X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=bd2862a3b8affddc0858182222080e86f83011fd;hb=875193c17720b95fa13a38703b1dd63949e12ca9;hp=8ad094f4bf88b2c15d1df4911ebd65712c1f9dd1;hpb=2677eb3d3744f321876e25eeaa70dfa8fde70184;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 8ad094f..bd2862a 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -31,7 +31,7 @@ import jalview.util.Comparison; import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; -import java.awt.AlphaComposite; // ok +import java.awt.AlphaComposite; import java.awt.BasicStroke; import java.awt.BorderLayout; import java.awt.Color; @@ -47,63 +47,58 @@ 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"; + private static final String ZEROS = "0000000000"; final FeatureRenderer fr; - final SequenceRenderer seqRdr; //ok - BufferedImage img; - Graphics2D gg; - - int imgWidth; - - int imgHeight; - AlignViewport av; - boolean fastPaint = false; - - boolean fastpainting = false; - int cursorX = 0; int cursorY = 0; + private final SequenceRenderer seqRdr; + + private boolean fastPaint = false; + + private boolean fastpainting = false; + private AnnotationPanel annotations; /* * measurements for drawing a wrapped alignment */ - int labelWidthWest; // label left width in pixels if shown - private int labelWidthEast; // label right width in pixels if shown + private int labelWidthWest; // label left width in pixels if shown + private int wrappedSpaceAboveAlignment; // gap between widths private int wrappedRepeatHeightPx; // height in pixels of wrapped width private int wrappedVisibleWidths; // number of wrapped widths displayed + private Graphics2D gg; + /** * Creates a new SeqCanvas object. * - * @param av - * DOCUMENT ME! + * @param ap */ public SeqCanvas(AlignmentPanel ap) { this.av = ap.av; fr = new FeatureRenderer(ap); - seqRdr = new SequenceRenderer(av); //ok + seqRdr = new SequenceRenderer(av); setLayout(new BorderLayout()); PaintRefresher.Register(this, av.getSequenceSetId()); setBackground(Color.white); @@ -113,7 +108,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public SequenceRenderer getSequenceRenderer() { - return seqRdr; //ok + return seqRdr; } public FeatureRenderer getFeatureRenderer() @@ -190,19 +185,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * @param left * if true, scale is left of residues, if false, scale is right */ - void drawVerticalScale(Graphics g, int startx, int endx, int ypos, - boolean left) + void drawVerticalScale(Graphics g, final int startx, final int endx, + final int ypos, final boolean left) { int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); - ypos += charHeight; + int yPos = ypos + charHeight; + int startX = startx; + int endX = endx; if (av.hasHiddenColumns()) { HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); - startx = hiddenColumns.adjustForHiddenColumns(startx); - endx = hiddenColumns.adjustForHiddenColumns(endx); + startX = hiddenColumns.adjustForHiddenColumns(startx); + endX = hiddenColumns.adjustForHiddenColumns(endx); } FontMetrics fm = getFontMetrics(av.getFont()); @@ -214,9 +211,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * 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 index = left ? startX : endX; int value = -1; - while (index >= startx && index <= endx) + while (index >= startX && index <= endX) { if (!Comparison.isGap(seq.getCharAt(index))) { @@ -237,29 +234,28 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * white fill the space for the scale */ g.setColor(Color.white); - int y = (ypos + (i * charHeight)) - (charHeight / 5); + 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) { - /* - * draw scale value, right justified, with half a character width - * separation from the sequence data + * 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 justify = fm.stringWidth(valueAsString) + charWidth; - int xpos = left ? labelWidthWest - justify + charWidth / 2 - : labelWidthEast - justify + charWidth / 2; + int labelLength = fm.stringWidth(valueAsString); + int xOffset = labelSpace - labelLength; g.setColor(Color.black); - g.drawString(valueAsString, xpos, y); + g.drawString(valueAsString, xOffset, y); } } } - //ok /** * 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 @@ -280,7 +276,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ public void fastPaint(int horizontal, int vertical) { - if (fastpainting || gg == null || img == null) //ok + if (fastpainting || gg == null || img == null) { return; } @@ -346,9 +342,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI fastpainting = false; } } - //ok - //ok @Override public void paintComponent(Graphics g) { @@ -370,11 +364,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI ranges.getStartRes(), ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq()); + BufferedImage cursorImage = drawCursor(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); + BufferedImage lcimg = buildLocalImage(selectImage, cursorImage); g.drawImage(lcimg, 