From 2677eb3d3744f321876e25eeaa70dfa8fde70184 Mon Sep 17 00:00:00 2001 From: kiramt Date: Tue, 10 Oct 2017 11:59:51 +0100 Subject: [PATCH] JAL-2690attemptedmerge partial merge --- src/jalview/gui/SeqCanvas.java | 937 ++++++++++++++++++++++++++++------------ 1 file changed, 670 insertions(+), 267 deletions(-) diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 4e896a0..8ad094f 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -27,10 +27,11 @@ 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.AlphaComposite; +import java.awt.AlphaComposite; // ok import java.awt.BasicStroke; import java.awt.BorderLayout; import java.awt.Color; @@ -57,31 +58,40 @@ public class SeqCanvas extends JComponent implements ViewportListenerI final FeatureRenderer fr; - final SequenceRenderer seqRdr; + final SequenceRenderer seqRdr; //ok BufferedImage img; Graphics2D gg; + int imgWidth; + + int imgHeight; + AlignViewport av; boolean fastPaint = false; - int labelWidthWest; - - int labelWidthEast; + boolean fastpainting = false; int cursorX = 0; int cursorY = 0; - int charHeight = 0; + private AnnotationPanel annotations; - int charWidth = 0; + /* + * measurements for drawing a wrapped alignment + */ + int labelWidthWest; // label left width in pixels if shown - boolean fastpainting = false; + private int labelWidthEast; // label right width in pixels if shown - AnnotationPanel annotations; + private int wrappedSpaceAboveAlignment; // gap between widths + + private int wrappedRepeatHeightPx; // height in pixels of wrapped width + + private int wrappedVisibleWidths; // number of wrapped widths displayed /** * Creates a new SeqCanvas object. @@ -92,9 +102,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public SeqCanvas(AlignmentPanel ap) { this.av = ap.av; - updateViewport(); fr = new FeatureRenderer(ap); - seqRdr = new SequenceRenderer(av); + seqRdr = new SequenceRenderer(av); //ok setLayout(new BorderLayout()); PaintRefresher.Register(this, av.getSequenceSetId()); setBackground(Color.white); @@ -104,7 +113,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public SequenceRenderer getSequenceRenderer() { - return seqRdr; + return seqRdr; //ok } public FeatureRenderer getFeatureRenderer() @@ -112,29 +121,36 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return fr; } - private void updateViewport() - { - charHeight = av.getCharHeight(); - charWidth = av.getCharWidth(); - } - /** - * DOCUMENT ME! + * Draws the scale above a region of a wrapped alignment, consisting of a + * column number every major interval (10 columns). * * @param g - * DOCUMENT ME! + * the graphics context to draw on, positioned at the start (bottom + * left) of the line on which to draw any scale marks * @param startx - * DOCUMENT ME! + * start alignment column (0..) * @param endx - * DOCUMENT ME! + * end alignment column (0..) * @param ypos - * DOCUMENT ME! + * y offset to draw at */ private void drawNorthScale(Graphics g, int startx, int endx, int ypos) { - updateViewport(); - for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx, - endx)) + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + + /* + * white fill the scale space (for the fastPaint case) + */ + g.setColor(Color.white); + g.fillRect(0, ypos - charHeight - charHeight / 2, getWidth(), + charHeight * 3 / 2 + 2); + g.setColor(Color.black); + + List marks = new ScaleRenderer().calculateMarks(av, startx, + endx); + for (ScaleMark mark : marks) { int mpos = mark.column; // (i - startx - 1) if (mpos < 0) @@ -149,155 +165,140 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2)); } - g.drawLine((mpos * charWidth) + (charWidth / 2), - (ypos + 2) - (charHeight / 2), - (mpos * charWidth) + (charWidth / 2), ypos - 2); + + /* + * draw a tick mark below the column number, centred on the column; + * height of tick mark is 4 pixels less than half a character + */ + int xpos = (mpos * charWidth) + (charWidth / 2); + g.drawLine(xpos, (ypos + 2) - (charHeight / 2), xpos, ypos - 2); } } } /** - * DOCUMENT ME! + * Draw the scale to the left or right of a wrapped alignment * * @param g - * DOCUMENT ME! + * graphics context, positioned at the start of the scale to be drawn * @param startx - * DOCUMENT ME! + * first column of wrapped