X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=b3fcc542f3c0f6f7d2fc3899b172bf0fe3b551b3;hb=87e1ada6a62777b415f14b0444fdcc63336c8f73;hp=2c8a5df3848d40fff3deb6bd8e8fdc3f85abd77c;hpb=67f498031a89aa97926db7be629e94ef031c10e4;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 2c8a5df..b3fcc54 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -22,16 +22,16 @@ package jalview.gui; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; -import jalview.datamodel.HiddenColumns.VisibleBlocksVisBoundsIterator; 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; @@ -43,57 +43,66 @@ 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; /** - * DOCUMENT ME! + * The Swing component on which the alignment sequences, and annotations (if + * shown), are drawn. This includes scales above, left and right (if shown) in + * Wrapped mode, but not the scale above in Unwrapped mode. * - * @author $author$ - * @version $Revision$ */ public class SeqCanvas extends JComponent implements ViewportListenerI { - private static String ZEROS = "0000000000"; + /* + * pixels gap between sequences and annotations when in wrapped mode + */ + static final int SEQS_ANNOTATION_GAP = 3; - final FeatureRenderer fr; + private static final String ZEROS = "0000000000"; - final SequenceRenderer seqRdr; + final FeatureRenderer fr; BufferedImage img; - Graphics2D gg; - AlignViewport av; - boolean fastPaint = false; + int cursorX = 0; + + int cursorY = 0; - int labelWidthWest; + private final SequenceRenderer seqRdr; - int labelWidthEast; + private boolean fastPaint = false; - int cursorX = 0; + private boolean fastpainting = false; - int cursorY = 0; + private AnnotationPanel annotations; + + /* + * measurements for drawing a wrapped alignment + */ + private int labelWidthEast; // label right width in pixels if shown + + private int labelWidthWest; // label left width in pixels if shown - int charHeight = 0; + int wrappedSpaceAboveAlignment; // gap between widths - int charWidth = 0; + int wrappedRepeatHeightPx; // height in pixels of wrapped width - boolean fastpainting = false; + private int wrappedVisibleWidths; // number of wrapped widths displayed - AnnotationPanel annotations; + private Graphics2D gg; /** * Creates a new SeqCanvas object. * - * @param av - * DOCUMENT ME! + * @param ap */ public SeqCanvas(AlignmentPanel ap) { this.av = ap.av; - updateViewport(); fr = new FeatureRenderer(ap); seqRdr = new SequenceRenderer(av); setLayout(new BorderLayout()); @@ -113,29 +122,36 @@ 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) @@ -150,137 +166,119 @@ 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, final int startx, final int endx, + final int ypos, final 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); - } + int yPos = ypos + charHeight; + int startX = startx; + int endX = endx; - int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth) - 1; + HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); + startX = hiddenColumns.visibleToAbsoluteColumn(startx); + endX = hiddenColumns.visibleToAbsoluteColumn(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 within its width less half a + * character width padding on the right + */ + int labelSpace = left ? labelWidthWest : labelWidthEast; + labelSpace -= charWidth / 2; // leave space to the right + String valueAsString = String.valueOf(value); + int labelLength = fm.stringWidth(valueAsString); + int xOffset = labelSpace - labelLength; + g.setColor(Color.black); + g.drawString(valueAsString, xOffset, y); } } } - /** - * 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) { @@ -290,113 +288,121 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } 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; - - gg.copyArea(horizontal * charWidth, vertical * charHeight, - img.getWidth(), img.getHeight(), -horizontal * charWidth, - -vertical * charHeight); - - if (horizontal > 0) // scrollbar pulled right, image to the left - { - transX = (endRes - startRes - horizontal) * charWidth; - startRes = endRes - horizontal; - } - else if (horizontal < 0) - { - endRes = startRes - horizontal; - } - else if (vertical > 0) // scroll down + try { - startSeq = endSeq - vertical; + 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, + -vertical * charHeight); - if (startSeq < ranges.getStartSeq()) - { // ie scrolling too fast, more than a page at a time - startSeq = ranges.getStartSeq(); + if (horizontal > 0) // scrollbar pulled right, image to the left + { + transX = (endRes - startRes - horizontal) * charWidth; + startRes = endRes - horizontal; } - else + else if (horizontal < 0) { - transY = img.getHeight() - ((vertical + 1) * charHeight); + endRes = startRes - horizontal; } - } - else if (vertical < 0) - { - endSeq = startSeq - vertical; - if (endSeq > ranges.getEndSeq()) + if (vertical > 0) // scroll