X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=795faffd3f0705eec5c09b2395c4bf2bf31e2804;hb=3cdfc5e46776dbb8127f0a5b64df3545b988e3d9;hp=1753a64139aafbb7fc7b2ca940d319e03c873fbb;hpb=72ac4a5ecabebe8c96feb08c32e5ce1adccc7d46;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 1753a64..795faff 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -32,7 +32,6 @@ import jalview.util.Comparison; import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; -import java.awt.AlphaComposite; import java.awt.BasicStroke; import java.awt.BorderLayout; import java.awt.Color; @@ -56,6 +55,11 @@ import javax.swing.JComponent; */ public class SeqCanvas extends JComponent implements ViewportListenerI { + /* + * pixels gap between sequences and annotations when in wrapped mode + */ + static final int SEQS_ANNOTATION_GAP = 3; + private static final String ZEROS = "0000000000"; final FeatureRenderer fr; @@ -83,9 +87,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI private int labelWidthWest; // label left width in pixels if shown - private int wrappedSpaceAboveAlignment; // gap between widths + int wrappedSpaceAboveAlignment; // gap between widths - private int wrappedRepeatHeightPx; // height in pixels of wrapped width + int wrappedRepeatHeightPx; // height in pixels of wrapped width private int wrappedVisibleWidths; // number of wrapped widths displayed @@ -365,31 +369,27 @@ public class SeqCanvas extends JComponent implements ViewportListenerI width -= (width % charWidth); height -= (height % charHeight); - // selectImage is the selection group outline image - BufferedImage selectImage = drawSelectionGroup( - ranges.getStartRes(), ranges.getEndRes(), - ranges.getStartSeq(), ranges.getEndSeq()); - if ((img != null) && (fastPaint || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g.getClipBounds().height))) { - BufferedImage lcimg = buildLocalImage(selectImage); - g.drawImage(lcimg, 0, 0, this); + g.drawImage(img, 0, 0, this); + + drawSelectionGroup((Graphics2D) g, ranges.getStartRes(), + ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq()); + fastPaint = false; } - else if ((width > 0) && (height > 0)) + else if (width > 0 && height > 0) { - // img is a cached version of the last view we drew, if any - // if we have no img or the size has changed, make a new one + /* + * img is a cached version of the last view we drew, if any + * if we have no img or the size has changed, make a new one + */ if (img == null || width != img.getWidth() || height != img.getHeight()) { - img = setupImage(); - if (img == null) - { - return; - } + img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); gg = (Graphics2D) img.getGraphics(); gg.setFont(av.getFont()); } @@ -412,11 +412,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq(), 0); } - - // lcimg is a local *copy* of img which we'll draw selectImage on top of - BufferedImage lcimg = buildLocalImage(selectImage); - g.drawImage(lcimg, 0, 0, this); + drawSelectionGroup(gg, ranges.getStartRes(), + ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq()); + + g.drawImage(img, 0, 0, this); } if (av.cursorMode) @@ -445,14 +445,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { drawPanel(g1, startRes, endRes, startSeq, endSeq, 0); - BufferedImage selectImage = drawSelectionGroup(startRes, endRes, + drawSelectionGroup((Graphics2D) g1, startRes, endRes, startSeq, endSeq); - if (selectImage != null) - { - ((Graphics2D) g1).setComposite(AlphaComposite - .getInstance(AlphaComposite.SRC_OVER)); - g1.drawImage(selectImage, 0, 0, this); - } } /** @@ -470,104 +464,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth, int canvasHeight, int startRes) { - SequenceGroup group = av.getSelectionGroup(); - drawWrappedPanel(g, canvasWidth, canvasHeight, startRes); + SequenceGroup group = av.getSelectionGroup(); if (group != null) { - BufferedImage selectImage = null; - try - { - selectImage = new BufferedImage(canvasWidth, canvasHeight, - BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works - } catch (OutOfMemoryError er) - { - System.gc(); - System.err.println("Print image OutOfMemory Error.