X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=785b71deff6bfc22de5e63722ca75a136179fadf;hb=f5be602fd7f0560f29d96748145aef5fa590beda;hp=226e0df95259ade61897b744b6c472f40e6ad66d;hpb=5edb685cf52a607834a82c10cb4dd9c139e31dde;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 226e0df..785b71d 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -21,11 +21,15 @@ package jalview.gui; import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.renderer.ScaleRenderer; import jalview.renderer.ScaleRenderer.ScaleMark; +import jalview.util.Comparison; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; import java.awt.BasicStroke; import java.awt.BorderLayout; @@ -36,6 +40,7 @@ import java.awt.Graphics2D; import java.awt.RenderingHints; import java.awt.Shape; import java.awt.image.BufferedImage; +import java.beans.PropertyChangeEvent; import java.util.List; import javax.swing.JComponent; @@ -46,8 +51,10 @@ import javax.swing.JComponent; * @author $author$ * @version $Revision$ */ -public class SeqCanvas extends JComponent +public class SeqCanvas extends JComponent implements ViewportListenerI { + private static String ZEROS = "0000000000"; + final FeatureRenderer fr; final SequenceRenderer sr; @@ -64,9 +71,11 @@ public class SeqCanvas extends JComponent boolean fastPaint = false; - int LABEL_WEST; + boolean fastpainting = false; + + int labelWidthWest; - int LABEL_EAST; + int labelWidthEast; int cursorX = 0; @@ -87,6 +96,8 @@ public class SeqCanvas extends JComponent setLayout(new BorderLayout()); PaintRefresher.Register(this, av.getSequenceSetId()); setBackground(Color.white); + + av.getRanges().addPropertyChangeListener(this); } public SequenceRenderer getSequenceRenderer() @@ -108,22 +119,25 @@ public class SeqCanvas extends JComponent } /** - * 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)) + List marks = new ScaleRenderer().calculateMarks(av, startx, + endx); + for (ScaleMark mark : marks) { int mpos = mark.column; // (i - startx - 1) if (mpos < 0) @@ -138,134 +152,115 @@ public class SeqCanvas extends JComponent { 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! * @param startx - * DOCUMENT ME! + * first column of wrapped width (0.. excluding any hidden columns) * @param endx - * DOCUMENT ME! + * last column of wrapped width (0.. excluding any hidden columns) * @param ypos - * DOCUMENT ME! + * vertical offset at which to begin the scale + * @param left + * if true, scale is left of residues, if false, scale is right */ - void drawWestScale(Graphics g, int startx, int endx, int ypos) + void drawVerticalScale(Graphics g, int startx, int endx, int ypos, + boolean left) { - FontMetrics fm = getFontMetrics(av.getFont()); ypos += charHeight; if (av.hasHiddenColumns()) { - startx = av.getColumnSelection().adjustForHiddenColumns(startx); - endx = av.getColumnSelection().adjustForHiddenColumns(endx); - } - - int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns()) - { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); + startx = hiddenColumns.adjustForHiddenColumns(startx); + endx = hiddenColumns.adjustForHiddenColumns(endx); } + FontMetrics fm = getFontMetrics(av.getFont()); - // WEST SCALE for (int i = 0; i < av.getAlignment().getHeight(); i++) { SequenceI seq = av.getAlignment().getSequenceAt(i); - int index = startx; - int value = -1; - while (index < endx) + /* + * find sequence position of first non-gapped position - + * to the right if scale left, to the left if scale right + */ + int index = left ? startx : endx; + int value = -1; + while (index >= startx && index <= endx) { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + if (!Comparison.isGap(seq.getCharAt(index))) + { + value = seq.findPosition(index); + break; + } + if (left) { index++; - - continue; } - - value = av.getAlignment().getSequenceAt(i).findPosition(index); - - break; - } - - if (value != -1) - { - int x = LABEL_WEST - 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.getColumnSelection().