import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
+import java.awt.AlphaComposite;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
final FeatureRenderer fr;
- final SequenceRenderer sr;
+ final SequenceRenderer seqRdr;
BufferedImage img;
Graphics2D gg;
- int imgWidth;
-
- int imgHeight;
-
AlignViewport av;
boolean fastPaint = false;
int cursorY = 0;
+ int charHeight = 0;
+
+ int charWidth = 0;
+
+ boolean fastpainting = false;
+
+ AnnotationPanel annotations;
+
/**
* Creates a new SeqCanvas object.
*
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);
public SequenceRenderer getSequenceRenderer()
{
- return sr;
+ return seqRdr;
}
public FeatureRenderer getFeatureRenderer()
return fr;
}
- int charHeight = 0, charWidth = 0;
-
private void updateViewport()
{
charHeight = av.getCharHeight();
}
}
- boolean fastpainting = false;
/**
* need to make this thread safe move alignment rendering in response to
int transX = 0;
int transY = 0;
- gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
- imgHeight, -horizontal * charWidth, -vertical * charHeight);
+ gg.copyArea(horizontal * charWidth, vertical * charHeight,
+ img.getWidth(), img.getHeight(), -horizontal * charWidth,
+ -vertical * charHeight);
if (horizontal > 0) // scrollbar pulled right, image to the left
{
}
else
{
- transY = imgHeight - ((vertical + 1) * charHeight);
+ transY = img.getHeight() - ((vertical + 1) * charHeight);
}
}
else if (vertical < 0)
@Override
public void paintComponent(Graphics g)
{
- updateViewport();
- BufferedImage lcimg = img; // take reference since other threads may null
- // img and call later.
super.paintComponent(g);
- if (lcimg != null && (fastPaint
+ updateViewport();
+
+ ViewportRanges ranges = av.getRanges();
+
+ int width = getWidth();
+ int height = getHeight();
+
+ width -= (width % charWidth);
+ height -= (height % charHeight);
+
+ // selectImage is the selection group outline image
+ BufferedImage selectImage = drawSelectionGroup(
+ ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq());
+
+ if ((img != null) && (fastPaint
|| (getVisibleRect().width != g.getClipBounds().width)
|| (getVisibleRect().height != g.getClipBounds().height)))
{
+ BufferedImage lcimg = buildLocalImage(selectImage);
g.drawImage(lcimg, 0, 0, this);
fastPaint = false;
- return;
}
-
- // this draws the whole of the alignment
- imgWidth = getWidth();
- imgHeight = getHeight();
-
- imgWidth -= (imgWidth % charWidth);
- imgHeight -= (imgHeight % charHeight);
-
- if ((imgWidth < 1) || (imgHeight < 1))
- {
- return;
- }
-
- if (lcimg == null || imgWidth != lcimg.getWidth()
- || imgHeight != lcimg.getHeight())
+ else if ((width > 0) && (height > 0))
{
- try
+ // 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())
{
- lcimg = img = new BufferedImage(imgWidth, imgHeight,
- BufferedImage.TYPE_INT_RGB);
+ img = setupImage();
+ if (img == null)
+ {
+ return;
+ }
gg = (Graphics2D) img.getGraphics();
gg.setFont(av.getFont());
- } catch (OutOfMemoryError er)
+ }
+
+ if (av.antiAlias)
{
- System.gc();
- System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
- new OOMWarning("Creating alignment image for display", er);
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
- return;
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, img.getWidth(), img.getHeight());
+
+ if (av.getWrapAlignment())
+ {
+ drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
}
+ else
+ {
+ 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);
}
+ }
+
+ /**
+ * 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 drawPanelForPrint(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+ BufferedImage selectImage = drawSelectionGroup(startRes, endRes,
+ startSeq, endSeq);
+ drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
+ ((Graphics2D) g1).setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g1.drawImage(selectImage, 0, 0, this);
+ }
- if (av.antiAlias)
+ /*
+ * Make a local image by combining the cached image img
+ * with any selection
+ */
+ private BufferedImage buildLocalImage(BufferedImage selectImage)
+ {
+ // clone the cached image
+ BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+ img.getType());
+ Graphics2D g2d = lcimg.createGraphics();
+ g2d.drawImage(img, 0, 0, null);
+
+ // overlay selection group on lcimg
+ if (selectImage != null)
{
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ g2d.setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g2d.drawImage(selectImage, 0, 0, this);
}
+ g2d.dispose();
- gg.setColor(Color.white);
- gg.fillRect(0, 0, imgWidth, imgHeight);
+ return lcimg;
+ }
- ViewportRanges ranges = av.getRanges();
- if (av.getWrapAlignment())
+ /*
+ * Set up a buffered image of the correct height and size for the sequence canvas
+ */
+ private BufferedImage setupImage()
+ {
+ BufferedImage lcimg = null;
+
+ int width = getWidth();
+ int height = getHeight();
+
+ width -= (width % charWidth);
+ height -= (height % charHeight);
+
+ if ((width < 1) || (height < 1))
{
- drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+ return null;
}
- else
+
+ try
{
- drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
- ranges.getStartSeq(), ranges.getEndSeq(), 0);
- }
+ 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);
- g.drawImage(lcimg, 0, 0, this);
+ return null;
+ }
+ return lcimg;
}
/**
}
}
- AnnotationPanel annotations;
+ /*
+ * 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 - labelWidthEast - labelWidthWest)
+ / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
+
+ int startx = startRes;
+ int endx;
+ int ypos = hgap; // vertical offset
+ int maxwidth = av.getAlignment().getWidth();
+
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(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))
+ {
+ // set end value to be start + width, or maxwidth, whichever is smaller
+ endx = startx + cWidth - 1;
+
+ if (endx > maxwidth)
+ {
+ endx = maxwidth;
+ }
+
+ g.translate(labelWidthWest, 0);
+
+ drawUnwrappedSelection(g, group, startx, endx, 0,
+ av.getAlignment().getHeight() - 1,
+ ypos);
+
+ g.translate(-labelWidthWest, 0);
+
+ // update vertical offset
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ // update horizontal offset
+ startx += cWidth;
+ }
+ }
int getAnnotationHeight()
{
return annotations.adjustPanelHeight();
}
+
/**
* 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
* marker.
