{
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)
updateViewport();
- // img is a cached version of the last view we drew
- // selectImage will hold any selection we have
- // lcimg is a local *copy* of img which we'll draw selectImage on top of
+ ViewportRanges ranges = av.getRanges();
- if (img == null)
- {
- setupImage();
- }
- if (img == null)
- {
- return;
- }
+ int width = getWidth();
+ int height = getHeight();
- BufferedImage selectImage = drawSelectionGroup();
+ width -= (width % charWidth);
+ height -= (height % charHeight);
- if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
- || (getVisibleRect().height != g.getClipBounds().height))
+ // 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;
- }
-
- if (av.antiAlias)
- {
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
}
-
- gg.setColor(Color.white);
- gg.fillRect(0, 0, imgWidth, imgHeight);
-
- ViewportRanges ranges = av.getRanges();
- if (av.getWrapAlignment())
+ else if ((width > 0) && (height > 0))
{
- drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
- }
- else
- {
- drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
- ranges.getStartSeq(), ranges.getEndSeq(), 0);
+ // img is a cached version of the last view we drew, if any
+ // if we have no img or the size has changed, make a new one
+ if (img == null || width != img.getWidth()
+ || height != img.getHeight())
+ {
+ img = setupImage();
+ if (img == null)
+ {
+ return;
+ }
+ gg = (Graphics2D) img.getGraphics();
+ gg.setFont(av.getFont());
+ }
+
+ if (av.antiAlias)
+ {
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, img.getWidth(), img.getHeight());
+
+ if (av.getWrapAlignment())
+ {
+ 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);
}
+ }
- 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);
}
/*
return lcimg;
}
- private void paintSeqGroup()
- {
- fastPaint = true;
- repaint();
- }
-
- private void setupImage()
- {
- // this draws the whole of the alignment
- imgWidth = getWidth();
- imgHeight = getHeight();
-
- imgWidth -= (imgWidth % charWidth);
- imgHeight -= (imgHeight % charHeight);
-
- if ((imgWidth < 1) || (imgHeight < 1))
- {
- return;
- }
-
-
- try
- {
- img = new BufferedImage(imgWidth, imgHeight,
- BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
- gg = (Graphics2D) img.getGraphics();
- gg.setFont(av.getFont());
- } catch (OutOfMemoryError er)
- {
- System.gc();
- System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
- new OOMWarning("Creating alignment image for display", er);
-
- return;
- }
-
- }
-
- private BufferedImage setupSelectionImage()
+ /*
+ * Set up a buffered image of the correct height and size for the sequence canvas
+ */
+ private BufferedImage setupImage()
{
BufferedImage lcimg = null;
{
System.gc();
System.err.println(
- "Selection Group image OutOfMemory Redraw Error.\n" + er);
+ "Group image OutOfMemory Redraw Error.\n" + er);
new OOMWarning("Creating alignment image for display", er);
return null;
}
}
- 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 - LABEL_EAST - LABEL_WEST) / 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(LABEL_WEST, 0);
+
+ drawUnwrappedSelection(g, group, startx, endx, 0,
+ av.getAlignment().getHeight() - 1,
+ ypos);
+
+ g.translate(-LABEL_WEST, 0);
+
+ // update vertical offset
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ // update horizontal offset
+ startx += cWidth;
+ }
+ }
int getAnnotationHeight()
{
return annotations.adjustPanelHeight();
}
- /**
- * DOCUMENT ME!
+ /*
+ * Draw an alignment panel for printing
*
* @param g1
- * DOCUMENT ME!
+ * Graphics object to draw with
* @param startRes
- * DOCUMENT ME!
+ * start residue of print area
* @param endRes
- * DOCUMENT ME!
+ * end residue of print area
* @param startSeq
- * DOCUMENT ME!
+ * start sequence of print area
* @param endSeq
- * DOCUMENT ME!
+ * end sequence of print area
* @param offset
- * DOCUMENT ME!