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; } if (value != -1) { - g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight)) - - (charHeight / 5)); + /* + * white fill the space for the scale + */ + g.setColor(Color.white); + int y = (ypos + (i * charHeight)) - (charHeight / 5); + y -= charHeight; // fillRect: origin is top left of rectangle + int xpos = left ? 0 : getWidth() - labelWidthEast; + g.fillRect(xpos, y, left ? labelWidthWest : labelWidthEast, + charHeight + 1); + y += charHeight; // drawString: origin is bottom left of text + + /* + * draw scale value, right justified, with half a character width + * separation from the sequence data + */ + String valueAsString = String.valueOf(value); + int justify = fm.stringWidth(valueAsString) + charWidth; + xpos = left ? labelWidthWest - justify + charWidth / 2 + : getWidth() - justify - charWidth / 2; + + g.setColor(Color.black); + g.drawString(valueAsString, xpos, y); } } } - boolean fastpainting = false; - /** - * 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) { @@ -276,33 +271,34 @@ public class SeqCanvas extends JComponent fastpainting = true; fastPaint = true; updateViewport(); - gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth, - imgHeight, -horizontal * charWidth, -vertical * charHeight); - int sr = av.getStartRes(); - int er = av.getEndRes(); - int ss = av.getStartSeq(); - int es = av.getEndSeq(); + 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, imgWidth, + imgHeight, -horizontal * charWidth, -vertical * charHeight); + if (horizontal > 0) // scrollbar pulled right, image to the left { - er++; - transX = (er - sr - horizontal) * charWidth; - sr = er - horizontal; + transX = (endRes - startRes - horizontal) * charWidth; + startRes = endRes - horizontal; } else if (horizontal < 0) { - er = sr - horizontal - 1; + endRes = startRes - horizontal; } else if (vertical > 0) // scroll down { - ss = es - vertical; + startSeq = endSeq - vertical; - if (ss < av.getStartSeq()) + if (startSeq < ranges.getStartSeq()) { // ie scrolling too fast, more than a page at a time - ss = av.getStartSeq(); + startSeq = ranges.getStartSeq(); } else { @@ -311,32 +307,22 @@ public class SeqCanvas extends JComponent } else if (vertical < 0) { - es = ss - vertical; + endSeq = startSeq - vertical; - if (es > av.getEndSeq()) + if (endSeq > ranges.getEndSeq()) { - es = av.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) { @@ -395,14 +381,15 @@ public class SeqCanvas extends JComponent gg.setColor(Color.white); gg.fillRect(0, 0, imgWidth, imgHeight); + ViewportRanges ranges = av.getRanges(); if (av.getWrapAlignment()) { - drawWrappedPanel(gg, getWidth(), getHeight(), av.getStartRes()); + drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); } else { - drawPanel(gg, av.getStartRes(), av.getEndRes(), av.getStartSeq(), - av.getEndSeq(), 0); + drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq(), 0); } g.drawImage(lcimg, 0, 0, this); @@ -410,88 +397,90 @@ public class SeqCanvas extends JComponent } /** - * 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)); } /** - * 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! + * available height in pixels * @param startRes - * DOCUMENT ME! + * the first visible column (0...) of the alignment to draw */ public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) { updateViewport(); - AlignmentI al = av.getAlignment(); - - FontMetrics fm = getFontMetrics(av.getFont()); - - 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()) @@ -499,113 +488,153 @@ public class SeqCanvas extends JComponent hgap += charHeight; } - int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth; - int cHeight = av.getAlignment().getHeight() * charHeight; + int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; av.setWrappedWidth(cWidth); - av.setEndRes(av.getStartRes() + cWidth); + av.getRanges().setViewportStartAndWidth(startRes, cWidth); - int endx; int ypos = hgap; - int maxwidth = av.getAlignment().getWidth() - 1; + int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth); } - while ((ypos <= canvasHeight) && (startRes < maxwidth)) - { - endx = startRes + cWidth - 1; + int annotationHeight = getAnnotationHeight(); + int sequencesHeight = av.getAlignment().getHeight() * charHeight; - if (endx > maxwidth) - { - endx = maxwidth; - } + /* + * draw one width at a time (including any scales or annotation shown), + * until we have run out of alignment or vertical space available + * (stop if not enough room left for at least one sequence) + */ + int yposMax = canvasHeight;// - hgap - charHeight + 1; + while ((ypos <= yposMax) && (startRes < maxwidth)) + { + drawWrappedWidth(g, startRes, canvasHeight, cWidth, maxwidth, ypos); - g.setFont(av.getFont()); - g.setColor(Color.black); + ypos += sequencesHeight + annotationHeight + hgap; - if (av.getScaleLeftWrapped()) - { - drawWestScale(g, startRes, endx, ypos); - } + startRes += cWidth; + } + } - if (av.getScaleRightWrapped()) - { - g.translate(canvasWidth - LABEL_EAST, 0); - drawEastScale(g, startRes, endx, ypos); - g.translate(-(canvasWidth - LABEL_EAST), 0); - } + /** + * Draws one width of a wrapped alignment, including scales left, right or + * above, and annnotations, if shown + * + * @param g + * @param startRes + * @param canvasHeight + * @param canvasWidth + * @param maxWidth + * @param ypos + */ + protected void drawWrappedWidth(Graphics g, int startRes, + int canvasHeight, int canvasWidth, int maxWidth, int ypos) + { + int endx; + endx = startRes + canvasWidth - 1; - g.translate(LABEL_WEST, 0); + if (endx > maxWidth) + { + endx = maxWidth; + } - if (av.getScaleAboveWrapped()) - { - drawNorthScale(g, startRes, endx, ypos); - } + g.setFont(av.getFont()); + g.setColor(Color.black); - if (av.hasHiddenColumns() && av.getShowHiddenMarkers()) - { - g.setColor(Color.blue); - int res; - for (int i = 0; i < av.getColumnSelection().getHiddenColumns() - .size(); i++) - { - res = av.getColumnSelection().findHiddenRegionPosition(i) - - startRes; + if (av.getScaleLeftWrapped()) + { + drawVerticalScale(g, startRes, endx, ypos, true); + } - if (res < 0 || res > endx - startRes) - { - continue; - } + if (av.getScaleRightWrapped()) + { + drawVerticalScale(g, startRes, endx, ypos, false); + } - 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); + drawWrappedRegion(g, startRes, endx, canvasHeight, canvasWidth, ypos); + } - } - } + /** + * Draws columns of a wrapped alignment from startRes to endRes, including + * scale above and annotations if shown, but not scale left or right. + * + * @param g + * @param startRes + * @param endRes + * @param canvasHeight + * @param canvasWidth + * @param ypos + */ + protected void drawWrappedRegion(Graphics g, int startRes, int endRes, + int canvasHeight, int canvasWidth, int ypos) + { + g.translate(labelWidthWest, 0); - // When printing we have an extra clipped region, - // the Printable page which we need to account for here - Shape clip = g.getClip(); + if (av.getScaleAboveWrapped()) + { + drawNorthScale(g, startRes, endRes, ypos); + } - if (clip == null) - { - g.setClip(0, 0, cWidth * charWidth, canvasHeight); - } - else + // todo can we let drawPanel() handle this? + if (av.hasHiddenColumns() && av.getShowHiddenMarkers()) + { + g.setColor(Color.blue); + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + List positions = hidden.findHiddenRegionPositions(); + for (int pos : positions) { - g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth, - (int) clip.getBounds().getHeight()); - } - - drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); + int res = pos - startRes; - if (av.isShowAnnotation()) - { - g.translate(0, cHeight + ypos + 3); - if (annotations == null) + if (res < 0 || res > endRes - startRes) { - annotations = new AnnotationPanel(av); + continue; } - annotations.renderer.drawComponent(annotations, av, g, -1, - startRes, endx + 1); - g.translate(0, -cHeight - ypos - 3); + 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); } - g.setClip(clip); - g.translate(-LABEL_WEST, 0); + } - ypos += cHeight + getAnnotationHeight() + hgap; + // When printing we have an extra clipped region, + // the Printable page which we need to account for here + Shape clip = g.getClip(); - startRes += cWidth; + if (clip == null) + { + g.setClip(0, 0, canvasWidth * charWidth, canvasHeight); + } + else + { + g.setClip(0, (int) clip.getBounds().getY(), canvasWidth * charWidth, + (int) clip.getBounds().getHeight()); } + + drawPanel(g, startRes, endRes, 0, av.getAlignment().getHeight() - 1, ypos); + + int cHeight = av.getAlignment().getHeight() * charHeight; + + if (av.isShowAnnotation()) + { + g.translate(0, cHeight + ypos + 3); + if (annotations == null) + { + annotations = new AnnotationPanel(av); + } + + annotations.renderer.drawComponent(annotations, av, g, -1, startRes, + endRes + 1); + g.translate(0, -cHeight - ypos - 3); + } + g.setClip(clip); + g.translate(-labelWidthWest, 0); } AnnotationPanel annotations; @@ -626,38 +655,41 @@ public class SeqCanvas extends JComponent } /** - * 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! + * the graphics context, positioned at the first residue to be drawn * @param startRes - * DOCUMENT ME! + * offset of the first column to draw (0..) * @param endRes - * DOCUMENT ME! + * offset of the last column to draw (0..) * @param startSeq - * DOCUMENT ME! + * offset of the first sequence to draw (0..) * @param endSeq - * DOCUMENT ME! - * @param offset - * DOCUMENT ME! + * offset of the last sequence to draw (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 { - List regions = av.getColumnSelection().getHiddenColumns(); - int screenY = 0; + final int screenYMax = endRes - startRes; int blockStart = startRes; int blockEnd = endRes; - for (int[] region : regions) + for (int[] region : av.getAlignment().getHiddenColumns() + .getHiddenColumnsCopy()) { int hideStart = region[0]; int hideEnd = region[1]; @@ -668,38 +700,47 @@ public class SeqCanvas extends JComponent 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) * 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); } @@ -707,8 +748,21 @@ public class SeqCanvas extends JComponent } - // int startRes, int endRes, int startSeq, int endSeq, int x, int y, - // int x1, int x2, int y1, int y2, int startx, int starty, + /** + * 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) { @@ -734,14 +788,16 @@ public class SeqCanvas extends JComponent if (av.isShowSequenceFeatures()) { fr.drawSequence(g, nextSeq, startRes, endRes, offset - + ((i - startSeq) * charHeight)); + + ((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) { @@ -959,17 +1015,694 @@ public class SeqCanvas extends JComponent } /** - * DOCUMENT ME! + * 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 - * DOCUMENT ME! + * @param noFastPaint + * @return */ - public void highlightSearchResults(SearchResultsI results) + public boolean highlightSearchResults(SearchResultsI results, + boolean noFastPaint) { - img = null; + 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; + } - av.setSearchResults(results); + /* + * if highlights were either removed or added, repaint + */ + if (redrawn) + { + repaint(); + } + + /* + * return true only if highlights were added + */ + return drawn; + + } finally + { + fastpainting = false; + } + } + + /** + * 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 + * @return + */ + protected boolean drawMappedPositions(SearchResultsI results) + { + if (results == null) + { + return false; + } + + /* + * 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; + + 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 + public void propertyChange(PropertyChangeEvent evt) + { + String eventName = evt.getPropertyName(); + + // if (av.getWrapAlignment()) + // { + // if (eventName.equals(ViewportRanges.STARTRES)) + // { + // repaint(); + // } + // } + // else + { + int scrollX = 0; + 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; + } + } + + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + if (eventName.equals(ViewportRanges.STARTRES)) + { + // scroll - startres and endres both change + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); + // fastPaintWrapped(scrollX > 0 ? 