*
* @param g1
+ * Graphics object to draw with
* @param startRes
* offset of the first column in the visible region (0..)
* @param endRes
* @param yOffset
* vertical offset at which to draw (for wrapped alignments)
*/
- public void drawPanel(Graphics g1, final int startRes, final int endRes,
- final int startSeq, final int endSeq, final int yOffset)
+ private void drawPanel(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int yOffset)
+
{
updateViewport();
if (!av.hasHiddenColumns())
}
+
/**
* Draws a region of the visible alignment
*
int endSeq, int offset)
{
g.setFont(av.getFont());
- sr.prepare(g, av.isRenderGaps());
+ seqRdr.prepare(g, av.isRenderGaps());
SequenceI nextSeq;
// 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())
{
for (int r = 0; r < visibleResults.length; r += 2)
{
- sr.drawHighlightedText(nextSeq, visibleResults[r],
- visibleResults[r + 1],
- (visibleResults[r] - startRes) * charWidth,
- offset + ((i - startSeq) * charHeight));
+ seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
+ visibleResults[r + 1], (visibleResults[r] - startRes)
+ * charWidth, offset
+ + ((i - startSeq) * charHeight));
}
}
}
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));
}
}
// ///////////////////////////////////
// Now outline any areas if necessary
// ///////////////////////////////////
- SequenceGroup group = av.getSelectionGroup();
- int sx = -1;
- int sy = -1;
- int ex = -1;
+ SequenceGroup group = null;
int groupIndex = -1;
- int visWidth = (endRes - startRes + 1) * charWidth;
- if ((group == null) && (av.getAlignment().getGroups().size() > 0))
+ if (av.getAlignment().getGroups().size() > 0)
{
group = av.getAlignment().getGroups().get(0);
groupIndex = 0;
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;
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
+ endSeq, offset);
+
+ groupIndex++;
- for (i = startSeq; i <= endSeq; i++)
+ g.setStroke(new BasicStroke());
+
+ if (groupIndex >= av.getAlignment().getGroups().size())
{
- sx = (group.getStartRes() - startRes) * charWidth;
- sy = offset + ((i - startSeq) * charHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
- - 1;
+ break;
+ }
- if (sx + ex < 0 || sx > visWidth)
- {
- continue;
- }
+ group = av.getAlignment().getGroups().get(groupIndex);
- 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;
- }
+ } while (groupIndex < av.getAlignment().getGroups().size());
- if (!inGroup)
- {
- if (((top == -1) && (i == 0)) || !group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i - 1)))
- {
- top = sy;
- }
+ }
- oldY = sy;
- inGroup = true;
+ }
- if (group == av.getSelectionGroup())
- {
- g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
- g.setColor(Color.RED);
- }
- else
- {
- g.setStroke(new BasicStroke());
- g.setColor(group.getOutlineColour());
- }
- }
- }
- else
- {
- if (inGroup)
- {
- if (sx >= 0 && sx < visWidth)
- {
- g.drawLine(sx, oldY, sx, sy);
- }
- if (sx + ex < visWidth)
- {
- g.drawLine(sx + ex, oldY, sx + ex, sy);
- }
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private BufferedImage drawSelectionGroup(int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+ // get a new image of the correct size
+ BufferedImage selectionImage = setupImage();
- if (sx < 0)
- {
- ex += sx;
- sx = 0;
- }
+ if (selectionImage == null)
+ {
+ return null;
+ }
- if (sx + ex > visWidth)
- {
- ex = visWidth;
- }
+ SequenceGroup group = av.getSelectionGroup();
+ if (group == null)
+ {
+ // nothing to draw
+ return null;
+ }
- else if (sx + ex >= (endRes - startRes + 1) * charWidth)
- {
- ex = (endRes - startRes + 1) * charWidth;
- }
+ // set up drawing colour
+ Graphics2D g = (Graphics2D) selectionImage.getGraphics();
- if (top != -1)
- {
- g.drawLine(sx, top, sx + ex, top);
- top = -1;
- }
+ // set background to transparent
+ g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
+ g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
- if (bottom != -1)
- {
- g.drawLine(sx, bottom, sx + ex, bottom);
- bottom = -1;
- }
+ // 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);
- inGroup = false;
- }
- }
+ if (!av.getWrapAlignment())
+ {
+ drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq,
+ 0);
+ }
+ else
+ {
+ drawWrappedSelection(g, group, getWidth(), getHeight(),
+ av.getRanges().getStartRes());
+ }
+
+ g.dispose();
+ return selectionImage;