+ * vertical offset
*/
- public void drawPanel(Graphics g1, int startRes, int endRes,
+ private void drawPanel(Graphics g1, int startRes, int endRes,
int startSeq, int endSeq, int offset)
{
updateViewport();
}
- // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
- // int x1, int x2, int y1, int y2, int startx, int starty,
private void draw(Graphics g, int startRes, int endRes, int startSeq,
int endSeq, int offset)
{
g.setFont(av.getFont());
- sr.prepare(g, av.isRenderGaps());
+ seqRdr.prepare(g, av.isRenderGaps());
SequenceI nextSeq;
// 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],
+ 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));
}
}
// ///////////////////////////////////
SequenceGroup group = null;
-
- int sx = -1;
- int sy = -1;
- int ex = -1;
int groupIndex = -1;
- int visWidth = (endRes - startRes + 1) * charWidth;
if (av.getAlignment().getGroups().size() > 0)
{
if (group != null)
{
+ g.setStroke(new BasicStroke());
+ g.setColor(group.getOutlineColour());
+
do
{
- int oldY = -1;
- int i = 0;
- boolean inGroup = false;
- int top = -1;
- int bottom = -1;
-
- for (i = startSeq; i <= endSeq; i++)
- {
- // position of start residue of group relative to startRes, in pixels
- sx = (group.getStartRes() - startRes) * charWidth;
- sy = offset + ((i - startSeq) * charHeight);
- // width of group in pixels
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - 1;
-
- if (sx + ex < 0 || sx > visWidth)
- {
- continue;
- }
-
- if ((sx <= (endRes - startRes) * charWidth)
- && group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i)))
- {
- if ((bottom == -1)
- && !group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i + 1)))
- {
- bottom = sy + charHeight;
- }
-
- if (!inGroup)
- {
- if (((top == -1) && (i == 0))
- || !group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i - 1)))
- {
- top = sy;
- }
-
- oldY = sy;
- inGroup = true;
-
- g.setStroke(new BasicStroke());
- g.setColor(group.getOutlineColour());
- }
- }
- else
- {
- if (inGroup)
- {
- // if start position is visible, draw vertical line to left of
- // group
- if (sx >= 0 && sx < visWidth)
- {
- g.drawLine(sx, oldY, sx, sy);
- }
-
- // if end position is visible, draw vertical line to right of
- // group
- if (sx + ex < visWidth)
- {
- g.drawLine(sx + ex, oldY, sx + ex, sy);
- }
-
- if (sx < 0)
- {
- // ex += sx;
- // sx = 0;
- }
-
- if (sx + ex > visWidth)
- {
- ex = visWidth;
- }
-
- else if (sx + ex >= (endRes - startRes + 1) * charWidth)
- {
- ex = (endRes - startRes + 1) * charWidth;
- }
-
- // draw horizontal line at top of group
- if (top != -1)
- {
- g.drawLine(sx, top, sx + ex, top);
- top = -1;
- }
-
- // draw horizontal line at bottom of group
- if (bottom != -1)
- {
- g.drawLine(sx, bottom, sx + ex, bottom);
- bottom = -1;
- }
-
- inGroup = false;
- }
- }
- }
-
- if (inGroup)
- {
- sy = offset + ((i - startSeq) * charHeight);
- if (sx >= 0 && sx < visWidth)
- {
- g.drawLine(sx, oldY, sx, sy);
- }
-
- if (sx + ex < visWidth)
- {
- g.drawLine(sx + ex, oldY, sx + ex, sy);
- }
-
- if (sx < 0)
- {
- ex += sx;
- sx = 0;
- }
-
- if (sx + ex > visWidth)
- {
- ex = visWidth;
- }
- else if (sx + ex >= (endRes - startRes + 1) * charWidth)
- {
- ex = (endRes - startRes + 1) * charWidth;
- }
-
- if (top != -1)
- {
- g.drawLine(sx, top, sx + ex, top);
- top = -1;
- }
-
- if (bottom != -1)
- {
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
- bottom = -1;
- }
-
- inGroup = false;
- }
-
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
+ endSeq, offset);
+
groupIndex++;
g.setStroke(new BasicStroke());
}
+
/*
* Draw the selection group as a separate image and overlay
*/
- private BufferedImage drawSelectionGroup()
