X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=4e896a0d9b7745b71a8a0614dc08ade86916b967;hb=bd894ca9f2aae448653d7431ab8a170e1105e85c;hp=646ecf8b810b6d21c132b430fbf2a3b3ddc7112f;hpb=8f6c457162137583ec6885d2f43d28052dd22dd9;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 646ecf8..4e896a0 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -53,9 +53,11 @@ import javax.swing.JComponent; */ public class SeqCanvas extends JComponent implements ViewportListenerI { + private static String ZEROS = "0000000000"; + final FeatureRenderer fr; - final SequenceRenderer sr; + final SequenceRenderer seqRdr; BufferedImage img; @@ -65,14 +67,22 @@ public class SeqCanvas extends JComponent implements ViewportListenerI boolean fastPaint = false; - int LABEL_WEST; + int labelWidthWest; - int LABEL_EAST; + int labelWidthEast; int cursorX = 0; int cursorY = 0; + int charHeight = 0; + + int charWidth = 0; + + boolean fastpainting = false; + + AnnotationPanel annotations; + /** * Creates a new SeqCanvas object. * @@ -84,7 +94,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI this.av = ap.av; updateViewport(); fr = new FeatureRenderer(ap); - sr = new SequenceRenderer(av); + seqRdr = new SequenceRenderer(av); setLayout(new BorderLayout()); PaintRefresher.Register(this, av.getSequenceSetId()); setBackground(Color.white); @@ -94,7 +104,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public SequenceRenderer getSequenceRenderer() { - return sr; + return seqRdr; } public FeatureRenderer getFeatureRenderer() @@ -102,8 +112,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return fr; } - int charHeight = 0, charWidth = 0; - private void updateViewport() { charHeight = av.getCharHeight(); @@ -141,9 +149,9 @@ 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); + g.drawLine((mpos * charWidth) + (charWidth / 2), + (ypos + 2) - (charHeight / 2), + (mpos * charWidth) + (charWidth / 2), ypos - 2); } } } @@ -203,10 +211,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (value != -1) { - int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) + int x = labelWidthWest - fm.stringWidth(String.valueOf(value)) - charWidth / 2; - g.drawString(value + "", x, (ypos + (i * charHeight)) - - (charHeight / 5)); + g.drawString(value + "", x, + (ypos + (i * charHeight)) - (charHeight / 5)); } } } @@ -257,13 +265,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (value != -1) { - g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight)) - - (charHeight / 5)); + g.drawString(String.valueOf(value), 0, + (ypos + (i * charHeight)) - (charHeight / 5)); } } } - boolean fastpainting = false; /** * need to make this thread safe move alignment rendering in response to @@ -276,7 +283,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ public void fastPaint(int horizontal, int vertical) { - if (fastpainting || gg == null) + if (fastpainting || gg == null || img == null) { return; } @@ -285,10 +292,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI updateViewport(); ViewportRanges ranges = av.getRanges(); - int sr = ranges.getStartRes(); - int er = ranges.getEndRes(); - int ss = ranges.getStartSeq(); - int es = ranges.getEndSeq(); + int startRes = ranges.getStartRes(); + int endRes = ranges.getEndRes(); + int startSeq = ranges.getStartSeq(); + int endSeq = ranges.getEndSeq(); int transX = 0; int transY = 0; @@ -298,20 +305,20 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (horizontal > 0) // scrollbar pulled right, image to the left { - transX = (er - sr - horizontal) * charWidth; - sr = er - horizontal; + transX = (endRes - startRes - horizontal) * charWidth; + startRes = endRes - horizontal; } else if (horizontal < 0) { - er = sr - horizontal; + endRes = startRes - horizontal; } else if (vertical > 0) // scroll down { - ss = es - vertical; + startSeq = endSeq - vertical; - if (ss < ranges.getStartSeq()) + if (startSeq < ranges.getStartSeq()) { // ie scrolling too fast, more than a page at a time - ss = ranges.getStartSeq(); + startSeq = ranges.getStartSeq(); } else { @@ -320,32 +327,22 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } else if (vertical < 0) { - es = ss - vertical; + endSeq = startSeq - vertical; - if (es > ranges.getEndSeq()) + if (endSeq > ranges.getEndSeq()) { - es = ranges.getEndSeq(); + endSeq = ranges.getEndSeq(); } } gg.translate(transX, transY); - drawPanel(gg, sr, er, ss, es, 0); + drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); gg.translate(-transX, -transY); repaint(); fastpainting = false; } - /** - * Definitions of startx and endx (hopefully): SMJS This is what I'm working - * towards! startx is the first residue (starting at 