1 : -1); // to debug: 1 at a time + } + else + { + fastPaint(scrollX, 0); + } + } + else if (eventName.equals(ViewportRanges.STARTSEQ)) + { + fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + } + } + } + + /** + * 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) + { + if (Math.abs(scrollX) > av.getRanges().getViewportWidth()) + { + /* + * shift of more than one view width is + * too complicated to handle in this method + */ + fastPaint = false; + repaint(); + return; + } + + fastPaint = true; + + /* + * relocate the regions of the alignment that are still visible + */ + shiftWrappedAlignment(-scrollX); + + /* + * add new columns (scale above, sequence, annotation) + * - at top left if scrollX < 0 + * - at right of last two widths if scrollX > 0 + * also West scale top left or East scale bottom right if shown + */ + if (scrollX < 0) + { + fastPaintWrappedAddLeft(-scrollX); + } + else + { + fastPaintWrappedAddRight(scrollX); + } repaint(); } + + /** + * Draws the specified number of columns at the 'end' (bottom right) of a + * wrapped alignment view, including scale above and right and annotations if + * shown. 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; + } + + /* + * how many widths are visible? we will be adding + * columns to the last visible width, right hand end + */ + int repeatHeight = getRepeatHeightWrapped(); + int canvasHeight = getHeight(); + int visibleWidths = canvasHeight / repeatHeight; + int remainder = canvasHeight % repeatHeight; + int hgap = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); + boolean lastWidthPartHeight = false; + if (remainder >= (hgap + charHeight)) + { + visibleWidths++; + lastWidthPartHeight = true; + } + + /* + * limit visible widths to max widths of alignment + */ + ViewportRanges ranges = av.getRanges(); + int visibleAlignmentWidth = ranges.getVisibleAlignmentWidth(); + int viewportWidth = ranges.getViewportWidth(); + int maxWidths = visibleAlignmentWidth / viewportWidth; + if (visibleAlignmentWidth % viewportWidth > 0) + { + maxWidths++; + } + visibleWidths = Math.min(visibleWidths, maxWidths); + int widthInColumns = (getWidth() - labelWidthEast - labelWidthWest) + / charWidth; + + /** + * draw full height alignment in the second last row, last columns, if the + * last row was not full height + */ + if (lastWidthPartHeight) + { + int widthsAbove = visibleWidths - 2; + int ypos = repeatHeight * widthsAbove + hgap; + int endRes = ranges.getEndRes(); + endRes += widthsAbove * viewportWidth; + int startRes = endRes - columns; + int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth) + * charWidth; + gg.translate(xOffset, 0); + + /* + * white fill first to erase annotations + */ + gg.setColor(Color.white); + gg.fillRect(labelWidthWest, ypos, + (endRes - startRes + 1) * charWidth, repeatHeight); + + drawWrappedRegion(gg, startRes, endRes, canvasHeight, widthInColumns, + ypos); + gg.translate(-xOffset, 0); + } + + /* + * y-offset for drawing is height of widths above, + * plus one gap row + */ + int widthsAbove = visibleWidths - 1; + int ypos = repeatHeight * widthsAbove + hgap; + int endRes = ranges.getEndRes(); + endRes += widthsAbove * viewportWidth; + endRes = Math.min(endRes, ranges.getVisibleAlignmentWidth()); + + /* + * draw one extra column than strictly needed - this is a (harmless) + * fudge to ensure scale marks get drawn (JAL-2636) + */ + int startRes = endRes - columns; + + /* + * x-offset is x-start modulo viewport start residue; + * doesn't include label West (offset is applied in drawWrappedRegion) + */ + + int leftEndColumn = ranges.getStartRes() + widthsAbove + * ranges.getViewportWidth(); + // startRes = Math.max(startRes - 0, leftEndColumn); + int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth) + * charWidth; + gg.translate(xOffset, 0); + + /* + * white fill the region to be drawn including scale left or above; + * extend to right hand margin so as to erase scale above when + * scrolling right beyond end of alignment + */ + gg.setColor(Color.white); + int width = getWidth() - labelWidthWest - xOffset; + gg.fillRect(labelWidthWest, ypos - hgap, width, repeatHeight); + + gg.setFont(av.getFont()); + gg.setColor(Color.black); + + drawWrappedRegion(gg, startRes, endRes, canvasHeight, widthInColumns, + ypos); + gg.translate(-xOffset, 0); + + /* + * draw scale right if shown, passing in the start/end columns + * for the whole line, not just the last