0, 0, this); fastPaint = false; } @@ -414,11 +411,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } // lcimg is a local *copy* of img which we'll draw selectImage on top of - BufferedImage lcimg = buildLocalImage(selectImage); + BufferedImage lcimg = buildLocalImage(selectImage, cursorImage); g.drawImage(lcimg, 0, 0, this); } } -//ok /** * Draw an alignment panel for printing @@ -500,7 +496,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * Make a local image by combining the cached image img * with any selection */ - private BufferedImage buildLocalImage(BufferedImage selectImage) + private BufferedImage buildLocalImage(BufferedImage selectImage, + BufferedImage cursorImage) { // clone the cached image BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), @@ -515,6 +512,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); g2d.drawImage(selectImage, 0, 0, this); } + // overlay cursor on lcimg + if (cursorImage != null) + { + g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); + g2d.drawImage(cursorImage, 0, 0, this); + } g2d.dispose(); return lcimg; @@ -527,6 +530,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { BufferedImage lcimg = null; + int charWidth = av.getCharWidth(); + int charHeight = av.getCharHeight(); + int width = getWidth(); int height = getHeight(); @@ -570,27 +576,26 @@ public class SeqCanvas extends JComponent implements ViewportListenerI FontMetrics fm = getFontMetrics(av.getFont()); - labelWidthEast = 0; - labelWidthWest = 0; - - 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 @@ -608,13 +613,13 @@ 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(); } /** @@ -679,19 +684,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI protected int calculateWrappedGeometry(int canvasWidth, int canvasHeight) { int charHeight = av.getCharHeight(); - int charWidth = av.getCharWidth(); - - /* - * width of labels in pixels left and right (if shown) - */ - int labelWidth = 0; - if (av.getScaleRightWrapped() || av.getScaleLeftWrapped()) - { - FontMetrics fm = getFontMetrics(av.getFont()); - labelWidth = getLabelWidth(fm); - } - labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0; - labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; /* * vertical space in pixels between wrapped widths of alignment @@ -711,19 +703,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI wrappedRepeatHeightPx += getAnnotationHeight(); /* - * number of residue columns we can show in each row; - * this is just canvas width less scale left and right (if shown), - * as a whole multiple of character widths - */ - int wrappedWidthInResidues = (canvasWidth - labelWidthEast - - labelWidthWest) / charWidth; - - /* * number of visible widths (the last one may be part height), * ensuring a part height includes at least one sequence */ ViewportRanges ranges = av.getRanges(); - int xMax = ranges.getVisibleAlignmentWidth(); wrappedVisibleWidths = canvasHeight / wrappedRepeatHeightPx; int remainder = canvasHeight % wrappedRepeatHeightPx; if (remainder >= (wrappedSpaceAboveAlignment + charHeight)) @@ -732,10 +715,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } /* + * compute width in residues; this also sets East and West label widths + */ + int wrappedWidthInResidues = getWrappedCanvasWidth(canvasWidth); + + /* * limit visibleWidths to not exceed width of alignment */ - int maxWidths = (xMax - ranges.getStartRes()) / wrappedWidthInResidues; - if (xMax % wrappedWidthInResidues > 0) + int xMax = ranges.getVisibleAlignmentWidth(); + int startToEnd = xMax - ranges.getStartRes(); + int maxWidths = startToEnd / wrappedWidthInResidues; + if (startToEnd % wrappedWidthInResidues > 0) { maxWidths++; } @@ -757,9 +747,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI protected void drawWrappedWidth(Graphics g, int ypos, int startColumn, int endColumn, int canvasHeight) { - int charHeight = av.getCharHeight(); - int charWidth = av.getCharWidth(); - ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); @@ -770,9 +757,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * 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; + * charWidth; g.translate(xOffset, 0); // When printing we have an extra clipped region, @@ -785,8 +773,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } else { - g.setClip(0, (int) clip.getBounds().getY(), viewportWidth * charWidth, - (int) clip.getBounds().getHeight()); + g.setClip(0, (int) clip.getBounds().getY(), + viewportWidth * charWidth, (int) clip.getBounds().getHeight()); } /* @@ -800,7 +788,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1, ypos); - int cHeight = av.getAlignment().getHeight() * charHeight; + int cHeight = av.getAlignment().getHeight() * av.getCharHeight(); if (av.isShowAnnotation()) { @@ -825,7 +813,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * @param g * @param startColumn */ - protected void drawWrappedDecorators(Graphics g, int