width (0.. excluding any hidden columns) * @param endx - * DOCUMENT ME! + * last column of wrapped width (0.. excluding any hidden columns) * @param ypos - * DOCUMENT ME! + * vertical offset at which to begin the scale + * @param left + * if true, scale is left of residues, if false, scale is right */ - void drawWestScale(Graphics g, int startx, int endx, int ypos) + void drawVerticalScale(Graphics g, int startx, int endx, int ypos, + boolean left) { - FontMetrics fm = getFontMetrics(av.getFont()); - ypos += charHeight; + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); - if (av.hasHiddenColumns()) - { - startx = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(startx); - endx = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(endx); - } + ypos += charHeight; - int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth) - 1; + HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); + startx = hiddenColumns.adjustForHiddenColumns(startx); + endx = hiddenColumns.adjustForHiddenColumns(endx); } + FontMetrics fm = getFontMetrics(av.getFont()); - // WEST SCALE for (int i = 0; i < av.getAlignment().getHeight(); i++) { SequenceI seq = av.getAlignment().getSequenceAt(i); - int index = startx; - int value = -1; - while (index < endx) + /* + * find sequence position of first non-gapped position - + * to the right if scale left, to the left if scale right + */ + int index = left ? startx : endx; + int value = -1; + while (index >= startx && index <= endx) { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + if (!Comparison.isGap(seq.getCharAt(index))) + { + value = seq.findPosition(index); + break; + } + if (left) { index++; - - continue; } - - value = av.getAlignment().getSequenceAt(i).findPosition(index); - - break; - } - - if (value != -1) - { - int x = labelWidthWest - fm.stringWidth(String.valueOf(value)) - - charWidth / 2; - g.drawString(value + "", x, - (ypos + (i * charHeight)) - (charHeight / 5)); - } - } - } - - /** - * DOCUMENT ME! - * - * @param g - * DOCUMENT ME! - * @param startx - * DOCUMENT ME! - * @param endx - * DOCUMENT ME! - * @param ypos - * DOCUMENT ME! - */ - void drawEastScale(Graphics g, int startx, int endx, int ypos) - { - ypos += charHeight; - - if (av.hasHiddenColumns()) - { - endx = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(endx); - } - - SequenceI seq; - // EAST SCALE - for (int i = 0; i < av.getAlignment().getHeight(); i++) - { - seq = av.getAlignment().getSequenceAt(i); - int index = endx; - int value = -1; - - while (index > startx) - { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + else { index--; - - continue; } - - value = seq.findPosition(index); - - break; } + /* + * white fill the space for the scale + */ + g.setColor(Color.white); + int y = (ypos + (i * charHeight)) - (charHeight / 5); + // fillRect origin is top left of rectangle + g.fillRect(0, y - charHeight, left ? labelWidthWest : labelWidthEast, + charHeight + 1); + if (value != -1) { - g.drawString(String.valueOf(value), 0, - (ypos + (i * charHeight)) - (charHeight / 5)); + + /* + * draw scale value, right justified, with half a character width + * separation from the sequence data + */ + String valueAsString = String.valueOf(value); + int justify = fm.stringWidth(valueAsString) + charWidth; + int xpos = left ? labelWidthWest - justify + charWidth / 2 + : labelWidthEast - justify + charWidth / 2; + g.setColor(Color.black); + g.drawString(valueAsString, xpos, y); } } } - + //ok /** - * need to make this thread safe move alignment rendering in response to - * slider adjustment + * Does a fast paint of an alignment in response to a scroll. Most of the + * visible region is simply copied and shifted, and then any newly visible + * columns or rows are drawn. The scroll may be horizontal or vertical, but + * not both at once. Scrolling may be the result of + * * * @param horizontal - * shift along + * columns to shift right (positive) or left (negative) * @param vertical - * shift up or down in repaint + * rows to shift down (positive) or up (negative) */ public void fastPaint(int horizontal, int vertical) { - if (fastpainting || gg == null || img == null) + if (fastpainting || gg == null || img == null) //ok { return; } fastpainting = true; fastPaint = true; - updateViewport(); - ViewportRanges ranges = av.getRanges(); - int startRes = ranges.getStartRes(); - int endRes = ranges.getEndRes(); - int startSeq = ranges.getStartSeq(); - int endSeq = ranges.getEndSeq(); - int transX = 0; - int transY = 0; + try + { + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + + ViewportRanges ranges = av.getRanges(); + int startRes = ranges.getStartRes(); + int endRes = ranges.getEndRes(); + int startSeq = ranges.getStartSeq(); + int endSeq = ranges.getEndSeq(); + int transX = 0; + int transY = 0; gg.copyArea(horizontal * charWidth, vertical * charHeight, img.getWidth(), img.getHeight(), -horizontal * charWidth, @@ -340,15 +341,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI gg.translate(-transX, -transY); repaint(); - fastpainting = false; + } finally + { + fastpainting = false; + } } + //ok + //ok @Override public void paintComponent(Graphics g) { - super.paintComponent(g); - - updateViewport(); + super.paintComponent(g); + + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); ViewportRanges ranges = av.getRanges(); @@ -411,7 +418,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI g.drawImage(lcimg, 0, 0, this); } } - +//ok + /** * Draw an alignment panel for printing * @@ -558,6 +566,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ public int getWrappedCanvasWidth(int canvasWidth) { + int charWidth = av.getCharWidth(); + FontMetrics fm = getFontMetrics(av.getFont()); labelWidthEast = 0; @@ -608,150 +618,306 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } /** - * DOCUMENT ME! + * Draws as many widths of a wrapped alignment as can fit in the visible + * window * * @param g - * DOCUMENT ME! * @param canvasWidth - * DOCUMENT ME! + * available width in pixels * @param canvasHeight - * DOCUMENT ME! - * @param startRes - * DOCUMENT ME! + * available height in pixels + * @param startColumn + * the first column (0...) of the alignment to draw */ - private void drawWrappedPanel(Graphics g, int canvasWidth, - int canvasHeight, int startRes) + public void drawWrappedPanel(Graphics g, int canvasWidth, + int canvasHeight, final int startColumn) + { + int wrappedWidthInResidues = calculateWrappedGeometry(canvasWidth, + canvasHeight); + + av.setWrappedWidth(wrappedWidthInResidues); + + ViewportRanges ranges = av.getRanges(); + ranges.setViewportStartAndWidth(startColumn, wrappedWidthInResidues); + + /* + * draw one width at a time (including any scales or annotation shown), + * until we have run out of either alignment or vertical space available + */ + int ypos = wrappedSpaceAboveAlignment; + int maxWidth = ranges.getVisibleAlignmentWidth(); + + int start = startColumn; + int currentWidth = 0; + while ((currentWidth < wrappedVisibleWidths) && (start < maxWidth)) + { + int endColumn = Math + .min(maxWidth, start + wrappedWidthInResidues - 1); + drawWrappedWidth(g, ypos, start, endColumn, canvasHeight); + ypos += wrappedRepeatHeightPx; + start += wrappedWidthInResidues; + currentWidth++; + } + + drawWrappedDecorators(g, startColumn); + } + + /** + * Calculates and saves values needed when rendering a wrapped alignment. + * These depend on many factors, including + * + * + * @param canvasWidth + * @param canvasHeight + * @return the number of residue columns in each width + */ + protected int calculateWrappedGeometry(int canvasWidth, int canvasHeight) { - updateViewport(); - AlignmentI al = av.getAlignment(); + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + /* + * width of labels in pixels left and right (if shown) + */ int labelWidth = 0; if (av.getScaleRightWrapped() || av.getScaleLeftWrapped()) { FontMetrics fm = getFontMetrics(av.getFont()); labelWidth = getLabelWidth(fm); } - labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0; labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; - int hgap = charHeight; - if (av.getScaleAboveWrapped()) + /* + * 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 + */ + wrappedRepeatHeightPx = wrappedSpaceAboveAlignment; + // add sequences + wrappedRepeatHeightPx += av.getRanges().getViewportHeight() + * charHeight; + // add annotations panel height if shown + wrappedRepeatHeightPx += getAnnotationHeight(); + + /* + * number