\n" + er); - new OOMWarning("Creating wrapped alignment image for printing", er); - } - if (selectImage != null) - { - Graphics2D g2 = selectImage.createGraphics(); - setupSelectionGroup(g2, selectImage); - drawWrappedSelection(g2, group, canvasWidth, canvasHeight, + drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight, startRes); - - g2.setComposite( - AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); - g.drawImage(selectImage, 0, 0, this); - g2.dispose(); - } } } - /* - * Make a local image by combining the cached image img - * with any selection - */ - private BufferedImage buildLocalImage(BufferedImage selectImage) - { - // clone the cached image - BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), - img.getType()); - - // BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), - // img.getType()); - Graphics2D g2d = lcimg.createGraphics(); - g2d.drawImage(img, 0, 0, null); - - // overlay selection group on lcimg - if (selectImage != null) - { - g2d.setComposite( - AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); - g2d.drawImage(selectImage, 0, 0, this); - } - - g2d.dispose(); - - return lcimg; - } - - /* - * Set up a buffered image of the correct height and size for the sequence canvas - */ - private BufferedImage setupImage() - { - BufferedImage lcimg = null; - - int charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - - int width = getWidth(); - int height = getHeight(); - - width -= (width % charWidth); - height -= (height % charHeight); - - if ((width < 1) || (height < 1)) - { - return null; - } - - try - { - lcimg = new BufferedImage(width, height, - BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works - } catch (OutOfMemoryError er) - { - System.gc(); - System.err.println( - "Group image OutOfMemory Redraw Error.\n" + er); - new OOMWarning("Creating alignment image for display", er); - - return null; - } - - return lcimg; - } - /** * Returns the visible width of the canvas in residues, after allowing for * East or West scales (if shown) @@ -594,6 +500,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0; + System.out.println(Thread.currentThread().getName() + + " " + System.currentTimeMillis() + " labelWidthWest: " + + labelWidthWest); return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth; } @@ -658,7 +567,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI calculateWrappedGeometry(canvasWidth, canvasHeight); /* - * draw one width at a time (excluding any scales or annotation shown), + * draw one width at a time (excluding any scales shown), * until we have run out of either alignment or vertical space available */ int ypos = wrappedSpaceAboveAlignment; @@ -705,14 +614,22 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * (av.getScaleAboveWrapped() ? 2 : 1); /* - * height in pixels of the wrapped widths + * compute height in pixels of the wrapped widths + * - start with space above plus sequences */ wrappedRepeatHeightPx = wrappedSpaceAboveAlignment; - // add sequences wrappedRepeatHeightPx += av.getAlignment().getHeight() * charHeight; - // add annotations panel height if shown - wrappedRepeatHeightPx += getAnnotationHeight(); + + /* + * add annotations panel height if shown + * also gap between sequences and annotations + */ + if (av.isShowAnnotation()) + { + wrappedRepeatHeightPx += getAnnotationHeight(); + wrappedRepeatHeightPx += SEQS_ANNOTATION_GAP; // 3px + } /* * number of visible widths (the last one may be part height), @@ -756,8 +673,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * @param endColumn * @param canvasHeight */ - protected void drawWrappedWidth(Graphics g, int ypos, int startColumn, - int endColumn, int canvasHeight) + protected void drawWrappedWidth(Graphics g, final int ypos, + final int startColumn, final int endColumn, + final int canvasHeight) { ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); @@ -804,7 +722,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.isShowAnnotation()) { - g.translate(0, cHeight + ypos + 3); + final int yShift = cHeight + ypos + SEQS_ANNOTATION_GAP; + g.translate(0, yShift); if (annotations == null) { annotations = new AnnotationPanel(av); @@ -812,7 +731,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI annotations.renderer.drawComponent(annotations, av, g, -1, startColumn, endx + 1); - g.translate(0, -cHeight - ypos - 3); + g.translate(0, -yShift); } g.setClip(clip); g.translate(-xOffset, 0); @@ -954,16 +873,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int startx = startRes; int endx; int ypos = hgap; // vertical offset - int maxwidth = av.getAlignment().getWidth(); - - if (av.hasHiddenColumns()) - { - maxwidth = av.getAlignment().getHiddenColumns() - .absoluteToVisibleColumn(maxwidth); - } + int maxwidth = av.getAlignment().getVisibleWidth(); // chop the wrapped alignment extent up into panel-sized blocks and treat // each block as if it were a block from an unwrapped