+ }
+
+ /*
+ * 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())
+ {
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
+ offset);
+ }
+ else
+ {
+ // package into blocks of visible columns
+ int screenY = 0;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ for (int[] region : av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy())
+ {
+ int hideStart = region[0];
+ int hideEnd = region[1];
+
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
+
+ blockEnd = hideStart - 1;
+
+ g.translate(screenY * charWidth, 0);
+ drawPartialGroupOutline(g, group,
+ blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g.translate(-screenY * charWidth, 0);
+ screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
+
+ if (screenY > (endRes - startRes))
+ {
+ // already rendered last block
+ break;
}
+ }
+ if (screenY <= (endRes - startRes))
+ {
+ // remaining visible region to render
+ blockEnd = blockStart + (endRes - startRes) - screenY;
+ g.translate(screenY * charWidth, 0);
+ drawPartialGroupOutline(g, group,
+ blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g.translate(-screenY * charWidth, 0);
+ }
+ }
+ }
+
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq,
+ int verticalOffset)
+ {
+ int visWidth = (endRes - startRes + 1) * charWidth;
+
+ int oldY = -1;
+ int i = 0;
+ boolean inGroup = false;
+ int top = -1;
+ int bottom = -1;
+
+ int sx = -1;
+ int sy = -1;
+ int xwidth = -1;
+
+ for (i = startSeq; i <= endSeq; i++)
+ {
+ // position of start residue of group relative to startRes, in pixels
+ sx = (group.getStartRes() - startRes) * charWidth;
+
+ // width of group in pixels
+ xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
+ - 1;
+
+ sy = verticalOffset + (i - startSeq) * charHeight;
+
+ if (sx + xwidth < 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;
+ }
+ }
+ else
+ {
if (inGroup)
{
- sy = offset + ((i - startSeq) * charHeight);
+ // if start position is visible, draw vertical line to left of
+ // group
if (sx >= 0 && sx < visWidth)
{
g.drawLine(sx, oldY, sx, sy);
}
- if (sx + ex < visWidth)
+ // if end position is visible, draw vertical line to right of
+ // group
+ if (sx + xwidth < visWidth)
{
- g.drawLine(sx + ex, oldY, sx + ex, sy);
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
}
if (sx < 0)
{
- ex += sx;
+ xwidth += sx;
sx = 0;
}
- if (sx + ex > visWidth)
- {
- ex = visWidth;
- }
- else if (sx + ex >= (endRes - startRes + 1) * charWidth)
+ // don't let width extend beyond current block, or group extent
+ // fixes JAL-2672
+ if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
{
- ex = (endRes - startRes + 1) * charWidth;
+ xwidth = (endRes - startRes + 1) * charWidth - sx;
}
-
+
+ // draw horizontal line at top of group
if (top != -1)
{
- g.drawLine(sx, top, sx + ex, top);
+ g.drawLine(sx, top, sx + xwidth, top);
top = -1;
}
+ // draw horizontal line at bottom of group
if (bottom != -1)
{
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+ g.drawLine(sx, bottom, sx + xwidth, bottom);
bottom = -1;
}
inGroup = false;
}
+ }
+ }
- groupIndex++;
+ if (inGroup)
+ {
+ sy = verticalOffset + ((i - startSeq) * charHeight);
+ if (sx >= 0 && sx < visWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
- g.setStroke(new BasicStroke());
+ if (sx + xwidth < visWidth)
+ {
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
+ }
- if (groupIndex >= av.getAlignment().getGroups().size())
- {
- break;
- }
+ if (sx < 0)
+ {
+ xwidth += sx;
+ sx = 0;
+ }
- group = av.getAlignment().getGroups().get(groupIndex);
+ if (sx + xwidth > visWidth)
+ {
+ xwidth = visWidth;
+ }
+ else if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
+ {
+ xwidth = (endRes - startRes + 1) * charWidth;
+ }
- } while (groupIndex < av.getAlignment().getGroups().size());
+ if (top != -1)
+ {
+ g.drawLine(sx, top, sx + xwidth, top);
+ top = -1;
+ }
- }
+ if (bottom != -1)
+ {
+ g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1);
+ bottom = -1;
+ }
+ 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
{
String eventName = evt.getPropertyName();
- if (av.getWrapAlignment())
+ if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
+ {
+ fastPaint = true;
+ repaint();
+ }
+ else if (av.getWrapAlignment())
{
if (eventName.equals(ViewportRanges.STARTRES))
{
git://source.jalview.org / jalview.git / blobdiff