarning("Creating alignment image for display", er); + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } + + gg.setColor(Color.white); + gg.fillRect(0, 0, img.getWidth(), img.getHeight()); - return; + if (av.getWrapAlignment()) + { + drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); } + else + { + drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); + } + + drawSelectionGroup(gg, startRes, endRes, startSeq, endSeq); + + g.drawImage(img, 0, 0, this); + gg.dispose(); } - if (av.antiAlias) + if (av.cursorMode) { - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + drawCursor(g, startRes, endRes, startSeq, endSeq); } + } - gg.setColor(Color.white); - gg.fillRect(0, 0, imgWidth, imgHeight); + /** + * 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); - ViewportRanges ranges = av.getRanges(); - if (av.getWrapAlignment()) - { - drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); - } - else - { - drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), - ranges.getStartSeq(), ranges.getEndSeq(), 0); - } + drawSelectionGroup((Graphics2D) g1, startRes, endRes, startSeq, endSeq); + } - g.drawImage(lcimg, 0, 0, this); + /** + * Draw a wrapped alignment panel for printing + * + * @param g + * Graphics object to draw with + * @param canvasWidth + * width of drawing area + * @param canvasHeight + * height of drawing area + * @param startRes + * start residue of print area + */ + public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth, + int canvasHeight, int startRes) + { + drawWrappedPanel(g, canvasWidth, canvasHeight, startRes); + SequenceGroup group = av.getSelectionGroup(); + if (group != null) + { + drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight, + startRes); + } } /** @@ -436,29 +532,30 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ public int getWrappedCanvasWidth(int canvasWidth) { + int charWidth = av.getCharWidth(); + FontMetrics fm = getFontMetrics(av.getFont()); - labelWidthEast = 0; - labelWidthWest = 0; + int labelWidth = 0; - if (av.getScaleRightWrapped()) + if (av.getScaleRightWrapped() || av.getScaleLeftWrapped()) { - labelWidthEast = getLabelWidth(fm); + labelWidth = getLabelWidth(fm); } - if (av.getScaleLeftWrapped()) - { - labelWidthWest = labelWidthEast > 0 ? labelWidthEast - : getLabelWidth(fm); - } + labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0; + + labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; return (canvasWidth - 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 @@ -476,13 +573,13 @@ public class SeqCanvas extends JComponent implements ViewportListenerI maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd()); } - int length = 2; + 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(); } /** @@ -500,8 +597,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, final int startColumn) { - updateViewport(); - int wrappedWidthInResidues = calculateWrappedGeometry(canvasWidth, canvasHeight); @@ -510,24 +605,28 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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 (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 yposMax = canvasHeight; - // ensure room for at least one sequence - yposMax -= wrappedSpaceAboveAlignment - charHeight; int ypos = wrappedSpaceAboveAlignment; int maxWidth = ranges.getVisibleAlignmentWidth(); int start = startColumn; - while ((ypos <= yposMax) && (start < maxWidth)) + int currentWidth = 0; + while ((currentWidth < wrappedVisibleWidths) && (start < maxWidth)) { - int endColumn = Math - .min(maxWidth, start + wrappedWidthInResidues - 1); + int endColumn = Math.min(maxWidth, + start + wrappedWidthInResidues - 1); drawWrappedWidth(g, ypos, start, endColumn, canvasHeight); ypos += wrappedRepeatHeightPx; start += wrappedWidthInResidues; + currentWidth++; } drawWrappedDecorators(g, startColumn); @@ -549,38 +648,37 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ protected int calculateWrappedGeometry(int canvasWidth, int canvasHeight) { - /* - * 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 + * - one character height, or two if scale above is drawn */ wrappedSpaceAboveAlignment = charHeight * (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 += av.getAlignment().getHeight() * charHeight; /* - * number of visible widths (the last one may be part height) + * add annotations panel height if shown + * also gap between sequences and annotations + */ + if (av.isShowAnnotation()) + { + wrappedRepeatHeightPx += getAnnotationHeight(); + wrappedRepeatHeightPx += SEQS_ANNOTATION_GAP; // 3px + } + + /* + * number of visible widths (the last one may be part height), + * ensuring a part height includes at