few columns + */ + if (av.getScaleRightWrapped()) + { + drawVerticalScale(gg, leftEndColumn, endRes, ypos, false); + } + } + + /** + * Draws the specified number of columns at the 'start' (top left) of a + * wrapped alignment view, including scale above and left and annotations if + * shown + * + * @param columns + */ + protected void fastPaintWrappedAddLeft(int columns) + { + int startRes = av.getRanges().getStartRes(); + + /* + * draw one extra column than strictly needed - this is a (harmless) + * fudge to ensure scale marks get drawn (JAL-2636) + */ + int endx = startRes + columns; + int ypos = 0; + + /* + * white fill the region to be drawn including scale left or above + */ + gg.setColor(Color.white); + int height = getRepeatHeightWrapped(); + gg.fillRect(0, ypos, labelWidthWest + columns * charWidth, height); + ypos += charHeight * (av.getScaleAboveWrapped() ? 2 : 1); + + gg.setFont(av.getFont()); + gg.setColor(Color.black); + + if (av.getScaleLeftWrapped()) + { + drawVerticalScale(gg, startRes, endx, ypos, true); + } + + int cWidth = (getWidth() - labelWidthEast - labelWidthWest) / charWidth; + + drawWrappedRegion(gg, startRes, endx, getHeight(), cWidth, ypos); + } + + /** + * Shifts the visible alignment by the specified number of columns - left if + * negative, right if positive. Includes scale above, left or right and + * annotations (if shown). Does not draw newly visible columns. + * + * @param positions + */ + protected void shiftWrappedAlignment(int positions) + { + if (positions == 0) + { + return; + } + + int repeatHeight = getRepeatHeightWrapped(); + ViewportRanges ranges = av.getRanges(); + int xMax = ranges.getVisibleAlignmentWidth(); + int widthToCopy = (ranges.getViewportWidth() - Math.abs(positions)) + * charWidth; + int canvasHeight = getHeight(); + int visibleWidths = canvasHeight / repeatHeight; + if (canvasHeight % repeatHeight > 0) + { + visibleWidths++; + } + int viewportWidth = ranges.getViewportWidth(); + int hgap = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); + + int remainder = canvasHeight % repeatHeight; + if (remainder >= (hgap + charHeight)) + { + visibleWidths++; + } + + 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 + */ + int xpos = ranges.getStartRes() + (visibleWidths - 1) * viewportWidth; + + /* + * get y-offset of last wrapped width + */ + int y = canvasHeight / repeatHeight * repeatHeight; + int copyFromLeftStart = labelWidthWest; + int copyFromRightStart = copyFromLeftStart + widthToCopy; + + while (y >= 0) + { + gg.copyArea(copyFromLeftStart, y, widthToCopy, repeatHeight, + positions * charWidth, 0); + if (y > 0) + { + gg.copyArea(copyFromRightStart, y - repeatHeight, positions + * charWidth, repeatHeight, -widthToCopy, repeatHeight); + } + + if (av.getScaleLeftWrapped()) + { + drawVerticalScale(gg, xpos, xpos + viewportWidth - 1, y + hgap, + true); + } + if (av.getScaleRightWrapped()) + { + drawVerticalScale(gg, xpos, xpos + viewportWidth - 1, y + hgap, + false); + } + + y -= repeatHeight; + xpos -= viewportWidth; + } + } + 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 = ranges.getStartRes(); + int y = 0; + int copyFromRightStart = labelWidthWest - positions * charWidth; + + while (y < canvasHeight) + { + gg.copyArea(copyFromRightStart, y, widthToCopy, repeatHeight, + positions * charWidth, 0); + if (y + repeatHeight < canvasHeight - repeatHeight + && (xpos + viewportWidth <= xMax)) + { + gg.copyArea(labelWidthWest, y + repeatHeight, -positions + * charWidth, repeatHeight, widthToCopy, -repeatHeight); + } + + if (av.getScaleLeftWrapped()) + { + drawVerticalScale(gg, xpos, xpos + viewportWidth, y + hgap, true); + } + if (av.getScaleRightWrapped()) + { + drawVerticalScale(gg, xpos, xpos + viewportWidth, y + hgap, false); + } + + y += repeatHeight; + xpos += viewportWidth; + } + } + } + + /** + * Redraws any positions in the search results in the visible region of a + * wrapped alignment. Any highlights are drawn depending on the search results + * set on the Viewport, not the results argument. This allows + * 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; + } }