alignment + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f)); + g.setColor(Color.RED); while ((ypos <= canvasHeight) && (startx < maxwidth)) { // set end value to be start + width, or maxwidth, whichever is smaller @@ -988,6 +905,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // update horizontal offset startx += cWidth; } + g.setStroke(new BasicStroke()); } int getAnnotationHeight() @@ -1154,14 +1072,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } + /** + * Draws the outlines of any groups defined on the alignment (excluding the + * current selection group, if any) + * + * @param g1 + * @param startRes + * @param endRes + * @param startSeq + * @param endSeq + * @param offset + */ void drawGroupsBoundaries(Graphics g1, int startRes, int endRes, int startSeq, int endSeq, int offset) { Graphics2D g = (Graphics2D) g1; - // - // /////////////////////////////////// - // Now outline any areas if necessary - // /////////////////////////////////// SequenceGroup group = null; int groupIndex = -1; @@ -1174,18 +1099,15 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (group != null) { - g.setStroke(new BasicStroke()); - g.setColor(group.getOutlineColour()); - do { + g.setColor(group.getOutlineColour()); + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, offset); groupIndex++; - g.setStroke(new BasicStroke()); - if (groupIndex >= av.getAlignment().getGroups().size()) { break; @@ -1199,33 +1121,28 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } - - /* - * Draw the selection group as a separate image and overlay + /** + * Draws the outline of the current selection group (if any) + * + * @param g + * @param startRes + * @param endRes + * @param startSeq + * @param endSeq */ - private BufferedImage drawSelectionGroup(int startRes, int endRes, + private void drawSelectionGroup(Graphics2D g, int startRes, int endRes, int startSeq, int endSeq) { - // get a new image of the correct size - BufferedImage selectionImage = setupImage(); - - if (selectionImage == null) - { - return null; - } - SequenceGroup group = av.getSelectionGroup(); if (group == null) { - // nothing to draw - return null; + return; } - // set up drawing colour - Graphics2D g = (Graphics2D) selectionImage.getGraphics(); - - setupSelectionGroup(g, selectionImage); - + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f)); + g.setColor(Color.RED); if (!av.getWrapAlignment()) { drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq, @@ -1236,9 +1153,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawWrappedSelection(g, group, getWidth(), getHeight(), av.getRanges().getStartRes()); } - - g.dispose(); - return selectionImage; + g.setStroke(new BasicStroke()); } /** @@ -1329,33 +1244,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } - /* - * 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) + * + * @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) @@ -1393,8 +1298,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } - /* - * Draw the selection group as a separate image and overlay + /** + * Draws part of a selection group outline + * + * @param g + * @param group + * @param startRes + * @param endRes + * @param startSeq + * @param endSeq + * @param verticalOffset */ private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group, int startRes, int endRes, int startSeq, int endSeq, @@ -1745,7 +1658,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } ViewportRanges vpRanges = av.getRanges(); - int range = vpRanges.getEndRes() - vpRanges.getStartRes(); + int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1; if (scrollX > range) { scrollX = range; @@ -1814,10 +1727,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { ViewportRanges ranges = av.getRanges(); - if (Math.abs(scrollX) > ranges.getViewportWidth()) + if (Math.abs(scrollX) >= ranges.getViewportWidth()) { /* - * shift of more than one view width is + * shift of one view width or more is * overcomplicated to handle in this method */ fastPaint = false; @@ -2008,10 +1921,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI while (y >= 0) { + /* + * shift 'widthToCopy' residues by 'positions' places to the right + */ gg.copyArea(copyFromLeftStart, y, widthToCopy, heightToCopy, positions * charWidth, 0); if (y > 0) { + /* + * copy 'positions' residue from the row above (right hand end) + * to this row's left hand end + */ gg.copyArea(copyFromRightStart, y - wrappedRepeatHeightPx, positions * charWidth, heightToCopy, -widthToCopy, wrappedRepeatHeightPx);