import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
+import java.awt.AlphaComposite;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
Graphics2D gg;
- int imgWidth;
-
- int imgHeight;
-
AlignViewport av;
boolean fastPaint = false;
fastpainting = true;
fastPaint = true;
updateViewport();
- gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
- imgHeight, -horizontal * charWidth, -vertical * charHeight);
ViewportRanges ranges = av.getRanges();
int sr = ranges.getStartRes();
int transX = 0;
int transY = 0;
+ gg.copyArea(horizontal * charWidth, vertical * charHeight,
+ img.getWidth(), img.getHeight(), -horizontal * charWidth,
+ -vertical * charHeight);
+
if (horizontal > 0) // scrollbar pulled right, image to the left
{
transX = (er - sr - horizontal) * charWidth;
}
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
- || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g
- .getClipBounds().height)))
+ 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();
+ BufferedImage selectImage = drawSelectionGroup(
+ av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq());
+
+ if (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();
+ int width = getWidth();
+ int height = getHeight();
- imgWidth -= (imgWidth % charWidth);
- imgHeight -= (imgHeight % charHeight);
+ width -= (width % charWidth);
+ height -= (height % charHeight);
- if ((imgWidth < 1) || (imgHeight < 1))
+ if ((width < 1) || (height < 1))
{
return;
}
- if (lcimg == null || imgWidth != lcimg.getWidth()
- || imgHeight != lcimg.getHeight())
+ if (img == null || width != img.getWidth() || height != img.getHeight())
{
- try
- {
- lcimg = img = new BufferedImage(imgWidth, imgHeight,
- BufferedImage.TYPE_INT_RGB);
- 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;
- }
+ img = setupImage();
+ gg = (Graphics2D) img.getGraphics();
+ gg.setFont(av.getFont());
+ }
+ if (img == null)
+ {
+ 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();
+ gg.fillRect(0, 0, img.getWidth(), img.getHeight());
+
if (av.getWrapAlignment())
{
drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
ranges.getStartSeq(), ranges.getEndSeq(), 0);
}
+ BufferedImage lcimg = buildLocalImage(selectImage);
g.drawImage(lcimg, 0, 0, this);
+ }
+
+ /*
+ * 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)
+ {
+ g2d.setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g2d.drawImage(selectImage, 0, 0, this);
+ }
+ g2d.dispose();
+
+ return lcimg;
+ }
+
+ private void paintSeqGroup()
+ {
+ fastPaint = true;
+ repaint();
+ }
+
+ private BufferedImage setupImage()
+ {
+ BufferedImage lcimg = null;
+
+ 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(
+ "Selection Group image OutOfMemory Redraw Error.\n" + er);
+ new OOMWarning("Creating alignment image for display", er);
+
+ return null;
+ }
+
+ return lcimg;
}
/**
FontMetrics fm = getFontMetrics(av.getFont());
+ LABEL_EAST = 0;
+ LABEL_WEST = 0;
+
if (av.getScaleRightWrapped())
{
LABEL_EAST = fm.stringWidth(getMask());
av.setWrappedWidth(cWidth);
- av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth - 1);
+ 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.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
+ .findColumnPosition(maxwidth);
}
while ((ypos <= canvasHeight) && (startRes < maxwidth))
int blockEnd = endRes;
for (int[] region : av.getAlignment().getHiddenColumns()
- .getHiddenColumnsCopyAsList())
+ .getHiddenColumnsCopy())
{
int hideStart = region[0];
int hideEnd = region[1];
// ///////////////////////////////////
// Now outline any areas if necessary
// ///////////////////////////////////
- SequenceGroup group = av.getSelectionGroup();
+
+ SequenceGroup group = null;
int sx = -1;
int sy = -1;
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;
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)
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());
- }
+ 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);
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);
}
+
+ /*
+ * 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 (selectionImage == null)
+ {
+ return null;
+ }
+
+ SequenceGroup group = av.getSelectionGroup();
+ if (group == null)
+ {
+ // nothing to draw
+ return null;
+ }
+
+ // set up drawing colour
+ Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+ g.translate(LABEL_WEST, 0);
+ // set background to transparent
+ g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
+ g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
+
+ 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);
+
+ if (!av.hasHiddenColumns())
+ {
+ drawSelectionGroupPart(g, group, startRes, endRes, startSeq, endSeq);
+ }
+ else
+ {