0) to display. endx is - * the last residue to display (starting at 0). starty is the first sequence - * to display (starting at 0). endy is the last sequence to display (starting - * at 0). NOTE 1: The av limits are set in setFont in this class and in the - * adjustment listener in SeqPanel when the scrollbars move. - */ - - // Set this to false to force a full panel paint @Override public void paintComponent(Graphics g) { @@ -353,69 +350,142 @@ public class SeqCanvas extends JComponent implements ViewportListenerI updateViewport(); - // img is a cached version of the last view we drew - // selectImage will hold any selection we have - // lcimg is a local *copy* of img which we'll draw selectImage on top of - 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( - av.getRanges().getStartRes(), av.getRanges().getEndRes(), + ranges.getStartRes(), ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq()); - if (fastPaint || (getVisibleRect().width != g.getClipBounds().width) - || (getVisibleRect().height != g.getClipBounds().height)) + if ((img != null) && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) + || (getVisibleRect().height != g.getClipBounds().height))) { BufferedImage lcimg = buildLocalImage(selectImage); g.drawImage(lcimg, 0, 0, this); - fastPaint = false; - return; } + 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 + if (img == null || width != img.getWidth() + || height != img.getHeight()) + { + img = setupImage(); + if (img == null) + { + return; + } + gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + } - int width = getWidth(); - int height = getHeight(); + if (av.antiAlias) + { + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } - width -= (width % charWidth); - height -= (height % charHeight); + gg.setColor(Color.white); + gg.fillRect(0, 0, img.getWidth(), img.getHeight()); - if ((width < 1) || (height < 1)) - { - return; - } + if (av.getWrapAlignment()) + { + drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); + } + else + { + drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq(), 0); + } - if (img == null || width != img.getWidth() || height != img.getHeight()) - { - img = setupImage(); - gg = (Graphics2D) img.getGraphics(); - gg.setFont(av.getFont()); - } - if (img == null) - { - return; + // 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); } + } - - 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()) + /** + * Draw an alignment panel for printing + * + * @param g1 + * Graphics object to draw with + * @param startRes + * start residue of print area + * @param endRes + * end residue of print area + * @param startSeq + * start sequence of print area + * @param endSeq + * end sequence of print area + */ + public void drawPanelForPrinting(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq) + { + drawPanel(g1, startRes, endRes, startSeq, endSeq, 0); + + BufferedImage selectImage = drawSelectionGroup(startRes, endRes, + startSeq, endSeq); + if (selectImage != null) { - drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); + ((Graphics2D) g1).setComposite(AlphaComposite + .getInstance(AlphaComposite.SRC_OVER)); + g1.drawImage(selectImage, 0, 0, this); } - else + } + + /** + * Draw a wrapped alignment panel for printing + * + * @param g + * Graphics object to draw with + * @param canvasWidth + * width of drawing area + * @param canvasHeight + * height of drawing area + * @param startRes + * start residue of print area + */ + public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth, + int canvasHeight, int startRes) + { + SequenceGroup group = av.getSelectionGroup(); + + drawWrappedPanel(g, canvasWidth, canvasHeight, startRes); + + if (group != null) { - drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), - ranges.getStartSeq(), ranges.getEndSeq(), 0); + BufferedImage selectImage = null; + try + { + selectImage = new BufferedImage(canvasWidth, canvasHeight, + BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works + } catch (OutOfMemoryError er) + { + System.gc(); + System.err.println("Print image OutOfMemory Error.\n" + er); + new OOMWarning("Creating wrapped alignment image for printing", er); + } + if (selectImage != null) + { + Graphics2D g2 = selectImage.createGraphics(); + setupSelectionGroup(g2, selectImage); + drawWrappedSelection(g2, group, canvasWidth, canvasHeight, + startRes); + + g2.setComposite( + AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); + g.drawImage(selectImage, 0, 0, this); + g2.dispose(); + } } - - BufferedImage lcimg = buildLocalImage(selectImage); - g.drawImage(lcimg, 0, 0, this); } /* @@ -442,12 +512,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return lcimg; } - private void paintSeqGroup() - { - fastPaint = true; - repaint(); - } - + /* + * Set up a buffered image of the correct height and size for the sequence canvas + */ private BufferedImage setupImage() { BufferedImage lcimg = null; @@ -471,7 +538,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { System.gc(); System.err.println( - "Selection Group image OutOfMemory Redraw Error.