down { - endSeq = ranges.getEndSeq(); + startSeq = endSeq - vertical; + + if (startSeq < ranges.getStartSeq()) + { // ie scrolling too fast, more than a page at a time + startSeq = ranges.getStartSeq(); + } + else + { + transY = img.getHeight() - ((vertical + 1) * charHeight); + } } - } + else if (vertical < 0) + { + endSeq = startSeq - vertical; - gg.translate(transX, transY); - drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); - gg.translate(-transX, -transY); + if (endSeq > ranges.getEndSeq()) + { + endSeq = ranges.getEndSeq(); + } + } + + gg.translate(transX, transY); + drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); + gg.translate(-transX, -transY); - repaint(); - fastpainting = false; + // 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; + } } @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(); - + 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()); @@ -407,12 +413,19 @@ 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) + { + drawCursor(g, ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq()); + } + } + /** * Draw an alignment panel for printing * @@ -432,14 +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); - } } /** @@ -457,97 +464,16 @@ 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, + 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 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) @@ -559,29 +485,30 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ public int getWrappedCanvasWidth(int canvasWidth) { - FontMetrics fm = getFontMetrics(av.getFont()); + int charWidth = av.getCharWidth(); - labelWidthEast = 0; - labelWidthWest = 0; + FontMetrics fm = getFontMetrics(av.getFont()); - if (av.getScaleRightWrapped()) + int labelWidth = 0; + + if (av.getScaleRightWrapped() || av.getScaleLeftWrapped()) { - labelWidthEast = getLabelWidth(fm); + labelWidth = getLabelWidth(fm); } - if (av.getScaleLeftWrapped()) - { - labelWidthWest = labelWidthEast > 0 ? labelWidthEast - : getLabelWidth(fm); - } + labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0; + + labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; } /** - * Returns a pixel width suitable for showing the largest sequence coordinate - * (end position) in the alignment. Returns 2 plus the number of decimal - * digits to be shown (3 for 1-10, 4 for 11-99 etc). + * Returns a pixel width sufficient to show the largest sequence coordinate + * (end position) in the alignment, calculated as the FontMetrics width of + * zeroes "0000000" limited to the number of decimal digits to be shown (3 for + * 1-10, 4 for 11-99 etc). One character width is added to this, to allow for + * half a character width space on either side. * * @param fm * @return @@ -599,154 +526,323 @@ public class SeqCanvas extends JComponent implements ViewportListenerI maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd()); } - int length = 2; + int length = 0; for (int i = maxWidth; i > 0; i /= 10) { length++; } - return fm.stringWidth(ZEROS.substring(0, length)); + return fm.stringWidth(ZEROS.substring(0, length)) + av.getCharWidth(); } /** - * 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) { - updateViewport(); - AlignmentI al = av.getAlignment(); + int wrappedWidthInResidues = calculateWrappedGeometry(canvasWidth, + canvasHeight); - int labelWidth = 0; - if (av.getScaleRightWrapped() || av.getScaleLeftWrapped()) + av.setWrappedWidth(wrappedWidthInResidues); + + ViewportRanges ranges = av.getRanges(); + ranges.setViewportStartAndWidth(startColumn, wrappedWidthInResidues); + + // we need to call this again to make sure the startColumn + + // wrappedWidthInResidues values are used to calculate wrappedVisibleWidths + // correctly. + calculateWrappedGeometry(canvasWidth, canvasHeight); + + /* + * 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; + int maxWidth = ranges.getVisibleAlignmentWidth(); + + int start = startColumn; + int currentWidth = 0; + while ((currentWidth < wrappedVisibleWidths) && (start < maxWidth)) { - FontMetrics fm = getFontMetrics(av.getFont()); - labelWidth = getLabelWidth(fm); + int endColumn = Math + .min(maxWidth, start + wrappedWidthInResidues - 1); + drawWrappedWidth(g, ypos, start, endColumn, canvasHeight); + ypos += wrappedRepeatHeightPx; + start += wrappedWidthInResidues; + currentWidth++; } - labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0; - labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; + drawWrappedDecorators(g, startColumn); + } - int hgap = charHeight; - if (av.getScaleAboveWrapped()) + /** + * 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) + { + int charHeight = av.getCharHeight(); + + /* + * vertical space in pixels between wrapped widths of alignment + * - one character height, or two if scale above is drawn + */ + wrappedSpaceAboveAlignment = charHeight + * (av.getScaleAboveWrapped() ? 