*/
package jalview.renderer.seqfeatures;
+import java.awt.AlphaComposite;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.util.List;
+
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
+import jalview.datamodel.ContiguousI;
import jalview.datamodel.MappedFeatures;
-import jalview.datamodel.Range;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.util.ReverseListIterator;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-import java.awt.AlphaComposite;
-import java.awt.Color;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.util.List;
-
public class FeatureRenderer extends FeatureRendererModel
{
private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
continue;
}
+ /*
+ * JAL-3045 text is always drawn over features, even if
+ * 'Show Text' is unchecked in the format menu
+ */
g.setColor(Color.white);
int charOffset = (charWidth - fm.charWidth(s)) / 2;
g.drawString(String.valueOf(s),
/*
* if columns are all gapped, or sequence has no features, nothing to do
*/
- Range visiblePositions = seq.findPositions(start+1, end+1);
- if (visiblePositions == null || (!seq.getFeatures().hasFeatures()
- && !av.isShowComplementFeatures()))
+ ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1);
+ if (visiblePositions == null || !seq.getFeatures().hasFeatures()
+ && !av.isShowComplementFeatures())
{
return null;
}
List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
visiblePositions.getBegin(), visiblePositions.getEnd(), type);
- if (fc.isSimpleColour())
+ if (overlaps.size() > 1 && fc.isSimpleColour())
{
filterFeaturesForDisplay(overlaps);
}
*/
Color drawComplementFeatures(final Graphics g, final SequenceI seq,
int start, int end, int y1, boolean colourOnly,
- Range visiblePositions, Color drawnColour)
+ ContiguousI visiblePositions, Color drawnColour)
{
AlignViewportI comp = av.getCodingComplement();
FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
.getFeatureRenderer();
- for (int pos = visiblePositions.start; pos <= visiblePositions.end; pos++)
+
+ final int visibleStart = visiblePositions.getBegin();
+ final int visibleEnd = visiblePositions.getEnd();
+
+ for (int pos = visibleStart; pos <= visibleEnd; pos++)
{
int column = seq.findIndex(pos);
MappedFeatures mf = fr2
continue;
}
+ /*
+ * find features of this type, and the colour of the _last_ one
+ * (the one that would be drawn on top) that has a colour
+ */
List<SequenceFeature> overlaps = seq.findFeatures(column, column,
type);
- for (SequenceFeature sequenceFeature : overlaps)
+ for (int i = overlaps.size() - 1 ; i >= 0 ; i--)
{
+ SequenceFeature sequenceFeature = overlaps.get(i);
if (!featureGroupNotShown(sequenceFeature))
{
Color col = getColour(sequenceFeature);