\n" + er); + "Group image OutOfMemory Redraw Error.\n" + er); new OOMWarning("Creating alignment image for display", er); return null; @@ -481,57 +548,63 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } /** - * DOCUMENT ME! + * Returns the visible width of the canvas in residues, after allowing for + * East or West scales (if shown) * - * @param cwidth - * DOCUMENT ME! + * @param canvasWidth + * the width in pixels (possibly including scales) * - * @return DOCUMENT ME! + * @return */ - public int getWrappedCanvasWidth(int cwidth) + public int getWrappedCanvasWidth(int canvasWidth) { FontMetrics fm = getFontMetrics(av.getFont()); - LABEL_EAST = 0; - LABEL_WEST = 0; + labelWidthEast = 0; + labelWidthWest = 0; if (av.getScaleRightWrapped()) { - LABEL_EAST = fm.stringWidth(getMask()); + labelWidthEast = getLabelWidth(fm); } if (av.getScaleLeftWrapped()) { - LABEL_WEST = fm.stringWidth(getMask()); + labelWidthWest = labelWidthEast > 0 ? labelWidthEast + : getLabelWidth(fm); } - return (cwidth - LABEL_EAST - LABEL_WEST) / charWidth; + return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; } /** - * Generates a string of zeroes. + * 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). * - * @return String + * @param fm + * @return */ - String getMask() + protected int getLabelWidth(FontMetrics fm) { - String mask = "00"; + /* + * find the biggest sequence end position we need to show + * (note this is not necessarily the sequence length) + */ int maxWidth = 0; - int tmp; - for (int i = 0; i < av.getAlignment().getHeight(); i++) + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) { - tmp = av.getAlignment().getSequenceAt(i).getEnd(); - if (tmp > maxWidth) - { - maxWidth = tmp; - } + maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd()); } + int length = 2; for (int i = maxWidth; i > 0; i /= 10) { - mask += "0"; + length++; } - return mask; + + return fm.stringWidth(ZEROS.substring(0, length)); } /** @@ -546,26 +619,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * @param startRes * DOCUMENT ME! */ - public void drawWrappedPanel(Graphics g, int canvasWidth, + private void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) { updateViewport(); AlignmentI al = av.getAlignment(); - FontMetrics fm = getFontMetrics(av.getFont()); - - LABEL_EAST = 0; - LABEL_WEST = 0; - - if (av.getScaleRightWrapped()) + int labelWidth = 0; + if (av.getScaleRightWrapped() || av.getScaleLeftWrapped()) { - LABEL_EAST = fm.stringWidth(getMask()); + FontMetrics fm = getFontMetrics(av.getFont()); + labelWidth = getLabelWidth(fm); } - if (av.getScaleLeftWrapped()) - { - LABEL_WEST = fm.stringWidth(getMask()); - } + labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0; + labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; int hgap = charHeight; if (av.getScaleAboveWrapped()) @@ -573,7 +641,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI hgap += charHeight; } - int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth; + int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; int cHeight = av.getAlignment().getHeight() * charHeight; av.setWrappedWidth(cWidth); @@ -590,6 +658,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI .findColumnPosition(maxwidth); } + int annotationHeight = getAnnotationHeight(); + while ((ypos <= canvasHeight) && (startRes < maxwidth)) { endx = startRes + cWidth - 1; @@ -609,12 +679,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.getScaleRightWrapped()) { - g.translate(canvasWidth - LABEL_EAST, 0); + g.translate(canvasWidth - labelWidthEast, 0); drawEastScale(g, startRes, endx, ypos); - g.translate(-(canvasWidth - LABEL_EAST), 0); + g.translate(-(canvasWidth - labelWidthEast), 0); } - g.translate(LABEL_WEST, 0); + g.translate(labelWidthWest, 0); if (av.getScaleAboveWrapped()) { @@ -637,10 +707,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } gg.fillPolygon( - new int[] { res * charWidth - charHeight / 4, + new int[] + { res * charWidth - charHeight / 4, res * charWidth + charHeight / 4, res * charWidth }, - new int[] { ypos - (charHeight / 2), - ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 }, + new int[] + { ypos - (charHeight / 2), ypos - (charHeight / 2), + ypos - (charHeight / 2) + 8 }, 3); } @@ -670,34 +742,40 @@ public class SeqCanvas extends JComponent implements ViewportListenerI annotations = new AnnotationPanel(av); } - annotations.renderer.drawComponent(annotations, av, g, -1, - startRes, endx + 1); + annotations.renderer.drawComponent(annotations, av, g, -1, startRes, + endx + 1); g.translate(0, -cHeight - ypos - 3); } g.setClip(clip); - g.translate(-LABEL_WEST, 0); + g.translate(-labelWidthWest, 0); - ypos += cHeight + getAnnotationHeight() + hgap; + ypos += cHeight + annotationHeight + hgap; startRes += cWidth; } } - public void drawWrappedSelection(Graphics2D g, SequenceGroup group, + /* + * Draw a selection group over a wrapped alignment + */ + private void drawWrappedSelection(Graphics2D g, SequenceGroup group, int canvasWidth, int canvasHeight, int startRes) { + // height gap above each panel int hgap = charHeight; if (av.getScaleAboveWrapped()) { hgap += charHeight; } - int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth; + int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) + / charWidth; int cHeight = av.getAlignment().getHeight() * charHeight; + int startx = startRes; int endx; - int ypos = hgap; + int ypos = hgap; // vertical offset int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) @@ -706,31 +784,34 @@ public class SeqCanvas extends JComponent implements ViewportListenerI .findColumnPosition(maxwidth); } - while ((ypos <= canvasHeight) && (startRes < maxwidth)) + // chop the wrapped alignment extent up into panel-sized blocks and treat + // each block as if it were a block from an unwrapped alignment + while ((ypos <= canvasHeight) && (startx < maxwidth)) { - endx = startRes + cWidth - 1; + // set end value to be start + width, or maxwidth, whichever is smaller + endx = startx + cWidth - 1; if (endx > maxwidth) { endx = maxwidth; } - g.translate(LABEL_WEST, 0); + g.translate(labelWidthWest, 0); - drawUnwrappedSelection(g, group, startRes, endx, 0, + drawUnwrappedSelection(g, group, startx, endx, 0, av.getAlignment().getHeight() - 1, ypos); - g.translate(-LABEL_WEST, 0); + g.translate(-labelWidthWest, 0); + // update vertical offset ypos += cHeight + getAnnotationHeight() + hgap; - startRes += cWidth; + // update horizontal offset + startx += cWidth; } } - AnnotationPanel annotations; - int getAnnotationHeight() { if (!av.isShowAnnotation()) @@ -747,32 +828,36 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } /** - * DOCUMENT ME! + * Draws the visible region of the alignment on the graphics context. If there + * are hidden column markers in the visible region, then each sub-region + * between the markers is drawn separately, followed by the hidden column + * marker. * * @param g1 - * DOCUMENT ME! + * Graphics object to draw with * @param startRes - * DOCUMENT ME! + * offset of the first column in the visible region (0..) * @param endRes - * DOCUMENT ME! + * offset of the last column in the visible region (0..) * @param startSeq - * DOCUMENT ME! + * offset of the first sequence in the visible region (0..) * @param endSeq - * DOCUMENT ME! - * @param offset - * DOCUMENT ME! + * offset of the last sequence in the visible region (0..) + * @param yOffset + * vertical offset at which to draw (for wrapped alignments) */ - public void drawPanel(Graphics g1, int startRes, int endRes, - int startSeq, int endSeq, int offset) + public void drawPanel(Graphics g1, final int startRes, final int endRes, + final int startSeq, final int endSeq, final int yOffset) { updateViewport(); if (!av.hasHiddenColumns()) { - draw(g1, startRes, endRes, startSeq, endSeq, offset); + draw(g1, startRes, endRes, startSeq, endSeq, yOffset); } else { int screenY = 0; + final int screenYMax = endRes - startRes; int blockStart = startRes; int blockEnd = endRes; @@ -788,38 +873,47 @@ public class SeqCanvas extends JComponent implements ViewportListenerI continue; } - blockEnd = hideStart - 1; + /* + * draw up to just before the next hidden region, or the end of + * the visible region, whichever comes first + */ + blockEnd = Math.min(hideStart - 1, blockStart + screenYMax + - screenY); g1.translate(screenY * charWidth, 0); - draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); - if (av.getShowHiddenMarkers()) + /* + * draw the downline of the hidden column marker (ScalePanel draws the + * triangle on top) if we reached it + */ + if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1) { g1.setColor(Color.blue); g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1, - 0 + offset, (blockEnd - blockStart + 1) * charWidth - 1, - (endSeq - startSeq + 1) * charHeight + offset); + 0 + yOffset, (blockEnd - blockStart + 1) * charWidth - 1, + (endSeq - startSeq + 1) * charHeight + yOffset); } g1.