X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=795faffd3f0705eec5c09b2395c4bf2bf31e2804;hb=3cdfc5e46776dbb8127f0a5b64df3545b988e3d9;hp=1e1105f86d1a8413d931835502e8cd1a7e19ebb0;hpb=f5cadfa2a55d78a08268a0df9a7c3f64d1c43e8a;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 1e1105f..795faff 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -25,13 +25,13 @@ 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; @@ -42,6 +42,7 @@ 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; @@ -54,6 +55,11 @@ import javax.swing.JComponent; */ public class SeqCanvas extends JComponent implements ViewportListenerI { + /* + * pixels gap between sequences and annotations when in wrapped mode + */ + static final int SEQS_ANNOTATION_GAP = 3; + private static final String ZEROS = "0000000000"; final FeatureRenderer fr; @@ -81,9 +87,9 @@ 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 @@ -198,8 +204,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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()); @@ -295,7 +301,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int endSeq = ranges.getEndSeq(); int transX = 0; int transY = 0; - + gg.copyArea(horizontal * charWidth, vertical * charHeight, img.getWidth(), img.getHeight(), -horizontal * charWidth, -vertical * charHeight); @@ -337,7 +343,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); gg.translate(-transX, -transY); - 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. + av.getAlignPanel().repaint(); } finally { fastpainting = false; @@ -351,53 +360,49 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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()); - + if ((img != null) && (fastPaint || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g.getClipBounds().height))) { - BufferedImage lcimg = buildLocalImage(selectImage); - g.drawImage(lcimg, 0, 0, this); + g.drawImage(img, 0, 0, this); + + drawSelectionGroup((Graphics2D) g, ranges.getStartRes(), + ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq()); + fastPaint = false; } - else if ((width > 0) && (height > 0)) + else if (width > 0 && height > 0) { - // 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 any + * 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; - } + img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); gg = (Graphics2D) img.getGraphics(); gg.setFont(av.getFont()); } - + if (av.antiAlias) { gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); } - + gg.setColor(Color.white); gg.fillRect(0, 0, img.getWidth(), img.getHeight()); - + if (av.getWrapAlignment()) { drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); @@ -408,10 +413,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI ranges.getStartSeq(), ranges.getEndSeq(), 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, ranges.getStartRes(), + ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq()); + g.drawImage(img, 0, 0, this); } if (av.cursorMode) @@ -440,14 +445,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { drawPanel(g1, startRes, endRes, startSeq, endSeq, 0); - BufferedImage selectImage = drawSelectionGroup(startRes, endRes, + drawSelectionGroup((Graphics2D) g1, startRes, endRes, startSeq, endSeq); - if (selectImage != null) - { - ((Graphics2D) g1).setComposite(AlphaComposite - .getInstance(AlphaComposite.SRC_OVER)); - g1.drawImage(selectImage, 0, 0, this); - } } /** @@ -465,99 +464,14 @@ 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, + drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight, startRes); - - g2.setComposite( - AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); - g.drawImage(selectImage, 0, 0, this); - g2.dispose(); - } - } - } - - /* - * Make a local image by combining the cached image img - * with any selection - */ - private BufferedImage buildLocalImage(BufferedImage selectImage) - { - // clone the cached image - BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), - img.getType()); - Graphics2D g2d = lcimg.createGraphics(); - g2d.drawImage(img, 0, 0, null); - - // overlay selection group on lcimg - if (selectImage != null) - { - g2d.setComposite( - AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); - g2d.drawImage(selectImage, 0, 0, this); - } - - 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; } /** @@ -586,6 +500,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; + System.out.println(Thread.currentThread().getName() + + " " + System.currentTimeMillis() + " labelWidthWest: " + + labelWidthWest); return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; } @@ -644,8 +561,13 @@ 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; @@ -692,14 +614,22 @@ 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() + wrappedRepeatHeightPx += av.getAlignment().getHeight() * charHeight; - // add annotations panel height if shown - wrappedRepeatHeightPx += getAnnotationHeight(); + + /* + * 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), @@ -743,8 +673,9 @@ 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(); @@ -791,7 +722,8 @@ 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); @@ -799,7 +731,7 @@ 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); @@ -890,11 +822,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int charWidth = av.getCharWidth(); g.setColor(Color.blue); + int res; HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - List positions = hidden.findHiddenRegionPositions(); - for (int pos : positions) + + Iterator it = hidden.getStartRegionIterator(startColumn, + endColumn); + while (it.hasNext()) { - int res = pos - startColumn; + res = it.next() - startColumn; if (res < 0 || res > endColumn - startColumn + 1) { @@ -938,16 +873,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int startx = startRes; int endx; int ypos = hgap; // vertical offset - int maxwidth = av.getAlignment().getWidth(); - - if (av.hasHiddenColumns()) - { - maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth); - } + int maxwidth = av.getAlignment().getVisibleWidth(); // 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); while ((ypos <= canvasHeight) && (startx < maxwidth)) { // set end value to be start + width, or maxwidth, whichever is smaller @@ -972,6 +905,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // update horizontal offset startx += cWidth; } + g.setStroke(new BasicStroke()); } int getAnnotationHeight() @@ -1021,29 +955,23 @@ 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); @@ -1052,7 +980,8 @@ 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); @@ -1063,23 +992,6 @@ 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); } } @@ -1137,16 +1049,16 @@ 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)); } } } @@ -1160,14 +1072,21 @@ 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; @@ -1180,18 +1099,15 @@ 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; @@ -1205,33 +1121,28 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } - - /* - * 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, @@ -1242,9 +1153,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawWrappedSelection(g, group, getWidth(), getHeight(), av.getRanges().getStartRes()); } - - g.dispose(); - return selectionImage; + g.setStroke(new BasicStroke()); } /** @@ -1278,7 +1187,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // convert the cursorX into a position on the visible alignment int cursor_xpos = av.getAlignment().getHiddenColumns() - .findColumnPosition(cursorX); + .absoluteToVisibleColumn(cursorX); if (av.getAlignment().getHiddenColumns().isVisible(cursorX)) { @@ -1335,33 +1244,23 @@ 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) @@ -1377,22 +1276,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { // package into blocks of visible columns int screenY = 0; - int blockStart = startRes; - int blockEnd = endRes; + int blockStart; + int blockEnd; - for (int[] region : av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy()) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + VisibleContigsIterator regions = hidden + .getVisContigsIterator(startRes, endRes + 1, true); + while (regions.hasNext()) { - int hideStart = region[0]; - int hideEnd = region[1]; - - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } - - blockEnd = hideStart - 1; + int[] region = regions.next(); + blockEnd = region[1]; + blockStart = region[0]; g.translate(screenY * charWidth, 0); drawPartialGroupOutline(g, group, @@ -1400,30 +1294,20 @@ public class SeqCanvas extends JComponent implements ViewportListenerI g.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - - if (screenY > (endRes - startRes)) - { - // already rendered last block - break; - } - } - - if (screenY <= (endRes - startRes)) - { - // remaining visible region to render - blockEnd = blockStart + (endRes - startRes) - screenY; - g.translate(screenY * charWidth, 0); - drawPartialGroupOutline(g, group, - blockStart, blockEnd, startSeq, endSeq, offset); - - g.translate(-screenY * charWidth, 0); } } } - /* - * Draw the selection group as a separate image and overlay + /** + * Draws part of a selection group outline + * + * @param g + * @param group + * @param startRes + * @param endRes + * @param startSeq + * @param endSeq + * @param verticalOffset */ private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group, int startRes, int endRes, int startSeq, int endSeq, @@ -1681,9 +1565,9 @@ 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 @@ -1726,8 +1610,8 @@ 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(); @@ -1774,7 +1658,7 @@ 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; @@ -1784,14 +1668,30 @@ 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)) - { - if (av.getWrapAlignment()) + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + if (eventName.equals(ViewportRanges.STARTRES)) + { + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); + } + else + { + fastPaint(scrollX, 0); + } + } + else if (eventName.equals(ViewportRanges.STARTSEQ)) + { + // scroll + fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + } + else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) + { + if (av.getWrapAlignment()) { fastPaintWrapped(scrollX); } @@ -1811,14 +1711,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { 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. } } @@ -1835,12 +1727,10 @@ 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; @@ -2031,10 +1921,17 @@ 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); @@ -2115,9 +2012,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(firstVisibleColumn); + .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(lastVisibleColumn); + .visibleToAbsoluteColumn(lastVisibleColumn); } int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); @@ -2156,7 +2053,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { displayColumn = alignment.getHiddenColumns() - .findColumnPosition(displayColumn); + .absoluteToVisibleColumn(displayColumn); } /*