2 : 1); + + /* + * compute height in pixels of the wrapped widths + * - start with space above plus sequences + */ + wrappedRepeatHeightPx = wrappedSpaceAboveAlignment; + wrappedRepeatHeightPx += av.getAlignment().getHeight() + * charHeight; + + /* + * add annotations panel height if shown + * also gap between sequences and annotations + */ + if (av.isShowAnnotation()) { - hgap += charHeight; + wrappedRepeatHeightPx += getAnnotationHeight(); + wrappedRepeatHeightPx += SEQS_ANNOTATION_GAP; // 3px } - int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; - int cHeight = av.getAlignment().getHeight() * charHeight; + /* + * number of visible widths (the last one may be part height), + * ensuring a part height includes at least one sequence + */ + ViewportRanges ranges = av.getRanges(); + wrappedVisibleWidths = canvasHeight / wrappedRepeatHeightPx; + int remainder = canvasHeight % wrappedRepeatHeightPx; + if (remainder >= (wrappedSpaceAboveAlignment + charHeight)) + { + wrappedVisibleWidths++; + } - av.setWrappedWidth(cWidth); + /* + * compute width in residues; this also sets East and West label widths + */ + int wrappedWidthInResidues = getWrappedCanvasWidth(canvasWidth); - av.getRanges().setViewportStartAndWidth(startRes, cWidth); + /* + * limit visibleWidths to not exceed width of alignment + */ + int xMax = ranges.getVisibleAlignmentWidth(); + int startToEnd = xMax - ranges.getStartRes(); + int maxWidths = startToEnd / wrappedWidthInResidues; + if (startToEnd % wrappedWidthInResidues > 0) + { + maxWidths++; + } + wrappedVisibleWidths = Math.min(wrappedVisibleWidths, maxWidths); - int endx; - int ypos = hgap; - int maxwidth = av.getAlignment().getWidth(); + return wrappedWidthInResidues; + } - if (av.hasHiddenColumns()) + /** + * 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, final int ypos, + final int startColumn, final int endColumn, + final int canvasHeight) + { + ViewportRanges ranges = av.getRanges(); + int viewportWidth = ranges.getViewportWidth(); + + int endx = Math.min(startColumn + viewportWidth - 1, endColumn); + + /* + * 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 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(); + + 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) + */ + g.setColor(Color.white); + g.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() * av.getCharHeight(); + + if (av.isShowAnnotation()) + { + final int yShift = cHeight + ypos + SEQS_ANNOTATION_GAP; + g.translate(0, yShift); + 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, -yShift); + } + 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, final 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; + int startCol = startColumn; + + while (widthsDrawn < wrappedVisibleWidths) + { + int endColumn = Math.min(maxWidth, startCol + viewportWidth - 1); if (av.getScaleLeftWrapped()) { - drawWestScale(g, startRes, endx, ypos); + drawVerticalScale(g, startCol, 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, startCol, endColumn, ypos, false); + g.translate(-x, 0); } + /* + * white fill region of scale above and hidden column markers + * (to support incremental fast paint of image) + */ + g.translate(labelWidthWest, 0); + g.setColor(Color.white); + g.fillRect(0, ypos - wrappedSpaceAboveAlignment, viewportWidth + * charWidth + labelWidthWest, wrappedSpaceAboveAlignment); + g.setColor(Color.black); + g.translate(-labelWidthWest, 0); + g.translate(labelWidthWest, 0); if (av.getScaleAboveWrapped()) { - drawNorthScale(g, startRes, endx, ypos); + drawNorthScale(g, startCol, endColumn, ypos); } if (av.hasHiddenColumns() && av.getShowHiddenMarkers()) { - g.setColor(Color.blue); - int res; - HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - - Iterator it = hidden.getBoundedStartIterator(startRes, - endx + 1); - while (it.hasNext()) - { - res = it.next() - startRes; - 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, startCol, 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); - if (clip == null) - { - g.setClip(0, 0, cWidth * charWidth, canvasHeight); - } - else - { - g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth, - (int) clip.getBounds().getHeight()); - } + ypos += wrappedRepeatHeightPx; + startCol += viewportWidth; + widthsDrawn++; + } + } - drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos); + /** + * Draws markers (triangles) above hidden column positions between startColumn + * and endColumn. + * + * @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(); - if (av.isShowAnnotation()) - { - g.translate(0, cHeight + ypos + 3); - if (annotations == null) - { - annotations = new AnnotationPanel(av); - } + g.setColor(Color.blue); + int res; + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - annotations.renderer.drawComponent(annotations, av, g, -1, startRes, - endx + 1); - g.translate(0, -cHeight - ypos - 3); - } - g.setClip(clip); - g.translate(-labelWidthWest, 0); + Iterator it = hidden.getStartRegionIterator(startColumn, + endColumn); + while (it.hasNext()) + { + res = it.next() - startColumn; - ypos += cHeight + annotationHeight + hgap; + if (res < 0 || res > endColumn - startColumn + 1) + { + continue; + } - 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); } } @@ -757,6 +853,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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()) @@ -771,16 +870,14 @@ 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 @@ -805,6 +902,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // update horizontal offset startx += cWidth; } + g.setStroke(new BasicStroke()); } int getAnnotationHeight() @@ -829,22 +927,24 @@ 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); @@ -852,35 +952,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI else { int screenY = 0; - final int screenYMax = endRes - startRes; - int blockStart = startRes; - int blockEnd = endRes; // equals blockStart + screenYMax - screenY; + int blockStart; + int blockEnd; HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - VisibleBlocksVisBoundsIterator regions = (VisibleBlocksVisBoundsIterator) hidden - .getVisibleBlocksIterator(startRes, endRes, true);// hidden.iterator(); + VisibleContigsIterator regions = hidden + .getVisContigsIterator(startRes, endRes + 1, true); + while (regions.hasNext()) { int[] region = regions.next(); blockEnd = region[1]; blockStart = region[0]; -/* int hideStart = region[0]; - int hideEnd = region[1]; - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; // convert startRes to an - // absolute value - blockEnd += (hideEnd - hideStart) + 1; - continue; - } -*/ /* * draw up to just before the next hidden region, or the end of * the visible region, whichever comes first */ -// blockEnd = Math.min(hideStart - 1, -// blockEnd); g1.translate(screenY * charWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); @@ -890,8 +978,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * triangle on top) if we reached it */ if (av.getShowHiddenMarkers() - && (regions.hasNext() || regions.endsAtHidden()))// blockEnd == - // hideStart - 1) + && (regions.hasNext() || regions.endsAtHidden())) { g1.setColor(Color.blue); @@ -902,25 +989,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI g1.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; - /* blockStart = hideEnd + 1; - blockEnd = blockStart + screenYMax - screenY; - - 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); - }*/ } } @@ -943,6 +1012,9 @@ 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()); @@ -974,26 +1046,19 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasSearchResults()) { SearchResultsI searchResults = av.getSearchResults(); - int[] visibleResults = searchResults.getResults(nextSeq, - startRes, endRes); + int[] visibleResults = searchResults.getResults(nextSeq, startRes, + endRes); if (visibleResults != null) { for (int r = 0; r < visibleResults.length; r += 2) { seqRdr.drawHighlightedText(nextSeq, visibleResults[r], - visibleResults[r + 1], (visibleResults[r] - startRes) - * charWidth, offset - + ((i - startSeq) * charHeight)); + visibleResults[r + 1], + (visibleResults[r] - startRes) * charWidth, + offset + ((i - startSeq) * charHeight)); } } } - - if (av.cursorMode && cursorY == i && cursorX >= startRes - && cursorX <= endRes) - { - seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth, - offset + ((i - startSeq) * charHeight)); - } } if (av.getSelectionGroup() != null @@ -1004,14 +1069,21 @@ 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; @@ -1024,18 +1096,15 @@ 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; @@ -1049,33 +1118,28 @@ 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, @@ -1086,42 +1150,120 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawWrappedSelection(g, group, getWidth(), getHeight(), av.getRanges().getStartRes()); } - - g.dispose(); - return selectionImage; + g.setStroke(new BasicStroke()); } - /* - * Set up graphics for selection group + /** + * Draw the cursor as a separate image and overlay + * + * @param startRes + * start residue of area to draw cursor in + * @param endRes + * end residue of area to draw cursor in + * @param startSeq + * start sequence of area to draw cursor in + * @param endSeq + * end sequence of are to draw cursor in + * @return a transparent image of the same size as the sequence canvas, with + * the cursor drawn on it, if any */ - private void setupSelectionGroup(Graphics2D g, - BufferedImage selectionImage) + private void drawCursor(Graphics g, int startRes, int endRes, + int startSeq, + int endSeq) { - // set background to transparent - g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); - g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight()); + // convert the cursorY into a position on the visible alignment + int cursor_ypos = cursorY; - // set up foreground to draw red dashed line - g.setComposite(AlphaComposite.Src); - g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, - BasicStroke.JOIN_ROUND, 3f, new float[] - { 5f, 3f }, 0f)); - g.setColor(Color.RED); + // don't do work unless we have to + if (cursor_ypos >= startSeq && cursor_ypos <= endSeq) + { + int yoffset = 0; + int xoffset = 0; + int startx = startRes; + int endx = endRes; + + // convert the cursorX into a position on the visible alignment + int cursor_xpos = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(cursorX); + + if (av.getAlignment().getHiddenColumns().isVisible(cursorX)) + { + + if (av.getWrapAlignment()) + { + // work out the correct offsets for the cursor + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + int canvasWidth = getWidth(); + int canvasHeight = getHeight(); + + // height gap above each panel + int hgap = charHeight; + if (av.getScaleAboveWrapped()) + { + hgap += charHeight; + } + + int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) + / charWidth; + int cHeight = av.getAlignment().getHeight() * charHeight; + + endx = startx + cWidth - 1; + int ypos = hgap; // vertical offset + + // iterate down the wrapped panels + while ((ypos <= canvasHeight) && (endx < cursor_xpos)) + { + // update vertical offset + ypos += cHeight + getAnnotationHeight() + hgap; + + // update horizontal offset + startx += cWidth; + endx = startx + cWidth - 1; + } + yoffset = ypos; + xoffset = labelWidthWest; + } + + // now check if cursor is within range for x values + if (cursor_xpos >= startx && cursor_xpos <= endx) + { + // get the character the cursor is drawn at + SequenceI seq = av.getAlignment().getSequenceAt(cursorY); + char s = seq.getCharAt(cursorX); + + seqRdr.drawCursor(g, s, + xoffset + (cursor_xpos - startx) * av.getCharWidth(), + yoffset + (cursor_ypos - startSeq) * av.getCharHeight()); + } + } + } } - /* + + /** * Draw a selection group over an unwrapped alignment - * @param g graphics object to draw with - * @param group selection group - * @param startRes start residue of area to draw - * @param endRes end residue of area to draw - * @param startSeq start sequence of area to draw - * @param endSeq end sequence of area to draw - * @param offset vertical offset (used when called from wrapped alignment code) + * + * @param g + * graphics object to draw with + * @param group + * selection group + * @param startRes + * start residue of area to draw + * @param endRes + * end residue of area to draw + * @param startSeq + * start sequence of area to draw + * @param endSeq + * end sequence of area to draw + * @param offset + * vertical offset (used when called from wrapped alignment code) */ private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group, int startRes, int endRes, int startSeq, int endSeq, int offset) { + int charWidth = av.getCharWidth(); + if (!av.hasHiddenColumns()) { drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, @@ -1129,62 +1271,47 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } else { - // package into blocks of visible columns - int screenY = 0; - int blockStart = startRes; - int blockEnd = endRes; - - HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - Iterator regions = hidden.iterator(); - while (regions.hasNext()) - { - int[] region = regions.next(); - int hideStart = region[0]; - int hideEnd = region[1]; - - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } - - blockEnd = hideStart - 1; - - g.translate(screenY * charWidth, 0); - drawPartialGroupOutline(g, group, - blockStart, blockEnd, startSeq, endSeq, offset); - - g.translate(-screenY * charWidth, 0); - screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - - if (screenY > (endRes - startRes)) - { - // already rendered last block - break; - } - } + // package into blocks of visible columns + int screenY = 0; + int blockStart; + int blockEnd; - if (screenY <= (endRes - startRes)) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + VisibleContigsIterator regions = hidden + .getVisContigsIterator(startRes, endRes + 1, true); + while (regions.hasNext()) { - // remaining visible region to render - blockEnd = blockStart + (endRes - startRes) - screenY; + int[] region = regions.next(); + blockEnd = region[1]; + blockStart = region[0]; + g.translate(screenY * charWidth, 0); drawPartialGroupOutline(g, group, blockStart, blockEnd, startSeq, endSeq, offset); - + g.translate(-screenY * charWidth, 0); + screenY += blockEnd - blockStart + 1; } } } - /* - * 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 visWidth = (endRes - startRes + 1) * charWidth; int oldY = -1; @@ -1192,140 +1319,141 @@ 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) - { - xwidth = (endRes - startRes + 1) * charWidth - sx; - } - - // draw horizontal line at top of group - if (top != -1) + if (!inGroup) { - 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); } } @@ -1353,14 +1481,11 @@ 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 @@ -1415,7 +1540,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ protected boolean drawMappedPositions(SearchResultsI results) { - if (results == null) + if ((results == null) || (gg == null)) // JAL-2784 check gg is not null { return false; } @@ -1437,9 +1562,9 @@ 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 @@ -1482,8 +1607,8 @@ 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(); @@ -1504,34 +1629,42 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { fastPaint = true; repaint(); + return; } - else if (av.getWrapAlignment()) + else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT)) { - if (eventName.equals(ViewportRanges.STARTRES)) - { - repaint(); - } + fastPaint = false; + repaint(); + return; } - else + + int scrollX = 0; + if (eventName.equals(ViewportRanges.STARTRES) + || eventName.equals(ViewportRanges.STARTRESANDSEQ)) { - int scrollX = 0; + // Make sure we're not trying to draw a panel + // larger than the visible window if (eventName.equals(ViewportRanges.STARTRES)) { - // Make sure we're not trying to draw a panel - // larger than the visible window - ViewportRanges vpRanges = av.getRanges(); scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); - int range = vpRanges.getEndRes() - vpRanges.getStartRes(); - if (scrollX > range) - { - scrollX = range; - } - else if (scrollX < -range) - { - scrollX = -range; - } } + else + { + scrollX = ((int[]) evt.getNewValue())[0] + - ((int[]) evt.getOldValue())[0]; + } + ViewportRanges vpRanges = av.getRanges(); + int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1; + if (scrollX > range) + { + scrollX = range; + } + else if (scrollX < -range) + { + scrollX = -range; + } + } // Both scrolling and resizing change viewport ranges: scrolling changes // both start and end points, but resize only changes end values. // Here we only want to fastpaint on a scroll, with resize using a normal @@ -1539,17 +1672,303 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // vertical start value. if (eventName.equals(ViewportRanges.STARTRES)) { - // scroll - startres and endres both change - fastPaint(scrollX, 0); + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); + } + else + { + fastPaint(scrollX, 0); + } } else if (eventName.equals(ViewportRanges.STARTSEQ)) { // scroll fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); } + else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) + { + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); + } + else + { + fastPaint(scrollX, 0); + } + } + 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); + } + } + } + + /** + * 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 one view width or more 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) + { + /* + * 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); + } + + 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 @@ -1562,15 +1981,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ protected boolean drawMappedPositionsWrapped(SearchResultsI results) { - if (results == null) + if ((results == null) || (gg == null)) // JAL-2784 check gg is not null { return false; } - + int charHeight = av.getCharHeight(); + boolean matchFound = false; + calculateWrappedGeometry(getWidth(), getHeight()); int wrappedWidth = av.getWrappedWidth(); - int wrappedHeight = getRepeatHeightWrapped(); + int wrappedHeight = wrappedRepeatHeightPx; ViewportRanges ranges = av.getRanges(); int canvasHeight = getHeight(); @@ -1588,9 +2009,9 @@ 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); @@ -1629,7 +2050,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { displayColumn = alignment.getHiddenColumns() - .findColumnPosition(displayColumn); + .absoluteToVisibleColumn(displayColumn); } /* @@ -1669,23 +2090,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } /** - * Answers the height in pixels of a repeating section of the wrapped - * alignment, including space above, scale above if shown, sequences, and - * annotation panel if shown + * Answers the width in pixels of the left scale labels (0 if not shown) * * @return */ - protected int getRepeatHeightWrapped() + int getLabelWidthWest() { - // gap (and maybe scale) above - int repeatHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); - - // add sequences - repeatHeight += av.getRanges().getViewportHeight() * charHeight; - - // add annotations panel height if shown - repeatHeight += getAnnotationHeight(); - - return repeatHeight; + return labelWidthWest; } }