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; blockStart = hideEnd + 1; - if (screenY > (endRes - startRes)) + if (screenY > screenYMax) { // already rendered last block return; } } - if (screenY <= (endRes - startRes)) + if (screenY <= screenYMax) { // remaining visible region to render - blockEnd = blockStart + (endRes - startRes) - screenY; + blockEnd = blockStart + screenYMax - screenY; g1.translate(screenY * charWidth, 0); - draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); g1.translate(-screenY * charWidth, 0); } @@ -827,11 +921,26 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } + /** + * Draws a region of the visible alignment + * + * @param g1 + * @param startRes + * offset of the first column in the visible region (0..) + * @param endRes + * offset of the last column in the visible region (0..) + * @param startSeq + * offset of the first sequence in the visible region (0..) + * @param endSeq + * offset of the last sequence in the visible region (0..) + * @param yOffset + * vertical offset at which to draw (for wrapped alignments) + */ private void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset) { g.setFont(av.getFont()); - sr.prepare(g, av.isRenderGaps()); + seqRdr.prepare(g, av.isRenderGaps()); SequenceI nextSeq; @@ -846,26 +955,28 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // empty continue; } - sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), + seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), startRes, endRes, offset + ((i - startSeq) * charHeight)); if (av.isShowSequenceFeatures()) { - fr.drawSequence(g, nextSeq, startRes, endRes, offset - + ((i - startSeq) * charHeight), false); + fr.drawSequence(g, nextSeq, startRes, endRes, + offset + ((i - startSeq) * charHeight), false); } - // / Highlight search Results once all sequences have been drawn - // //////////////////////////////////////////////////////// + /* + * highlight search Results once sequence has been drawn + */ if (av.hasSearchResults()) { - int[] visibleResults = av.getSearchResults().getResults(nextSeq, + SearchResultsI searchResults = av.getSearchResults(); + int[] visibleResults = searchResults.getResults(nextSeq, startRes, endRes); if (visibleResults != null) { for (int r = 0; r < visibleResults.length; r += 2) { - sr.drawHighlightedText(nextSeq, visibleResults[r], + seqRdr.drawHighlightedText(nextSeq, visibleResults[r], visibleResults[r + 1], (visibleResults[r] - startRes) * charWidth, offset + ((i - startSeq) * charHeight)); @@ -876,7 +987,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.cursorMode && cursorY == i && cursorX >= startRes && cursorX <= endRes) { - sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth, + seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth, offset + ((i - startSeq) * charHeight)); } } @@ -899,12 +1010,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // /////////////////////////////////// SequenceGroup group = null; - - int sx = -1; - int sy = -1; - int ex = -1; int groupIndex = -1; - int visWidth = (endRes - startRes + 1) * charWidth; if (av.getAlignment().getGroups().size() > 0) { @@ -914,149 +1020,13 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (group != null) { + g.setStroke(new BasicStroke()); + g.setColor(group.getOutlineColour()); + do { - int oldY = -1; - int i = 0; - boolean inGroup = false; - int top = -1; - int bottom = -1; - - for (i = startSeq; i <= endSeq; i++) - { - // position of start residue of group relative to startRes, in pixels - sx = (group.getStartRes() - startRes) * charWidth; - sy = offset + ((i - startSeq) * charHeight); - // width of group in pixels - ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - - 1; - - if (sx + ex < 0 || sx > visWidth) - { - continue; - } - - if ((sx <= (endRes - startRes) * charWidth) - && group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i))) - { - if ((bottom == -1) - && !group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i + 1))) - { - bottom = sy + charHeight; - } - - if (!inGroup) - { - if (((top == -1) && (i == 0)) - || !group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i - 1))) - { - top = sy; - } - - oldY = sy; - inGroup = true; - - g.setStroke(new BasicStroke()); - g.setColor(group.getOutlineColour()); - } - } - else - { - if (inGroup) - { - // 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 + ex < visWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } - - if (sx < 0) - { - ex += sx; - sx = 0; - } - - if (sx + ex > visWidth) - { - ex = visWidth; - } - else if (sx + ex >= (endRes - startRes + 