+ // package into blocks of visible columns
+ // Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+ // Graphics g1 = selectionImage.getGraphics();
+
+ 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);
+
+ drawSelectionGroupPart(g, group,
+ blockStart, blockEnd, startSeq, endSeq);
+
+ 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);
+ drawSelectionGroupPart(g, group,
+ blockStart, blockEnd, startSeq, endSeq);
+
+ g.translate(-screenY * charWidth, 0);
+ }
+ }
+ g.translate(-LABEL_WEST, 0);
+ return selectionImage;
+ }
+
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private void drawSelectionGroupPart(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq)
+ {
+ // set up values in case the alignment is wrapped
+ int verticalOffset = 0;
+ int horizontalOffset = 0;
+ if (av.getWrapAlignment())
+ {
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += charHeight;
+ }
+
+ // get the start res of the group and work out the offsets for it in the wrapped alignment
+ int groupstart = group.getStartRes();
+ int cWidth = (getWidth() - LABEL_EAST - LABEL_WEST) / charWidth;
+
+ // group is in which slice of alignment? res position / width in residues
+ int slice = groupstart / cWidth;
+ // vertical offset is increased by slice number * number of sequences * height of each sequence
+ verticalOffset = slice * (av.getAlignment().getHeight() * charHeight
+ + getAnnotationHeight() + hgap) + hgap;
+
+ // horizontal offset is number of residues to subtract from group residue
+ // position
+ horizontalOffset = (slice * cWidth);
+ }
+
+ int visWidth = av.getRanges().getViewportWidth() * charWidth;
+
+ // set x start and end positions of group
+ int startx = (group.getStartRes() - startRes - horizontalOffset)
+ * charWidth;
+ int endx = (group.getEndRes() - startRes + 1 - horizontalOffset)
+ * charWidth;
+
+ int oldY = -1;
+ int i = 0;
+ boolean inGroup = false;
+ int top = -1;
+ int bottom = -1;
+
+ // get sequences to determine y positions of group
+ for (i = startSeq; i <= endSeq; ++i)
+ {
+ int sy = verticalOffset + (i - startSeq) * charHeight;
+
+ if (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)
+ {
+ // if start position is visible, draw vertical line to left of
+ // group
+ if (startx >= 0 && startx < visWidth * charWidth)
+ {
+ g.drawLine(startx, oldY, startx, sy);
+ }
+
+ // if end position is visible, draw vertical line to right of
+ // group
+ if (endx <= visWidth * charWidth)
+ {
+ g.drawLine(endx, oldY, endx, sy);
+ }
+
+ if (endx > visWidth * charWidth)
+ {
+ endx = visWidth * charWidth;
+ }
+
+ // draw horizontal line at top of group
+ if (top != -1)
+ {
+ g.drawLine(startx, top, endx, top);
+ top = -1;
+ }
+
+ // draw horizontal line at bottom of group
+ if (bottom != -1)
+ {
+ g.drawLine(startx, bottom, endx, bottom);
+ bottom = -1;
+ }
+
+ inGroup = false;
+ }
+ }
+ }
+ if (inGroup)
+ {
+ int sy = verticalOffset + (i - startSeq) * charHeight;
+ if (startx >= 0 && startx < visWidth)
+ {
+ g.drawLine(startx, oldY, startx, sy);
+ }
+
+ if (endx < visWidth)
+ {
+ g.drawLine(endx, oldY, endx, sy);
+ }
+
+ if (endx > visWidth)
+ {
+ endx = visWidth;
+ }
+
+ if (top != -1)
+ {
+ g.drawLine(startx, top, endx, top);
+ top = -1;
+ }
+
+ if (bottom != -1)
+ {
+ g.drawLine(startx, bottom - 1, endx, bottom - 1);
+ bottom = -1;
+ }
+
+ inGroup = false;
+ }
+ }
+
/**
* DOCUMENT ME!
*
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- if (!av.getWrapAlignment())
+ String eventName = evt.getPropertyName();
+
+ if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
+ {
+ paintSeqGroup();
+ }
+ else if (av.getWrapAlignment())
+ {
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ repaint();
+ }
+ }
+ else
{
- if (evt.getPropertyName().equals("startres")
- || evt.getPropertyName().equals("endres"))
+ 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();
- int scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
- if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
+ scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+ int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+ if (scrollX > range)
{
- scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
+ scrollX = range;
}
- else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
+ else if (scrollX < -range)
{
- scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
+ 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
fastPaint(scrollX, 0);
}
- else if (evt.getPropertyName().equals("startseq")
- || evt.getPropertyName().equals("endseq"))
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
{
+ // scroll
fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
}
}
git://source.jalview.org / jalview.git / blobdiff