of residue columns we can show in each row; + * this is just canvas width less scale left and right (if shown), + * as a whole multiple of character widths + */ + int wrappedWidthInResidues = (canvasWidth - labelWidthEast + - labelWidthWest) / charWidth; + + /* + * 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)) { - hgap += charHeight; + wrappedVisibleWidths++; } - int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; - int cHeight = av.getAlignment().getHeight() * charHeight; + /* + * limit visibleWidths to not exceed width of alignment + */ + int maxWidths = (xMax - ranges.getStartRes()) / wrappedWidthInResidues; + if (xMax % wrappedWidthInResidues > 0) + { + maxWidths++; + } + wrappedVisibleWidths = Math.min(wrappedVisibleWidths, maxWidths); + + return wrappedWidthInResidues; + } + + /** + * Draws one width of a wrapped alignment, including sequences and + * annnotations, if shown, but not scales or hidden column markers + * + * @param g + * @param ypos + * @param startColumn + * @param endColumn + * @param canvasHeight + */ + protected void drawWrappedWidth(Graphics g, int ypos, int startColumn, + int endColumn, int canvasHeight) + { + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); - av.setWrappedWidth(cWidth); + ViewportRanges ranges = av.getRanges(); + int viewportWidth = ranges.getViewportWidth(); - av.getRanges().setViewportStartAndWidth(startRes, cWidth); + int endx = Math.min(startColumn + viewportWidth - 1, endColumn); - int endx; - int ypos = hgap; - int maxwidth = av.getAlignment().getWidth(); + /* + * move right before drawing by the width of the scale left (if any) + * plus column offset from left margin (usually zero, but may be non-zero + * when fast painting is drawing just a few columns) + */ + int xOffset = labelWidthWest + + ((startColumn - ranges.getStartRes()) % viewportWidth) + * charWidth; + g.translate(xOffset, 0); - if (av.hasHiddenColumns()) + // 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) { - maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth); + g.setClip(0, 0, viewportWidth * charWidth, canvasHeight); + } + else + { + g.setClip(0, (int) clip.getBounds().getY(), viewportWidth * charWidth, + (int) clip.getBounds().getHeight()); } - int annotationHeight = getAnnotationHeight(); + /* + * 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, + wrappedRepeatHeightPx); - while ((ypos <= canvasHeight) && (startRes < maxwidth)) - { - endx = startRes + cWidth - 1; + drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1, + ypos); - if (endx > maxwidth) + int cHeight = av.getAlignment().getHeight() * charHeight; + + if (av.isShowAnnotation()) + { + g.translate(0, cHeight + ypos + 3); + if (annotations == null) { - endx = maxwidth; + annotations = new AnnotationPanel(av); } - g.setFont(av.getFont()); - g.setColor(Color.black); + annotations.renderer.drawComponent(annotations, av, g, -1, + startColumn, endx + 1); + g.translate(0, -cHeight - ypos - 3); + } + g.setClip(clip); + g.translate(-xOffset, 0); + } + + /** + * Draws scales left, right and above (if shown), and any hidden column + * markers, on all widths of the wrapped alignment + * + * @param g + * @param startColumn + */ + protected void drawWrappedDecorators(Graphics g, int startColumn) + { + int charWidth = av.getCharWidth(); + + g.setFont(av.getFont()); + g.setColor(Color.black); + + int ypos = wrappedSpaceAboveAlignment; + ViewportRanges ranges = av.getRanges(); + int viewportWidth = ranges.getViewportWidth(); + int maxWidth = ranges.getVisibleAlignmentWidth(); + int widthsDrawn = 0; + while (widthsDrawn < wrappedVisibleWidths) + { + int endColumn = Math.min(maxWidth, startColumn + viewportWidth - 1); if (av.getScaleLeftWrapped()) { - drawWestScale(g, startRes, endx, ypos); + drawVerticalScale(g, startColumn, endColumn - 1, ypos, true); } if (av.getScaleRightWrapped()) { - g.translate(canvasWidth - labelWidthEast, 0); - drawEastScale(g, startRes, endx, ypos); - g.translate(-(canvasWidth - labelWidthEast), 0); + int x = labelWidthWest + viewportWidth * charWidth; + g.translate(x, 0); + drawVerticalScale(g, startColumn, 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.setColor(Color.white); + g.fillRect(0, ypos - wrappedSpaceAboveAlignment, + viewportWidth * charWidth + labelWidthWest, + wrappedSpaceAboveAlignment); + g.setColor(Color.black); + g.translate(labelWidthWest, 0); if (av.getScaleAboveWrapped()) { - drawNorthScale(g, startRes, endx, ypos); + drawNorthScale(g, startColumn, endColumn, ypos); } if (av.hasHiddenColumns() && av.getShowHiddenMarkers()) { - g.setColor(Color.blue); - int res; - HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - List positions = hidden.findHiddenRegionPositions(); - for (int pos : positions) - { - res = pos - startRes; - - if (res < 0 || res > endx - startRes) - { - continue; - } - - gg.fillPolygon( - new int[] - { res * charWidth - charHeight / 4, - res * charWidth + charHeight / 4, res * charWidth }, - new int[] - { ypos - (charHeight / 2), ypos - (charHeight / 2), - ypos - (charHeight / 2) + 8 }, - 3); - - } + drawHiddenColumnMarkers(g, ypos, startColumn, endColumn); } - // When printing we have an extra clipped region, - // the Printable page which we need to account for here - Shape clip = g.getClip(); + g.translate(-labelWidthWest, 0); + + ypos += wrappedRepeatHeightPx; + startColumn += viewportWidth; + widthsDrawn++; + } + } - if (clip == null) - { - g.setClip(0, 0, cWidth * charWidth, canvasHeight); - } - else - { - g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth, - (int) clip.getBounds().getHeight()); - } + /** + * @param g + * @param ypos + * @param startColumn + * @param endColumn + */ + protected void drawHiddenColumnMarkers(Graphics g, int ypos, + int startColumn, int endColumn) + { + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); - drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos); + g.setColor(Color.blue); + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + List positions = hidden.findHiddenRegionPositions(); + for (int pos : positions) + { + int res = pos - startColumn; - if (av.isShowAnnotation()) + if (res < 0 || res > endColumn - startColumn) { - g.translate(0, cHeight + ypos + 3); - if (annotations == null) - { - annotations = new AnnotationPanel(av); - } - - annotations.renderer.drawComponent(annotations, av, g, -1, startRes, - endx + 1); - g.translate(0, -cHeight - ypos - 3); + continue; } - g.setClip(clip); - g.translate(-labelWidthWest, 0); - - ypos += cHeight + annotationHeight + hgap; - startRes += cWidth; + /* + * draw a downward-pointing triangle at the hidden columns location + * (before the following visible column) + */ + int xMiddle = res * charWidth; + int[] xPoints = new int[] { xMiddle - charHeight / 4, + xMiddle + charHeight / 4, xMiddle }; + int yTop = ypos - (charHeight / 2); + int[] yPoints = new int[] { yTop, yTop, yTop + 8 }; + g.fillPolygon(xPoints, yPoints, 3); } } @@ -834,22 +1000,24 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * marker. * * @param g1 - * Graphics object to draw with + * the graphics context, positioned at the first residue to be drawn * @param startRes - * offset of the first column in the visible region (0..) + * offset of the first column to draw (0..) * @param endRes - * offset of the last column in the visible region (0..) + * offset of the last column to draw (0..) * @param startSeq - * offset of the first sequence in the visible region (0..) + * offset of the first sequence to draw (0..) * @param endSeq - * offset of the last sequence in the visible region (0..) + * offset of the last sequence to draw (0..) * @param yOffset * vertical offset at which to draw (for wrapped alignments) */ 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); @@ -939,6 +1107,9 @@ 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()); seqRdr.prepare(g, av.isRenderGaps()); @@ -1118,6 +1289,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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, @@ -1179,6 +1352,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int startRes, int endRes, int startSeq, int endSeq, int verticalOffset) { + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + int visWidth = (endRes - startRes + 1) * charWidth; int oldY = -1; @@ -1347,14 +1523,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return false; } boolean wrapped = av.getWrapAlignment(); - try { fastPaint = !noFastPaint; fastpainting = fastPaint; - updateViewport(); - /* * to avoid redrawing the whole visible region, we instead * redraw just the minimal regions to remove previous highlights @@ -1499,14 +1672,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI fastPaint = true; repaint(); } - else if (av.getWrapAlignment()) - { - if (eventName.equals(ViewportRanges.STARTRES)) - { - repaint(); - } - } - else + else if (eventName.equals(ViewportRanges.STARTRES)) { int scrollX = 0; if (eventName.equals(ViewportRanges.STARTRES)) @@ -1524,17 +1690,22 @@ 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. + // scroll - startres and endres both change - fastPaint(scrollX, 0); + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); + } + else + { + fastPaint(scrollX, 0); + } } else if (eventName.equals(ViewportRanges.STARTSEQ)) { @@ -1545,6 +1716,257 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } /** + * Does a minimal update of the image for a scroll movement. This method + * handles scroll movements of up to one width of the wrapped alignment (one + * click in the vertical scrollbar). Larger movements (for example after a + * scroll to highlight a mapped position) trigger a full redraw instead. + * + * @param scrollX + * number of positions scrolled (right if positive, left if negative) + */ + protected void fastPaintWrapped(int scrollX) + { + ViewportRanges ranges = av.getRanges(); + + if (Math.abs(scrollX) > ranges.getViewportWidth()) + { + /* + * shift of more than one view width is + * overcomplicated to handle in this method + */ + fastPaint = false; + repaint(); + return; + } + + if (fastpainting || gg == null) + { + return; + } + + fastPaint = true; + fastpainting = true; + + try + { + calculateWrappedGeometry(getWidth(), getHeight()); + + /* + * relocate the regions of the alignment that are still visible + */ + shiftWrappedAlignment(-scrollX); + + /* + * add new columns (sequence, annotation) + * - at top left if scrollX < 0 + * - at right of last two widths if scrollX > 0 + */ + if (scrollX < 0) + { + int startRes = ranges.getStartRes(); + drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes, startRes + - scrollX - 1, getHeight()); + } + else + { + fastPaintWrappedAddRight(scrollX); + } + + /* + * draw all scales (if shown) and hidden column markers + */ + drawWrappedDecorators(gg, ranges.getStartRes()); + + repaint(); + } finally + { + fastpainting = false; + } + } + + /** + * Draws the specified number of columns at the 'end' (bottom right) of a + * wrapped alignment view, including sequences and annotations if shown, but + * not scales. Also draws the same number of columns at the right hand end of + * the second last width shown, if the last width is not full height (so + * cannot simply be copied from the graphics image). + * + * @param columns + */ + protected void fastPaintWrappedAddRight(int columns) + { + if (columns == 0) + { + return; + } + + ViewportRanges ranges = av.getRanges(); + int viewportWidth = ranges.getViewportWidth(); + int charWidth = av.getCharWidth(); + + /** + * draw full height alignment in the second last row, last columns, if the + * last row was not full height + */ + int visibleWidths = wrappedVisibleWidths; + int canvasHeight = getHeight(); + boolean lastWidthPartHeight = (wrappedVisibleWidths * wrappedRepeatHeightPx) > canvasHeight; + + if (lastWidthPartHeight) + { + int widthsAbove = Math.max(0, visibleWidths - 2); + int ypos = wrappedRepeatHeightPx * widthsAbove + + wrappedSpaceAboveAlignment; + int endRes = ranges.getEndRes(); + endRes += widthsAbove * viewportWidth; + int startRes = endRes - columns; + int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth) + * charWidth; + + /* + * white fill first to erase annotations + */ + gg.translate(xOffset, 0); + gg.setColor(Color.white); + gg.fillRect(labelWidthWest, ypos, + (endRes - startRes + 1) * charWidth, wrappedRepeatHeightPx); + gg.translate(-xOffset, 0); + + drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight); + } + + /* + * draw newly visible columns in last wrapped width (none if we + * have reached the end of the alignment) + * y-offset for drawing last width is height of widths above, + * plus one gap row + */ + int widthsAbove = visibleWidths - 1; + int ypos = wrappedRepeatHeightPx * widthsAbove + + wrappedSpaceAboveAlignment; + int endRes = ranges.getEndRes(); + endRes += widthsAbove * viewportWidth; + int startRes = endRes - columns + 1; + + /* + * white fill first to erase annotations + */ + int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth) + * charWidth; + gg.translate(xOffset, 0); + gg.setColor(Color.white); + int width = viewportWidth * charWidth - xOffset; + gg.fillRect(labelWidthWest, ypos, width, wrappedRepeatHeightPx); + gg.translate(-xOffset, 0); + + gg.setFont(av.getFont()); + gg.setColor(Color.black); + + if (startRes < ranges.getVisibleAlignmentWidth()) + { + drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight); + } + + /* + * and finally, white fill any space below the visible alignment + */ + int heightBelow = canvasHeight - visibleWidths * wrappedRepeatHeightPx; + if (heightBelow > 0) + { + gg.setColor(Color.white); + gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow); + } + } + + /** + * Shifts the visible alignment by the specified number of columns - left if + * negative, right if positive. Copies and moves sequences and annotations (if + * shown). Scales, hidden column markers and any newly visible columns must be + * drawn separately. + * + * @param positions + */ + protected void shiftWrappedAlignment(int positions) + { + if (positions == 0) + { + return; + } + int charWidth = av.getCharWidth(); + + int canvasHeight = getHeight(); + ViewportRanges ranges = av.getRanges(); + int viewportWidth = ranges.getViewportWidth(); + int widthToCopy = (ranges.getViewportWidth() - Math.abs(positions)) + * charWidth; + int heightToCopy = wrappedRepeatHeightPx - wrappedSpaceAboveAlignment; + int xMax = ranges.getVisibleAlignmentWidth(); + + if (positions > 0) + { + /* + * shift right (after scroll left) + * for each wrapped width (starting with the last), copy (width-positions) + * columns from the left margin to the right margin, and copy positions + * columns from the right margin of the row above (if any) to the + * left margin of the current row + */ + + /* + * get y-offset of last wrapped width, first row of sequences + */ + int y = canvasHeight / wrappedRepeatHeightPx * wrappedRepeatHeightPx; + y += wrappedSpaceAboveAlignment; + int copyFromLeftStart = labelWidthWest; + int copyFromRightStart = copyFromLeftStart + widthToCopy; + + while (y >= 0) + { + gg.copyArea(copyFromLeftStart, y, widthToCopy, heightToCopy, + positions * charWidth, 0); + if (y > 0) + { + gg.copyArea(copyFromRightStart, y - wrappedRepeatHeightPx, + positions * charWidth, heightToCopy, -widthToCopy, + wrappedRepeatHeightPx); + } + + y -= wrappedRepeatHeightPx; + } + } + else + { + /* + * shift left (after scroll right) + * for each wrapped width (starting with the first), copy (width-positions) + * columns from the right margin to the left margin, and copy positions + * columns from the left margin of the row below (if any) to the + * right margin of the current row + */ + int xpos = av.getRanges().getStartRes(); + int y = wrappedSpaceAboveAlignment; + int copyFromRightStart = labelWidthWest - positions * charWidth; + + while (y < canvasHeight) + { + gg.copyArea(copyFromRightStart, y, widthToCopy, heightToCopy, + positions * charWidth, 0); + if (y + wrappedRepeatHeightPx < canvasHeight - wrappedRepeatHeightPx + && (xpos + viewportWidth <= xMax)) + { + gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx, -positions + * charWidth, heightToCopy, widthToCopy, + -wrappedRepeatHeightPx); + } + + y += wrappedRepeatHeightPx; + xpos += viewportWidth; + } + } + } + + + /** * Redraws any positions in the search results in the visible region of a * wrapped alignment. Any highlights are drawn depending on the search results * set on the Viewport, not the results argument. This allows @@ -1560,11 +1982,13 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { 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(); @@ -1661,25 +2085,4 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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 - * - * @return - */ - protected int getRepeatHeightWrapped() - { - // 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; - } } -- 1.7.10.2