1) * charWidth) - { - ex = (endRes - startRes + 1) * charWidth; - } - - // draw horizontal line at top of group - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } - - // draw horizontal line at bottom of group - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } - - inGroup = false; - } - } - } - - if (inGroup) - { - sy = offset + ((i - startSeq) * charHeight); - if (sx >= 0 && sx < visWidth) - { - g.drawLine(sx, oldY, sx, sy); - } - - if (sx + ex < visWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } - - if (sx < 0) - { - ex += sx; - sx = 0; - } - - if (sx + ex > visWidth) - { - ex = visWidth; - } - else if (sx + ex >= (endRes - startRes + 1) * charWidth) - { - ex = (endRes - startRes + 1) * charWidth; - } - - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } - - if (bottom != -1) - { - g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); - bottom = -1; - } - - inGroup = false; - } + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, + endSeq, offset); groupIndex++; @@ -1099,16 +1069,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // set up drawing colour Graphics2D g = (Graphics2D) selectionImage.getGraphics(); - // g.translate(LABEL_WEST, 0); - // set background to transparent - g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); - g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight()); - 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); + setupSelectionGroup(g, selectionImage); if (!av.getWrapAlignment()) { @@ -1125,12 +1087,40 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return selectionImage; } + /* + * Set up graphics for selection group + */ + private void setupSelectionGroup(Graphics2D g, + BufferedImage selectionImage) + { + // set background to transparent + g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); + g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight()); + + // set up foreground to draw red dashed line + g.setComposite(AlphaComposite.Src); + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f)); + g.setColor(Color.RED); + } + + /* + * Draw a selection group over an unwrapped alignment + * @param g graphics object to draw with + * @param group selection group + * @param startRes start residue of area to draw + * @param endRes end residue of area to draw + * @param startSeq start sequence of area to draw + * @param endSeq end sequence of area to draw + * @param offset vertical offset (used when called from wrapped alignment code) + */ private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group, int startRes, int endRes, int startSeq, int endSeq, int offset) { if (!av.hasHiddenColumns()) { - drawSelectionGroupPart(g, group, startRes, endRes, startSeq, endSeq, + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, offset); } else @@ -1155,7 +1145,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI blockEnd = hideStart - 1; g.translate(screenY * charWidth, 0); - drawSelectionGroupPart(g, group, + drawPartialGroupOutline(g, group, blockStart, blockEnd, startSeq, endSeq, offset); g.translate(-screenY * charWidth, 0); @@ -1174,7 +1164,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // remaining visible region to render blockEnd = blockStart + (endRes - startRes) - screenY; g.translate(screenY * charWidth, 0); - drawSelectionGroupPart(g, group, + drawPartialGroupOutline(g, group, blockStart, blockEnd, startSeq, endSeq, offset); g.translate(-screenY * charWidth, 0); @@ -1185,7 +1175,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI /* * Draw the selection group as a separate image and overlay */ - private void drawSelectionGroupPart(Graphics2D g, SequenceGroup group, + private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group, int startRes, int endRes, int startSeq, int endSeq, int verticalOffset) { @@ -1263,6 +1253,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI sx = 0; } + // 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; @@ -1330,20 +1322,171 @@ public class SeqCanvas extends JComponent implements ViewportListenerI inGroup = false; } } + + /** + * Highlights search results in the visible region by rendering as white text + * on a black background. Any previous highlighting is removed. Answers true + * if any highlight was left on the visible alignment (so status bar should be + * set to match), else false. + *
+ * Currently fastPaint is not implemented for wrapped alignments. If a wrapped
+ * alignment had to be scrolled to show the highlighted region, then it should
+ * be fully redrawn, otherwise a fast paint can be performed. This argument
+ * could be removed if fast paint of scrolled wrapped alignment is coded in
+ * future (JAL-2609).
