package jalview.gui;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+import java.awt.AlphaComposite;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.RenderingHints;
import java.awt.Shape;
import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
import java.util.List;
import javax.swing.JComponent;
* @author $author$
* @version $Revision$
*/
-public class SeqCanvas extends JComponent
+public class SeqCanvas extends JComponent implements ViewportListenerI
{
final FeatureRenderer fr;
setLayout(new BorderLayout());
PaintRefresher.Register(this, av.getSequenceSetId());
setBackground(Color.white);
+
+ av.getRanges().addPropertyChangeListener(this);
}
public SequenceRenderer getSequenceRenderer()
if (av.hasHiddenColumns())
{
- startx = av.getColumnSelection().adjustForHiddenColumns(startx);
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ startx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(startx);
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
}
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
}
// WEST SCALE
if (av.hasHiddenColumns())
{
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
}
SequenceI seq;
fastpainting = true;
fastPaint = true;
updateViewport();
- gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
- imgHeight, -horizontal * charWidth, -vertical * charHeight);
- int sr = av.getStartRes();
- int er = av.getEndRes();
- int ss = av.getStartSeq();
- int es = av.getEndSeq();
+ ViewportRanges ranges = av.getRanges();
+ int sr = ranges.getStartRes();
+ int er = ranges.getEndRes();
+ int ss = ranges.getStartSeq();
+ int es = ranges.getEndSeq();
int transX = 0;
int transY = 0;
+ gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
+ imgHeight, -horizontal * charWidth, -vertical * charHeight);
+
if (horizontal > 0) // scrollbar pulled right, image to the left
{
- er++;
transX = (er - sr - horizontal) * charWidth;
sr = er - horizontal;
}
else if (horizontal < 0)
{
- er = sr - horizontal - 1;
+ er = sr - horizontal;
}
else if (vertical > 0) // scroll down
{
ss = es - vertical;
- if (ss < av.getStartSeq())
+ if (ss < ranges.getStartSeq())
{ // ie scrolling too fast, more than a page at a time
- ss = av.getStartSeq();
+ ss = ranges.getStartSeq();
}
else
{
- transY = imgHeight - (vertical * charHeight);
+ transY = imgHeight - ((vertical + 1) * charHeight);
}
}
else if (vertical < 0)
{
es = ss - vertical;
- if (es > av.getEndSeq())
+ if (es > ranges.getEndSeq())
{
- es = av.getEndSeq();
+ es = ranges.getEndSeq();
}
}
public void paintComponent(Graphics g)
{
updateViewport();
- BufferedImage lcimg = img; // take reference since other threads may null
+
+ // 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
+
+ if (img == null)
+ {
+ setupImage();
+ }
+ if (img == null)
+ {
+ return;
+ }
+ BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+ img.getType());
+ Graphics2D g2d = lcimg.createGraphics();
+ g2d.drawImage(img, 0, 0, null);
+ g2d.dispose();
+
+
+ // BufferedImage lcimg = img; // take reference since other threads may null
// img and call later.