startColumn) + protected void drawWrappedDecorators(Graphics g, final int startColumn) { int charWidth = av.getCharWidth(); @@ -837,20 +825,22 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int viewportWidth = ranges.getViewportWidth(); int maxWidth = ranges.getVisibleAlignmentWidth(); int widthsDrawn = 0; + int startCol = startColumn; + while (widthsDrawn < wrappedVisibleWidths) { - int endColumn = Math.min(maxWidth, startColumn + viewportWidth - 1); + int endColumn = Math.min(maxWidth, startCol + viewportWidth - 1); if (av.getScaleLeftWrapped()) { - drawVerticalScale(g, startColumn, endColumn - 1, ypos, true); + drawVerticalScale(g, startCol, endColumn - 1, ypos, true); } if (av.getScaleRightWrapped()) { int x = labelWidthWest + viewportWidth * charWidth; g.translate(x, 0); - drawVerticalScale(g, startColumn, endColumn, ypos, false); + drawVerticalScale(g, startCol, endColumn, ypos, false); g.translate(-x, 0); } @@ -858,33 +848,37 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * 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.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, startColumn, endColumn, ypos); + drawNorthScale(g, startCol, endColumn, ypos); } if (av.hasHiddenColumns() && av.getShowHiddenMarkers()) { - drawHiddenColumnMarkers(g, ypos, startColumn, endColumn); + drawHiddenColumnMarkers(g, ypos, startCol, endColumn); } g.translate(-labelWidthWest, 0); ypos += wrappedRepeatHeightPx; - startColumn += viewportWidth; + startCol += viewportWidth; widthsDrawn++; } } /** + * Draws markers (triangles) above hidden column positions between startColumn + * and endColumn. + * * @param g * @param ypos * @param startColumn @@ -903,7 +897,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { int res = pos - startColumn; - if (res < 0 || res > endColumn - startColumn) + if (res < 0 || res > endColumn - startColumn + 1) { continue; } @@ -928,6 +922,9 @@ 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()) @@ -1155,12 +1152,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } - if (av.cursorMode && cursorY == i && cursorX >= startRes + /* if (av.cursorMode && cursorY == i && cursorX >= startRes && cursorX <= endRes) { seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth, offset + ((i - startSeq) * charHeight)); - } + }*/ } if (av.getSelectionGroup() != null @@ -1258,6 +1255,60 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return selectionImage; } + /** + * 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 BufferedImage drawCursor(int startRes, int endRes, int startSeq, + int endSeq) + { + // define our cursor image + BufferedImage cursorImage = null; + + if (av.cursorMode && cursorY >= startSeq && cursorY <= endSeq + && cursorX >= startRes && cursorX <= endRes) + { + // get a new image of the correct size + cursorImage = setupImage(); + Graphics2D g = (Graphics2D) cursorImage.getGraphics(); + + // get the character the cursor is drawn at + SequenceI seq = av.getAlignment().getSequenceAt(cursorY); + char s = seq.getCharAt(cursorX); + + int offset = 0; + if (av.getWrapAlignment()) + { + // work out the correct offset for the cursor + offset = wrappedSpaceAboveAlignment; + int currentWidth = 0; + while ((currentWidth < wrappedVisibleWidths) + && (currentWidth < cursorX)) + { + offset += wrappedRepeatHeightPx; + currentWidth++; + } + } + + seqRdr.drawCursor(g, s, + (cursorX - startRes) * av.getCharWidth(), + offset + ((cursorY - startSeq) * av.getCharHeight())); + g.dispose(); + } + + return cursorImage; + } + /* * Set up graphics for selection group */ @@ -1671,48 +1722,50 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { fastPaint = true; repaint(); + return; } - else if (eventName.equals(ViewportRanges.STARTRES)) + + int scrollX = 0; + if (eventName.equals(ViewportRanges.STARTRES)) { - 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.getViewportWidth(); + if (scrollX > range) { - // 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; - } + 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. - - // scroll - startres and endres both change - if (av.getWrapAlignment()) - { - fastPaintWrapped(scrollX); - } - else - { - fastPaint(scrollX, 0); - } + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + + // scroll - startres and endres both change + if (eventName.equals(ViewportRanges.STARTRES)) + { + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); } - else if (eventName.equals(ViewportRanges.STARTSEQ)) + else { - // scroll - fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + fastPaint(scrollX, 0); } } + else if (eventName.equals(ViewportRanges.STARTSEQ)) + { + // scroll + fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + } } /** @@ -2085,4 +2138,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return matchFound; } + + /** + * Answers the width in pixels of the left scale labels (0 if not shown) + * + * @return + */ + int getLabelWidthWest() + { + return labelWidthWest; + } }