+ *
+ * @param results
+ * @param noFastPaint
+ * @return
+ */
+ public boolean highlightSearchResults(SearchResultsI results,
+ boolean noFastPaint)
+ {
+ if (fastpainting)
+ {
+ 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
+ * and add new ones
+ */
+ SearchResultsI previous = av.getSearchResults();
+ av.setSearchResults(results);
+ boolean redrawn = false;
+ boolean drawn = false;
+ if (wrapped)
+ {
+ redrawn = drawMappedPositionsWrapped(previous);
+ drawn = drawMappedPositionsWrapped(results);
+ redrawn |= drawn;
+ }
+ else
+ {
+ redrawn = drawMappedPositions(previous);
+ drawn = drawMappedPositions(results);
+ redrawn |= drawn;
+ }
+
+ /*
+ * if highlights were either removed or added, repaint
+ */
+ if (redrawn)
+ {
+ repaint();
+ }
+
+ /*
+ * return true only if highlights were added
+ */
+ return drawn;
+
+ } finally
+ {
+ fastpainting = false;
+ }
+ }
/**
- * DOCUMENT ME!
+ * Redraws the minimal rectangle in the visible region (if any) that includes
+ * mapped positions of the given search results. Whether or not positions are
+ * highlighted depends on the SearchResults set on the Viewport. This allows
+ * this method to be called to either clear or set highlighting. Answers true
+ * if any positions were drawn (in which case a repaint is still required),
+ * else false.
*
* @param results
- * DOCUMENT ME!
+ * @return
*/
- public void highlightSearchResults(SearchResultsI results)
+ protected boolean drawMappedPositions(SearchResultsI results)
{
- img = null;
+ if (results == null)
+ {
+ return false;
+ }
- av.setSearchResults(results);
+ /*
+ * calculate the minimal rectangle to redraw that
+ * includes both new and existing search results
+ */
+ int firstSeq = Integer.MAX_VALUE;
+ int lastSeq = -1;
+ int firstCol = Integer.MAX_VALUE;
+ int lastCol = -1;
+ boolean matchFound = false;
- repaint();
+ ViewportRanges ranges = av.getRanges();
+ int firstVisibleColumn = ranges.getStartRes();
+ int lastVisibleColumn = ranges.getEndRes();
+ AlignmentI alignment = av.getAlignment();
+ if (av.hasHiddenColumns())
+ {
+ firstVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(firstVisibleColumn);
+ lastVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(lastVisibleColumn);
+ }
+
+ for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
+ .getEndSeq(); seqNo++)
+ {
+ SequenceI seq = alignment.getSequenceAt(seqNo);
+
+ int[] visibleResults = results.getResults(seq, firstVisibleColumn,
+ lastVisibleColumn);
+ if (visibleResults != null)
+ {
+ for (int i = 0; i < visibleResults.length - 1; i += 2)
+ {
+ int firstMatchedColumn = visibleResults[i];
+ int lastMatchedColumn = visibleResults[i + 1];
+ if (firstMatchedColumn <= lastVisibleColumn
+ && lastMatchedColumn >= firstVisibleColumn)
+ {
+ /*
+ * found a search results match in the visible region -
+ * remember the first and last sequence matched, and the first
+ * and last visible columns in the matched positions
+ */
+ matchFound = true;
+ firstSeq = Math.min(firstSeq, seqNo);
+ lastSeq = Math.max(lastSeq, seqNo);
+ firstMatchedColumn = Math.max(firstMatchedColumn,
+ firstVisibleColumn);
+ lastMatchedColumn = Math.min(lastMatchedColumn,
+ lastVisibleColumn);
+ firstCol = Math.min(firstCol, firstMatchedColumn);
+ lastCol = Math.max(lastCol, lastMatchedColumn);
+ }
+ }
+ }
+ }
+
+ if (matchFound)
+ {
+ if (av.hasHiddenColumns())
+ {
+ firstCol = alignment.getHiddenColumns()
+ .findColumnPosition(firstCol);
+ lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol);
+ }
+ int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
+ int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
+ gg.translate(transX, transY);
+ drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0);
+ gg.translate(-transX, -transY);
+ }
+
+ return matchFound;
}
@Override
@@ -1353,7 +1496,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
{
- paintSeqGroup();
+ fastPaint = true;
+ repaint();
}
else if (av.getWrapAlignment())
{
@@ -1399,4 +1543,143 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
}
}
}
+
+ /**
+ * 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
+ * this method to be called either to clear highlights (passing the previous
+ * search results), or to draw new highlights.
