import jalview.api.AlignmentColsCollectionI;
import jalview.api.AlignmentRowsCollectionI;
+import jalview.api.RendererListenerI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.viewmodel.OverviewDimensions;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeSupport;
public class OverviewRenderer
{
+ public static final String UPDATE = "OverviewUpdate";
+
+ protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+
private FeatureColourFinder finder;
private jalview.api.SequenceRenderer sr;
// raw number of pixels to allocate to each row
private float pixelsPerSeq;
+ // height in pixels of graph
+ private int graphHeight;
+
+ // flag to indicate whether to halt drawing
+ private volatile boolean redraw = false;
+
public OverviewRenderer(jalview.api.SequenceRenderer seqRenderer,
- FeatureColourFinder colfinder, OverviewDimensions od)
+ FeatureRenderer fr, OverviewDimensions od)
{
sr = seqRenderer;
- finder = colfinder;
+ finder = new FeatureColourFinder(fr);
pixelsPerCol = od.getPixelsPerCol();
pixelsPerSeq = od.getPixelsPerSeq();
+ graphHeight = od.getGraphHeight();
miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
BufferedImage.TYPE_INT_RGB);
}
int rgbcolor = Color.white.getRGB();
int seqIndex = 0;
int pixelRow = 0;
+ int alignmentHeight = miniMe.getHeight() - graphHeight;
+
+ changeSupport.firePropertyChange(UPDATE, -1, 0);
+
for (int alignmentRow : rows)
{
+ if (redraw)
+ {
+ break;
+ }
+
// get details of this alignment row
boolean hidden = rows.isHidden(alignmentRow);
SequenceI seq = rows.getSequence(alignmentRow);
int pixelCol = 0;
for (int alignmentCol : cols)
{
+ if (redraw)
+ {
+ break;
+ }
+
// calculate where this column extends to in pixels
int endCol = Math.min(
Math.round((colIndex + 1) * pixelsPerCol) - 1,
miniMe.getWidth() - 1);
- // determine the colour based on the sequence and column position
- rgbcolor = getColumnColourFromSequence(seq,
- hidden || cols.isHidden(alignmentCol), alignmentCol, finder);
-
- // fill in the appropriate number of pixels
- for (int row = pixelRow; row <= endRow; ++row)
+ // don't do expensive colour determination if we're not going to use it
+ // NB this is important to avoid performance issues in the overview
+ // panel
+ if (pixelCol <= endCol)
{
- for (int col = pixelCol; col <= endCol; ++col)
+ // determine the colour based on the sequence and column position
+ rgbcolor = getColumnColourFromSequence(seq,
+ hidden || cols.isHidden(alignmentCol), alignmentCol,
+ finder);
+
+ // fill in the appropriate number of pixels
+ for (int row = pixelRow; row <= endRow; ++row)
{
- miniMe.setRGB(col, row, rgbcolor);
+ for (int col = pixelCol; col <= endCol; ++col)
+ {
+ miniMe.setRGB(col, row, rgbcolor);
+ }
}
- }
- pixelCol = endCol + 1;
+ pixelCol = endCol + 1;
+ }
colIndex++;
}
- pixelRow = endRow + 1;
+
+ if (pixelRow != endRow + 1)
+ {
+ changeSupport.firePropertyChange(UPDATE,
+ Math.round(100 * (float) pixelRow / alignmentHeight),
+ Math.round(
+ 100 * ((float) (endRow + 1) / alignmentHeight)));
+ pixelRow = endRow + 1;
+ }
seqIndex++;
}
+
+ // final update to progress bar if present
+ if (redraw)
+ {
+ changeSupport.firePropertyChange(UPDATE,
+ Math.round(100 * (float) (pixelRow - 1) / alignmentHeight),
+ 0);
+ }
+ else
+ {
+ changeSupport.firePropertyChange(UPDATE,
+ Math.round(100 * alignmentHeight / miniMe.getHeight() - 1),
+ Math.round(100 * alignmentHeight / miniMe.getHeight()));
+ }
return miniMe;
}
int pixelCol = 0;
for (int alignmentCol : cols)
{
+ if (redraw)
+ {
+ changeSupport.firePropertyChange(UPDATE, 99, 0);
+ break;
+ }
+
if (alignmentCol >= annotations.length)
{
break; // no more annotations to draw here
colIndex++;
}
}
+ changeSupport.firePropertyChange(UPDATE, 99, 100);
+ }
+
+ public void setRedraw(boolean b)
+ {
+ synchronized (this)
+ {
+ redraw = b;
+ }
+ }
+
+ public void addPropertyChangeListener(RendererListenerI listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ public void removePropertyChangeListener(RendererListenerI listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
}
}