+ private BufferedImage drawSelectionGroup(int startRes, int endRes,
+ int startSeq, int endSeq)
{
// get a new image of the correct size
- BufferedImage selectionImage = setupSelectionImage();
+ BufferedImage selectionImage = setupImage();
if (selectionImage == null)
{
// set up drawing colour
Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+
// 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);
- int visWidth = av.getRanges().getViewportWidth() * charWidth;
+ 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;
+ }
- int startRes = av.getRanges().getStartRes();
+ 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);
+ }
+ }
+ }
- // set x start and end positions of group
- int startx = (group.getStartRes() - startRes) * charWidth;
- int endx = (group.getEndRes() - startRes + 1) * charWidth;
+ /*
+ * 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;
int top = -1;
int bottom = -1;
- // get sequences to determine y positions of group
- int startSeq = av.getRanges().getStartSeq();
- for (i = startSeq; i <= av.getRanges().getEndSeq(); ++i)
+ int sx = -1;
+ int sy = -1;
+ int xwidth = -1;
+
+ for (i = startSeq; i <= endSeq; i++)
{
- int sy = (i - startSeq) * charHeight;
+ // 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;
- if (group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i)))
+ 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)))
{
// if start position is visible, draw vertical line to left of
// group
- if (startx >= 0 && startx < visWidth * charWidth)
+ if (sx >= 0 && sx < visWidth)
{
- g.drawLine(startx, oldY, startx, sy);
+ g.drawLine(sx, oldY, sx, sy);
}
// if end position is visible, draw vertical line to right of
// group
- if (endx <= visWidth * charWidth)
+ if (sx + xwidth < visWidth)
{
- g.drawLine(endx, oldY, endx, sy);
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
}
- if (endx > visWidth * charWidth)
+ if (sx < 0)
{
- endx = visWidth * charWidth;
+ xwidth += sx;
+ sx = 0;
}
+ // don't let width extend beyond current block, or group extent
+ // fixes JAL-2672
+ if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
+ {
+ xwidth = (endRes - startRes + 1) * charWidth - sx;
+ }
+
// draw horizontal line at top of group
if (top != -1)
{
- g.drawLine(startx, top, endx, top);
+ g.drawLine(sx, top, sx + xwidth, top);
top = -1;
}
// draw horizontal line at bottom of group
if (bottom != -1)
{
- g.drawLine(startx, bottom, endx, bottom);
+ g.drawLine(sx, bottom, sx + xwidth, bottom);
bottom = -1;
}
}
}
}
+
if (inGroup)
{
- int sy = (i - startSeq) * charHeight;
- if (startx >= 0 && startx < visWidth)
+ sy = verticalOffset + ((i - startSeq) * charHeight);
+ if (sx >= 0 && sx < visWidth)
{
- g.drawLine(startx, oldY, startx, sy);
+ g.drawLine(sx, oldY, sx, sy);
}
- if (endx < visWidth)
+ if (sx + xwidth < visWidth)
{
- g.drawLine(endx, oldY, endx, sy);
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
}
- if (endx > visWidth)
+ if (sx < 0)
{
- endx = visWidth;
+ xwidth += sx;
+ sx = 0;
+ }
+
+ if (sx + xwidth > visWidth)
+ {
+ xwidth = visWidth;
+ }
+ else if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
+ {
+ xwidth = (endRes - startRes + 1) * charWidth;
}
if (top != -1)
{
- g.drawLine(startx, top, endx, top);
+ g.drawLine(sx, top, sx + xwidth, top);
top = -1;
}
if (bottom != -1)
{
- g.drawLine(startx, bottom - 1, endx, bottom - 1);
+ g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1);
bottom = -1;
}
inGroup = false;
}
-
- return selectionImage;
}
-
+
/**
* DOCUMENT ME!
*
if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
{
- paintSeqGroup();
+ fastPaint = true;
+ repaint();
}
else if (av.getWrapAlignment())
{
git://source.jalview.org / jalview.git / blobdiff