X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=d15cdcf376b50ba2fe0d3c08738935304c85d260;hb=efba321f20b819819c0b1cd9c9133d9d1a2ab314;hp=cdf84b7d0f233ef4e96ec4511e3db884565ef787;hpb=15662a256b76221299688fff94288d9bd37f8453;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index cdf84b7..d15cdcf 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -20,33 +20,32 @@ */ 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.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; 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; /** * The Swing component on which the alignment sequences, and annotations (if @@ -54,8 +53,15 @@ import javax.swing.JComponent; * Wrapped mode, but not the scale above in Unwrapped mode. * */ -public class SeqCanvas extends JComponent implements ViewportListenerI +@SuppressWarnings("serial") +public class SeqCanvas extends JPanel implements ViewportListenerI { + /** + * vertical gap in pixels between sequences and annotations when in wrapped + * mode + */ + static final int SEQS_ANNOTATION_GAP = 3; + private static final String ZEROS = "0000000000"; final FeatureRenderer fr; @@ -70,7 +76,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI private final SequenceRenderer seqRdr; - private boolean fastPaint = false; + boolean fastPaint = false; private boolean fastpainting = false; @@ -83,13 +89,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI private int labelWidthWest; // label left width in pixels if shown - private int wrappedSpaceAboveAlignment; // gap between widths + 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 Graphics2D gg; + // Don't do this! Graphics handles are supposed to be transient + // private Graphics2D gg; /** * Creates a new SeqCanvas object. @@ -256,6 +263,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI g.drawString(valueAsString, xOffset, y); } } + } /** @@ -269,6 +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 @@ -278,18 +287,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ public void fastPaint(int horizontal, int vertical) { - if (fastpainting || gg == null || img == null) + + // 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(); @@ -298,10 +310,6 @@ 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; @@ -335,11 +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; @@ -349,48 +373,77 @@ public class SeqCanvas extends JComponent implements ViewportListenerI @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); - // selectImage is the selection group outline image - BufferedImage selectImage = drawSelectionGroup( - ranges.getStartRes(), ranges.getEndRes(), - ranges.getStartSeq(), ranges.getEndSeq()); + // BH 2019 can't possibly fastPaint if either width or height is 0 - if ((img != null) && (fastPaint - || (getVisibleRect().width != g.getClipBounds().width) - || (getVisibleRect().height != g.getClipBounds().height))) + if (width == 0 || height == 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 (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 + // img is a cached version of the last view we drew. + // If we have no img or the size has changed, make a new one. + // if (img == null || width != img.getWidth() || height != img.getHeight()) { - img = setupImage(); - if (img == null) - { - return; - } - gg = (Graphics2D) img.getGraphics(); - gg.setFont(av.getFont()); + img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); } + Graphics2D gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + if (av.antiAlias) { gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, @@ -406,23 +459,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } 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, ranges.getStartRes(), ranges.getEndRes(), - ranges.getStartSeq(), ranges.getEndSeq()); + drawCursor(g, startRes, endRes, startSeq, endSeq); } } - + /** * Draw an alignment panel for printing * @@ -442,14 +493,7 @@ 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); } /** @@ -467,101 +511,16 @@ 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(); - } + drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight, + startRes); } } - /* - * 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); - } - - 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) @@ -578,7 +537,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI FontMetrics fm = getFontMetrics(av.getFont()); int labelWidth = 0; - + if (av.getScaleRightWrapped() || av.getScaleLeftWrapped()) { labelWidth = getLabelWidth(fm); @@ -646,8 +605,13 @@ 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 ypos = wrappedSpaceAboveAlignment; @@ -657,8 +621,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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; @@ -694,14 +658,21 @@ 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 += av.getAlignment().getHeight() * charHeight; + + /* + * add annotations panel height if shown + * also gap between sequences and annotations + */ + if (av.isShowAnnotation()) + { + wrappedRepeatHeightPx += getAnnotationHeight(); + wrappedRepeatHeightPx += SEQS_ANNOTATION_GAP; // 3px + } /* * number of visible widths (the last one may be part height), @@ -719,7 +690,7 @@ 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 */ @@ -745,8 +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(); @@ -761,29 +733,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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, @@ -793,7 +752,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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); @@ -801,9 +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); } @@ -819,6 +778,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int charWidth = av.getCharWidth(); g.setFont(av.getFont()); + g.setColor(Color.black); int ypos = wrappedSpaceAboveAlignment; @@ -840,6 +800,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.getScaleRightWrapped()) { int x = labelWidthWest + viewportWidth * charWidth; + g.translate(x, 0); drawVerticalScale(g, startCol, endColumn, ypos, false); g.translate(-x, 0); @@ -851,8 +812,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ 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); @@ -923,40 +885,26 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * 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(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 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() - .absoluteToVisibleColumn(maxwidth); - } + int maxwidth = av.getAlignment().getVisibleWidth(); + 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) { @@ -964,21 +912,23 @@ 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 += wrappedRepeatHeightPx; - // update horizontal offset 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()) @@ -1120,16 +1070,16 @@ 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)); } } } @@ -1143,14 +1093,21 @@ 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; @@ -1163,58 +1120,44 @@ 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, @@ -1225,9 +1168,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawWrappedSelection(g, group, getWidth(), getHeight(), av.getRanges().getStartRes()); } - - g.dispose(); - return selectionImage; + g.setStroke(new BasicStroke()); } /** @@ -1245,8 +1186,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * the cursor drawn on it, if any */ private void drawCursor(Graphics g, int startRes, int endRes, - int startSeq, - int endSeq) + int startSeq, int endSeq) { // convert the cursorY into a position on the visible alignment int cursor_ypos = cursorY; @@ -1317,40 +1257,29 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } - - /* - * Set up graphics for selection group - */ - private void setupSelectionGroup(Graphics2D g, - BufferedImage selectionImage) - { - // set background to transparent - g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); - g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight()); - - // 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); - } - - /* + /** * 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(); - + if (!av.hasHiddenColumns()) { drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, @@ -1373,8 +1302,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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; @@ -1382,16 +1311,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } - /* - * 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; @@ -1399,161 +1335,184 @@ 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) - { - g.drawLine(sx + xwidth, oldY, sx + xwidth, sy); - } - - if (sx < 0) + if ((bottom == -1) + && !seqs.contains(av.getAlignment().getSequenceAt(i + 1))) { - xwidth += sx; - sx = 0; + bottom = sy + charHeight; } - // don't let width extend beyond current block, or group extent - // fixes JAL-2672 - if (sx + xwidth >= (endRes - startRes + 1) * charWidth) + if (!inGroup) { - 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) { @@ -1562,7 +1521,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI boolean wrapped = av.getWrapAlignment(); try { - fastPaint = !noFastPaint; + fastPaint = doFastPaint; fastpainting = fastPaint; /* @@ -1619,7 +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; } @@ -1687,13 +1646,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { firstCol = alignment.getHiddenColumns() .absoluteToVisibleColumn(firstCol); - lastCol = alignment.getHiddenColumns().absoluteToVisibleColumn(lastCol); + 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; @@ -1703,7 +1665,7 @@ 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; @@ -1713,6 +1675,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT)) { fastPaint = false; + // System.err.println("!!!! fastPaint false from MOVE_VIEWPORT"); repaint(); return; } @@ -1734,7 +1697,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } ViewportRanges vpRanges = av.getRanges(); - int range = vpRanges.getEndRes() - vpRanges.getStartRes(); + int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1; if (scrollX > range) { scrollX = range; @@ -1744,43 +1707,50 @@ 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 - // paint, so scroll events are identified as changes to the horizontal or - // vertical start value. - if (eventName.equals(ViewportRanges.STARTRES)) + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + if (eventName.equals(ViewportRanges.STARTRES)) + { + if (av.getWrapAlignment()) { - if (av.getWrapAlignment()) - { - fastPaintWrapped(scrollX); - } - else - { - fastPaint(scrollX, 0); - } + fastPaintWrapped(scrollX); } - else if (eventName.equals(ViewportRanges.STARTSEQ)) + 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()) { - // scroll - fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + fastPaintWrapped(scrollX); } - else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) + else { - if (av.getWrapAlignment()) - { - fastPaintWrapped(scrollX); - } - else - { - fastPaint(scrollX, 0); - } - // bizarrely, we only need to scroll on the x value here as fastpaint - // copies the full height of the image anyway. Passing in the y value - // causes nasty repaint artefacts, which only disappear on a full - // repaint. + 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); + } + } } /** @@ -1796,12 +1766,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { ViewportRanges ranges = av.getRanges(); - // if (Math.abs(scrollX) > ranges.getViewportWidth()) - // JAL-2836, 2836 temporarily removed wrapped fastpaint for release 2.10.3 - if (true) + 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; @@ -1809,7 +1777,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return; } - if (fastpainting || gg == null) + if (fastpainting || img == null) { return; } @@ -1819,6 +1787,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI try { + + Graphics gg = img.getGraphics(); + calculateWrappedGeometry(getWidth(), getHeight()); /* @@ -1834,8 +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 { @@ -1847,6 +1818,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ drawWrappedDecorators(gg, ranges.getStartRes()); + gg.dispose(); + repaint(); } finally { @@ -1870,6 +1843,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return; } + Graphics gg = img.getGraphics(); + ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); int charWidth = av.getCharWidth(); @@ -1880,7 +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) { @@ -1896,13 +1872,15 @@ 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); + } /* @@ -1946,6 +1924,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI gg.setColor(Color.white); gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow); } + gg.dispose(); } /** @@ -1962,6 +1941,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { return; } + + Graphics gg = img.getGraphics(); + int charWidth = av.getCharWidth(); int canvasHeight = getHeight(); @@ -1992,10 +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); @@ -2024,18 +2013,17 @@ 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 @@ -2048,7 +2036,7 @@ 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; } @@ -2069,8 +2057,8 @@ 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()) @@ -2083,6 +2071,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); + Graphics gg = img.getGraphics(); + for (int seqNo = ranges.getStartSeq(); seqNo <= ranges .getEndSeq(); seqNo++) { @@ -2124,8 +2114,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * 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 @@ -2152,7 +2142,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } } - + + gg.dispose(); + return matchFound; } @@ -2165,4 +2157,5 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { return labelWidthWest; } + }