+ *
+ * @param results
+ * @return
+ */
+ protected boolean drawMappedPositionsWrapped(SearchResultsI results)
+ {
+ if (results == null)
+ {
+ return false;
+ }
+
+ boolean matchFound = false;
+
+ int wrappedWidth = av.getWrappedWidth();
+ int wrappedHeight = getRepeatHeightWrapped();
+
+ ViewportRanges ranges = av.getRanges();
+ int canvasHeight = getHeight();
+ int repeats = canvasHeight / wrappedHeight;
+ if (canvasHeight / wrappedHeight > 0)
+ {
+ repeats++;
+ }
+
+ int firstVisibleColumn = ranges.getStartRes();
+ int lastVisibleColumn = ranges.getStartRes() + repeats
+ * ranges.getViewportWidth() - 1;
+
+ AlignmentI alignment = av.getAlignment();
+ if (av.hasHiddenColumns())
+ {
+ firstVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(firstVisibleColumn);
+ lastVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(lastVisibleColumn);
+ }
+
+ int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
+
+ for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
+ .getEndSeq(); seqNo++)
+ {
+ SequenceI seq = alignment.getSequenceAt(seqNo);
+
+ int[] visibleResults = results.getResults(seq, firstVisibleColumn,
+ lastVisibleColumn);
+ if (visibleResults != null)
+ {
+ for (int i = 0; i < visibleResults.length - 1; i += 2)
+ {
+ int firstMatchedColumn = visibleResults[i];
+ int lastMatchedColumn = visibleResults[i + 1];
+ if (firstMatchedColumn <= lastVisibleColumn
+ && lastMatchedColumn >= firstVisibleColumn)
+ {
+ /*
+ * found a search results match in the visible region
+ */
+ firstMatchedColumn = Math.max(firstMatchedColumn,
+ firstVisibleColumn);
+ lastMatchedColumn = Math.min(lastMatchedColumn,
+ lastVisibleColumn);
+
+ /*
+ * draw each mapped position separately (as contiguous positions may
+ * wrap across lines)
+ */
+ for (int mappedPos = firstMatchedColumn; mappedPos <= lastMatchedColumn; mappedPos++)
+ {
+ int displayColumn = mappedPos;
+ if (av.hasHiddenColumns())
+ {
+ displayColumn = alignment.getHiddenColumns()
+ .findColumnPosition(displayColumn);
+ }
+
+ /*
+ * transX: offset from left edge of canvas to residue position
+ */
+ int transX = labelWidthWest
+ + ((displayColumn - ranges.getStartRes()) % wrappedWidth)
+ * av.getCharWidth();
+
+ /*
+ * transY: offset from top edge of canvas to residue position
+ */
+ int transY = gapHeight;
+ transY += (displayColumn - ranges.getStartRes())
+ / wrappedWidth * wrappedHeight;
+ transY += (seqNo - ranges.getStartSeq()) * av.getCharHeight();
+
+ /*
+ * yOffset is from graphics origin to start of visible region
+ */
+ int yOffset = 0;// (displayColumn / wrappedWidth) * wrappedHeight;
+ if (transY < getHeight())
+ {
+ matchFound = true;
+ gg.translate(transX, transY);
+ drawPanel(gg, displayColumn, displayColumn, seqNo, seqNo,
+ yOffset);
+ gg.translate(-transX, -transY);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ 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;
+ }
}