least one sequence */ ViewportRanges ranges = av.getRanges(); - int xMax = ranges.getVisibleAlignmentWidth(); wrappedVisibleWidths = canvasHeight / wrappedRepeatHeightPx; int remainder = canvasHeight % wrappedRepeatHeightPx; if (remainder >= (wrappedSpaceAboveAlignment + charHeight)) @@ -589,21 +687,22 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } /* + * 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 viewportWidth = ranges.getViewportWidth(); - int maxWidths = (xMax - ranges.getStartRes()) / viewportWidth; - if (xMax % viewportWidth > 0) + int xMax = ranges.getVisibleAlignmentWidth(); + int startToEnd = xMax - ranges.getStartRes(); + int maxWidths = startToEnd / wrappedWidthInResidues; + if (startToEnd % wrappedWidthInResidues > 0) { maxWidths++; } wrappedVisibleWidths = Math.min(wrappedVisibleWidths, maxWidths); - /* - * number of whole width residue columns we can show in each row - */ - int wrappedWidthInResidues = (canvasWidth - labelWidthEast - labelWidthWest) - / charWidth; return wrappedWidthInResidues; } @@ -617,8 +716,9 @@ 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) { ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); @@ -630,41 +730,30 @@ 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); + * charWidth; - // When printing we have an extra clipped region, - // the Printable page which we need to account for here - Shape clip = g.getClip(); - - if (clip == null) - { - g.setClip(0, 0, 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); @@ -672,9 +761,8 @@ 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); } @@ -685,9 +773,12 @@ 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; @@ -695,50 +786,62 @@ 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()) { - drawVerticalScale(g, startColumn, endColumn, ypos, false); + int x = labelWidthWest + viewportWidth * charWidth; + + g.translate(x, 0); + drawVerticalScale(g, startCol, endColumn, ypos, false); + g.translate(-x, 0); } /* * white fill region of scale above and hidden column markers * (to support incremental fast paint of image) */ + g.translate(labelWidthWest, 0); g.setColor(Color.white); - g.fillRect(0, ypos - wrappedSpaceAboveAlignment, viewportWidth - * charWidth + labelWidthWest, wrappedSpaceAboveAlignment); + g.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 @@ -747,14 +850,20 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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(); - 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; } @@ -768,10 +877,58 @@ public class SeqCanvas extends JComponent implements ViewportListenerI xMiddle + charHeight / 4, xMiddle }; int yTop = ypos - (charHeight / 2); int[] yPoints = new int[] { yTop, yTop, yTop + 8 }; - gg.fillPolygon(xPoints, yPoints, 3); + g.fillPolygon(xPoints, yPoints, 3); } } + /* + * Draw a selection group over a wrapped alignment + */ + private void drawWrappedSelection(Graphics2D g, SequenceGroup group, + int canvasWidth, int canvasHeight, int startRes) + { + // chop the wrapped alignment extent up into panel-sized blocks and treat + // each block as if it were a block from an unwrapped alignment + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f)); + g.setColor(Color.RED); + + int charWidth = av.getCharWidth(); + int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) + / charWidth; + int startx = startRes; + int maxwidth = av.getAlignment().getVisibleWidth(); + int ypos = wrappedSpaceAboveAlignment; + + while ((ypos <= canvasHeight) && (startx < maxwidth)) + { + // set end value to be start + width, or maxwidth, whichever is smaller + int endx = startx + cWidth - 1; + + if (endx > maxwidth) + { + endx = maxwidth; + } + + g.translate(labelWidthWest, 0); + drawUnwrappedSelection(g, group, startx, endx, 0, + av.getAlignment().getHeight() - 1, ypos); + g.translate(-labelWidthWest, 0); + + ypos += wrappedRepeatHeightPx; + + startx += cWidth; + } + g.setStroke(new BasicStroke()); + } + + /** + * Answers zero if annotations are not shown, otherwise recalculates and + * answers the total height of all annotation rows in pixels + * + * @return + */ int getAnnotationHeight() { if (!av.isShowAnnotation()) @@ -809,7 +966,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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, yOffset); @@ -817,29 +976,23 @@ 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); @@ -848,7 +1001,8 @@ 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); @@ -859,23 +1013,6 @@ 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); } } @@ -899,8 +1036,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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; @@ -915,7 +1055,7 @@ 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()) @@ -930,26 +1070,19 @@ 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) { - sr.drawHighlightedText(nextSeq, visibleResults[r], + 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 @@ -960,23 +1093,26 @@ 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 = av.getSelectionGroup(); - int sx = -1; - int sy = -1; - int ex = -1; + SequenceGroup group = null; int groupIndex = -1; - int visWidth = (endRes - startRes + 1) * charWidth; - if ((group == null) && (av.getAlignment().getGroups().size() > 0)) + if (av.getAlignment().getGroups().size() > 0) { group = av.getAlignment().getGroups().get(0); groupIndex = 0; @@ -986,163 +1122,370 @@ 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()) { - sx = (group.getStartRes() - startRes) * charWidth; - sy = offset + ((i - startSeq) * charHeight); - ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - - 1; + break; + } + group = av.getAlignment().getGroups().get(groupIndex); + } while (groupIndex < av.getAlignment().getGroups().size()); + } + } - if (sx + ex < 0 || sx > visWidth) + /** + * Draws the outline of the current selection group (if any) + * + * @param g + * @param startRes + * @param endRes + * @param startSeq + * @param endSeq + */ + private void drawSelectionGroup(Graphics2D g, int startRes, int endRes, + int startSeq, int endSeq) + { + SequenceGroup group = av.getSelectionGroup(); + if (group == null) + { + return; + } + + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f)); + g.setColor(Color.RED); + if (!av.getWrapAlignment()) + { + drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq, + 0); + } + else + { + drawWrappedSelection(g, group, getWidth(), getHeight(), + av.getRanges().getStartRes()); + } + g.setStroke(new BasicStroke()); + } + + /** + * Draw the cursor as a separate image and overlay + * + * @param startRes + * start residue of area to draw cursor in + * @param endRes + * end residue of area to draw cursor in + * @param startSeq + * start sequence of area to draw cursor in + * @param endSeq + * end sequence of are to draw cursor in + * @return a transparent image of the same size as the sequence canvas, with + * the cursor drawn on it, if any + */ + private void drawCursor(Graphics g, int startRes, int endRes, + int startSeq, int endSeq) + { + // convert the cursorY into a position on the visible alignment + int cursor_ypos = cursorY; + + // don't do work unless we have to + if (cursor_ypos >= startSeq && cursor_ypos <= endSeq) + { + int yoffset = 0; + int xoffset = 0; + int startx = startRes; + int endx = endRes; + + // convert the cursorX into a position on the visible alignment + int cursor_xpos = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(cursorX); + + if (av.getAlignment().getHiddenColumns().isVisible(cursorX)) + { + + if (av.getWrapAlignment()) + { + // work out the correct offsets for the cursor + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + int canvasWidth = getWidth(); + int canvasHeight = getHeight(); + + // height gap above each panel + int hgap = charHeight; + if (av.getScaleAboveWrapped()) { - continue; + hgap += charHeight; } - 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; - } + int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) + / charWidth; + int cHeight = av.getAlignment().getHeight() * charHeight; - if (!inGroup) - { - if (((top == -1) && (i == 0)) || !group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i - 1))) - { - top = sy; - } + endx = startx + cWidth - 1; + int ypos = hgap; // vertical offset - oldY = sy; - inGroup = true; + // iterate down the wrapped panels + while ((ypos <= canvasHeight) && (endx < cursor_xpos)) + { + // update vertical offset + ypos += cHeight + getAnnotationHeight() + hgap; - if (group == av.getSelectionGroup()) - { - g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, - BasicStroke.JOIN_ROUND, 3f, new float[] - { 5f, 3f }, 0f)); - g.setColor(Color.RED); - } - else - { - g.setStroke(new BasicStroke()); - g.setColor(group.getOutlineColour()); - } - } + // update horizontal offset + startx += cWidth; + endx = startx + cWidth - 1; } - else - { - if (inGroup) - { - if (sx >= 0 && sx < visWidth) - { - g.drawLine(sx, oldY, sx, sy); - } + yoffset = ypos; + xoffset = labelWidthWest; + } - if (sx + ex < visWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } + // 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); - if (sx < 0) - { - ex += sx; - sx = 0; - } + seqRdr.drawCursor(g, s, + xoffset + (cursor_xpos - startx) * av.getCharWidth(), + yoffset + (cursor_ypos - startSeq) * av.getCharHeight()); + } + } + } + } - if (sx + ex > visWidth) - { - ex = visWidth; - } + /** + * Draw a selection group over an unwrapped alignment + * + * @param g + * graphics object to draw with + * @param group + * selection group + * @param startRes + * start residue of area to draw + * @param endRes + * end residue of area to draw + * @param startSeq + * start sequence of area to draw + * @param endSeq + * end sequence of area to draw + * @param offset + * vertical offset (used when called from wrapped alignment code) + */ + private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group, + int startRes, int endRes, int startSeq, int endSeq, int offset) + { + int charWidth = av.getCharWidth(); - else if (sx + ex >= (endRes - startRes + 1) * charWidth) - { - ex = (endRes - startRes + 1) * charWidth; - } + if (!av.hasHiddenColumns()) + { + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, + offset); + } + else + { + // package into blocks of visible columns + int screenY = 0; + int blockStart; + int blockEnd; - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -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]; - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } + g.translate(screenY * charWidth, 0); + drawPartialGroupOutline(g, group, blockStart, blockEnd, startSeq, + endSeq, offset); - inGroup = false; - } - } - } + g.translate(-screenY * charWidth, 0); + screenY += blockEnd - blockStart + 1; + } + } + } - if (inGroup) - { - sy = offset + ((i - startSeq) * charHeight); - if (sx >= 0 && sx < visWidth) - { - g.drawLine(sx, oldY, sx, sy); - } + /** + * 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; - if (sx + ex < visWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } + int oldY = -1; + int i = 0; + boolean inGroup = false; + int top = -1; + int bottom = -1; + int sy = -1; - if (sx < 0) - { - ex += sx; - sx = 0; - } + List seqs = group.getSequences(null); - if (sx + ex > visWidth) - { - ex = visWidth; - } - else if (sx + ex >= (endRes - startRes + 1) * charWidth) - { - ex = (endRes - startRes + 1) * charWidth; - } + // position of start residue of group relative to startRes, in pixels + int sx = (group.getStartRes() - startRes) * charWidth; - if (top != -1) + // width of group in pixels + int xwidth = (((group.getEndRes() + 1) - group.getStartRes()) + * charWidth) - 1; + + if (!(sx + xwidth < 0 || sx > visWidth)) + { + for (i = startSeq; i <= endSeq; i++) + { + sy = verticalOffset + (i - startSeq) * charHeight; + + if ((sx <= (endRes - startRes) * charWidth) + && seqs.contains(av.getAlignment().getSequenceAt(i))) + { + if ((bottom == -1) + && !seqs.contains(av.getAlignment().getSequenceAt(i + 1))) { - g.drawLine(sx, top, sx + ex, top); - top = -1; + bottom = sy + charHeight; } - if (bottom != -1) + if (!inGroup) { - g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); - bottom = -1; + if (((top == -1) && (i == 0)) || !seqs + .contains(av.getAlignment().getSequenceAt(i - 1))) + { + top = sy; + } + + oldY = sy; + inGroup = true; } + } + else if (inGroup) + { + drawVerticals(g, sx, xwidth, visWidth, oldY, 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); + drawVerticals(g, sx, xwidth, visWidth, oldY, sy); + drawHorizontals(g, sx, xwidth, visWidth, top, bottom); + } + } + } - groupIndex++; + /** + * 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; + } - g.setStroke(new BasicStroke()); + // don't let width extend beyond current block, or group extent + // fixes JAL-2672 + if (startx + width >= visWidth) + { + width = visWidth - startx; + } - if (groupIndex >= av.getAlignment().getGroups().size()) - { - break; - } + if (top != -1) + { + g.drawLine(startx, top, startx + width, top); + } - group = av.getAlignment().getGroups().get(groupIndex); + if (bottom != -1) + { + g.drawLine(startx, bottom - 1, startx + width, bottom - 1); + } + } - } while (groupIndex < av.getAlignment().getGroups().size()); + /** + * 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); } @@ -1152,32 +1495,35 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * 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) { return false; } boolean wrapped = av.getWrapAlignment(); - try { - fastPaint = !noFastPaint; + fastPaint = doFastPaint; fastpainting = fastPaint; - updateViewport(); - /* * to avoid redrawing the whole visible region, we instead * redraw just the minimal regions to remove previous highlights @@ -1232,7 +1578,7 @@ 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; } @@ -1254,9 +1600,9 @@ 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 @@ -1299,14 +1645,17 @@ 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; @@ -1316,15 +1665,39 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public void propertyChange(PropertyChangeEvent evt) { String eventName = evt.getPropertyName(); + // System.err.println(">>SeqCanvas propertyChange " + eventName); + 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; + } int scrollX = 0; - if (eventName.equals(ViewportRanges.STARTRES)) + 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(); - scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); - int range = vpRanges.getEndRes() - vpRanges.getStartRes(); + + int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1; if (scrollX > range) { scrollX = range; @@ -1334,7 +1707,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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 @@ -1342,7 +1714,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // vertical start value. if (eventName.equals(ViewportRanges.STARTRES)) { - // scroll - startres and endres both change if (av.getWrapAlignment()) { fastPaintWrapped(scrollX); @@ -1354,8 +1725,32 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } 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); + } + } } /** @@ -1371,10 +1766,10 @@ 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; @@ -1382,7 +1777,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return; } - if (fastpainting || gg == null) + if (fastpainting || img == null) { return; } @@ -1392,6 +1787,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI try { + + Graphics gg = img.getGraphics(); + calculateWrappedGeometry(getWidth(), getHeight()); /* @@ -1407,8 +1805,8 @@ 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 { @@ -1420,6 +1818,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ drawWrappedDecorators(gg, ranges.getStartRes()); + gg.dispose(); + repaint(); } finally { @@ -1443,8 +1843,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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 @@ -1452,7 +1855,8 @@ 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) { @@ -1468,16 +1872,20 @@ 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); + } /* + * 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 */ @@ -1486,7 +1894,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI + wrappedSpaceAboveAlignment; int endRes = ranges.getEndRes(); endRes += widthsAbove * viewportWidth; - endRes = Math.min(endRes, ranges.getVisibleAlignmentWidth()); int startRes = endRes - columns + 1; /* @@ -1503,7 +1910,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI gg.setFont(av.getFont()); gg.setColor(Color.black); - drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight); + if (startRes < ranges.getVisibleAlignmentWidth()) + { + drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight); + } /* * and finally, white fill any space below the visible alignment @@ -1514,6 +1924,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI gg.setColor(Color.white); gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow); } + gg.dispose(); } /** @@ -1531,6 +1942,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return; } + Graphics gg = img.getGraphics(); + + int charWidth = av.getCharWidth(); + int canvasHeight = getHeight(); ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); @@ -1559,10 +1974,17 @@ 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); @@ -1591,15 +2013,15 @@ 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(); } /** @@ -1614,15 +2036,17 @@ 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; } - + int charHeight = av.getCharHeight(); + boolean matchFound = false; + calculateWrappedGeometry(getWidth(), getHeight()); int wrappedWidth = av.getWrappedWidth(); - int wrappedHeight = getRepeatHeightWrapped(); + int wrappedHeight = wrappedRepeatHeightPx; ViewportRanges ranges = av.getRanges(); int canvasHeight = getHeight(); @@ -1633,20 +2057,22 @@ 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++) { @@ -1681,15 +2107,15 @@ 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 @@ -1716,28 +2142,20 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } } - + + gg.dispose(); + return matchFound; } /** - * Answers the height in pixels of a repeating section of the wrapped - * alignment, including space above, scale above if shown, sequences, and - * annotation panel if shown + * Answers the width in pixels of the left scale labels (0 if not shown) * * @return */ - protected int getRepeatHeightWrapped() + int getLabelWidthWest() { - // gap (and maybe scale) above - int repeatHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); - - // add sequences - repeatHeight += av.getRanges().getViewportHeight() * charHeight; - - // add annotations panel height if shown - repeatHeight += getAnnotationHeight(); - - return repeatHeight; + return labelWidthWest; } + }