super.paintComponent(g);
+ BufferedImage selectImage = drawSelectionGroup();
+
if (lcimg != null
&& (fastPaint
|| (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g
.getClipBounds().height)))
{
+ Graphics2D g2 = (Graphics2D) lcimg.getGraphics();
+
+ // overlay selection group on lcimg
+ if (selectImage != null)
+ {
+ g2.setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g2.drawImage(selectImage, 0, 0, this);
+ }
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())
+ {
+ drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+ }
+ else
+ {
+ drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq(), 0);
+ }
+
+ lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+ img.getType());
+ g2d = lcimg.createGraphics();
+ g2d.drawImage(img, 0, 0, null);
+ g2d.dispose();
+
+ Graphics2D g2 = (Graphics2D) lcimg.getGraphics();
+
+ // overlay selection group on lcimg
+ if (selectImage != null)
+ {
+ g2.setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g2.drawImage(selectImage, 0, 0, this);
+ }
+ g.drawImage(lcimg, 0, 0, this);
+ }
+
+ private void paintSeqGroup()
+ {
+ fastPaint = true;
+ repaint();
+ }
+ private void setupImage()
+ {
// this draws the whole of the alignment
imgWidth = getWidth();
imgHeight = getHeight();
return;
}
- if (lcimg == null || imgWidth != lcimg.getWidth()
- || imgHeight != lcimg.getHeight())
- {
+
try
{
- lcimg = img = new BufferedImage(imgWidth, imgHeight,
- BufferedImage.TYPE_INT_RGB);
+ 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.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
new OOMWarning("Creating alignment image for display", er);
- return;
+ return;
}
- }
- if (av.antiAlias)
- {
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
- }
+ }
- gg.setColor(Color.white);
- gg.fillRect(0, 0, imgWidth, imgHeight);
+ private BufferedImage setupSelectionImage()
+ {
+ BufferedImage lcimg = null;
- if (av.getWrapAlignment())
+ int width = getWidth();
+ int height = getHeight();
+
+ width -= (width % charWidth);
+ height -= (height % charHeight);
+
+ if ((width < 1) || (height < 1))
{
- drawWrappedPanel(gg, getWidth(), getHeight(), av.getStartRes());
+ return null;
}
- else
+
+ try
{
- drawPanel(gg, av.getStartRes(), av.getEndRes(), av.getStartSeq(),
- av.getEndSeq(), 0);
- }
+ 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);
- g.drawImage(lcimg, 0, 0, this);
+ 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.setEndRes(av.getStartRes() + cWidth);
+ 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.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth);
}
while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
g.setColor(Color.blue);
int res;
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
- .size(); i++)
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ List<Integer> positions = hidden.findHiddenRegionPositions();
+ for (int pos : positions)
{
- res = av.getColumnSelection().findHiddenRegionPosition(i)
- - startRes;
+ res = pos - startRes;
if (res < 0 || res > endx - startRes)
{
(int) clip.getBounds().getHeight());
}
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+ drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
if (av.isShowAnnotation())
{
}
else
{
- List<int[]> regions = av.getColumnSelection().getHiddenColumns();
-
int screenY = 0;
int blockStart = startRes;
int blockEnd = endRes;
- for (int[] region : regions)
+ for (int[] region : av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy())
{
int hideStart = region[0];
int hideEnd = region[1];
g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
0 + offset, (blockEnd - blockStart + 1) * charWidth - 1,
- (endSeq - startSeq) * charHeight + offset);
+ (endSeq - startSeq + 1) * charHeight + offset);
}
g1.translate(-screenY * charWidth, 0);
// / First draw the sequences
// ///////////////////////////
- for (int i = startSeq; i < endSeq; i++)
+ for (int i = startSeq; i <= endSeq; i++)
{
nextSeq = av.getAlignment().getSequenceAt(i);
if (nextSeq == null)
if (av.isShowSequenceFeatures())
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * charHeight));
+ + ((i - startSeq) * charHeight), false);
}
// / Highlight search Results once all sequences have been drawn
// ///////////////////////////////////
// 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;
int top = -1;
int bottom = -1;
- for (i = startSeq; i < endSeq; i++)
+ 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);
if (sx < 0)
{
- ex += sx;
- sx = 0;
+ // ex += sx;
+ // sx = 0;
}
if (sx + ex > visWidth)
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()
+ {
+ // get a new image of the correct size
+ BufferedImage selectionImage = setupSelectionImage();
+
+ 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();
+ // 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);
+
+ int visWidth = av.getRanges().getViewportWidth() * charWidth;
+
+ int startRes = av.getRanges().getStartRes();
+
+ // set x start and end positions of group
+ int startx = (group.getStartRes() - startRes) * charWidth;
+ int endx = (group.getEndRes() - startRes + 1) * charWidth;
+
+ int oldY = -1;
+ int i = 0;
+ boolean inGroup = false;
+ 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 sy = (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 = (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;
+ }
+
+ return selectionImage;
+ }
+
/**
* DOCUMENT ME!
*
repaint();
}
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ String eventName = evt.getPropertyName();
+
+ if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
+ {
+ paintSeqGroup();
+ }
+ else if (av.getWrapAlignment())
+ {
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ repaint();
+ }
+ }
+ else
+ {
+ 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.getEndRes() - vpRanges.getStartRes();
+ if (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.
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ // scroll - startres and endres both change
+ fastPaint(scrollX, 0);
+ }
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
+ {
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff