*/
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.Range;
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.MappedFeatures;
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;
}
Color drawnColour = null;
/*
+ * draw 'complement' features below ours if configured to do so
+ */
+ if (av.isShowComplementFeatures()
+ && !av.isShowComplementFeaturesOnTop())
+ {
+ drawnColour = drawComplementFeatures(g, seq, start, end, y1,
+ colourOnly, visiblePositions, drawnColour);
+ }
+
+ /*
* iterate over features in ordering of their rendering (last is on top)
*/
for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
visiblePositions.getBegin(), visiblePositions.getEnd(), type);
- if (fc.isSimpleColour())
+ if (overlaps.size() > 1 && fc.isSimpleColour())
{
filterFeaturesForDisplay(overlaps);
}
}
int featureStartCol = seq.findIndex(visibleStart);
- int featureEndCol = sf.begin == sf.end ? featureStartCol : seq
- .findIndex(visibleEnd);
+ int featureEndCol = sf.begin == sf.end ? featureStartCol
+ : seq.findIndex(visibleEnd);
// Color featureColour = getColour(sequenceFeature);
else
{
*/
- boolean drawn = renderFeature(g, seq,
- featureStartCol - 1,
- featureEndCol - 1, featureColour,
- start, end, y1, colourOnly);
- if (drawn)
- {
- drawnColour = featureColour;
- }
+ boolean drawn = renderFeature(g, seq, featureStartCol - 1,
+ featureEndCol - 1, featureColour, start, end, y1,
+ colourOnly);
+ if (drawn)
+ {
+ drawnColour = featureColour;
+ }
/*}*/
}
}
}
/*
- * if configured to do so, find and show complement's features
+ * draw 'complement' features above ours if configured to do so
*/
- if (av.isShowComplementFeatures())
+ if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop())
{
- AlignViewportI comp = av.getCodingComplement();
- FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
- .getFeatureRenderer();
- for (int pos = visiblePositions.start; pos <= visiblePositions.end; pos++)
- {
- int column = seq.findIndex(pos);
- List<SequenceFeature> features = fr2
- .findComplementFeaturesAtResidue(seq, pos);
- for (SequenceFeature sf : features)
- {
- FeatureColourI fc = fr2.getFeatureStyle(sf.getType());
- Color featureColour = fr2.getColor(sf, fc);
- renderFeature(g, seq, column - 1, column - 1, featureColour,
- start, end, y1, colourOnly);
- }
- }
+ drawnColour = drawComplementFeatures(g, seq, start, end, y1,
+ colourOnly, visiblePositions, drawnColour);
}
if (transparency != 1.0f && g != null)
}
/**
+ * Find any features on the CDS/protein complement of the sequence region and
+ * draw them, with visibility and colouring as configured in the complementary
+ * viewport
+ *
+ * @param g
+ * @param seq
+ * @param start
+ * @param end
+ * @param y1
+ * @param colourOnly
+ * @param visiblePositions
+ * @param drawnColour
+ * @return
+ */
+ Color drawComplementFeatures(final Graphics g, final SequenceI seq,
+ int start, int end, int y1, boolean colourOnly,
+ ContiguousI visiblePositions, Color drawnColour)
+ {
+ AlignViewportI comp = av.getCodingComplement();
+ FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
+ .getFeatureRenderer();
+
+ 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.findComplementFeaturesAtResidue(seq, pos);
+ if (mf != null)
+ {
+ for (SequenceFeature sf : mf.features)
+ {
+ FeatureColourI fc = fr2.getFeatureStyle(sf.getType());
+ Color featureColour = fr2.getColor(sf, fc);
+ renderFeature(g, seq, column - 1, column - 1, featureColour,
+ start, end, y1, colourOnly);
+ drawnColour = featureColour;
+ }
+ }
+ }
+ return drawnColour;
+ }
+
+ /**
* Called when alignment in associated view has new/modified features to
* discover and display.
*
/*
* show complement features on top (if configured to show them)
*/
- if (av.isShowComplementFeatures())
+ if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop())
{
- AlignViewportI complement = av.getCodingComplement();
- AlignFrame af = Desktop.getAlignFrameFor(complement);
- FeatureRendererModel fr2 = af.getFeatureRenderer();
- List<SequenceFeature> features = fr2.findComplementFeaturesAtResidue(
- seq, seq.findPosition(column - 1));
-
- ReverseListIterator<SequenceFeature> it = new ReverseListIterator<>(
- features);
- while (it.hasNext())
+ Color col = findComplementFeatureColour(seq, column);
+ if (col != null)
{
- SequenceFeature sf = it.next();
- if (!fr2.featureGroupNotShown(sf))
- {
- Color col = fr2.getColour(sf);
- if (col != null)
- {
- return col;
- }
- }
+ return col;
}
}
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);
}
/*
- * no displayed feature found at position
+ * show complement features underneath (if configured to show them)
*/
+ Color col = null;
+ if (av.isShowComplementFeatures()
+ && !av.isShowComplementFeaturesOnTop())
+ {
+ col = findComplementFeatureColour(seq, column);
+ }
+
+ return col;
+ }
+
+ Color findComplementFeatureColour(SequenceI seq, int column)
+ {
+ AlignViewportI complement = av.getCodingComplement();
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ FeatureRendererModel fr2 = af.getFeatureRenderer();
+ MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq,
+ seq.findPosition(column - 1));
+ if (mf == null)
+ {
+ return null;
+ }
+ ReverseListIterator<SequenceFeature> it = new ReverseListIterator<>(
+ mf.features);
+ while (it.hasNext())
+ {
+ SequenceFeature sf = it.next();
+ if (!fr2.featureGroupNotShown(sf))
+ {
+ Color col = fr2.getColour(sf);
+ if (col != null)
+ {
+ return col;
+ }
+ }
+ }
return null;
}
}
git://source.jalview.org / jalview.git / blobdiff