*/
package jalview.renderer.seqfeatures;
-import jalview.api.AlignViewportI;
-import jalview.api.FeatureColourI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.util.Comparison;
-import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-
import java.awt.AlphaComposite;
import java.awt.Color;
import java.awt.FontMetrics;
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.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.util.Comparison;
+import jalview.util.ReverseListIterator;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+
public class FeatureRenderer extends FeatureRendererModel
{
private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
g.setColor(featureColour);
- g.fillRect((i - start) * charWidth, y1, charWidth,
- charHeight);
+ g.fillRect((i - start) * charWidth, y1, charWidth, charHeight);
if (colourOnly || !validCharWidth)
{
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), charOffset
- + (charWidth * (i - start)), pady);
+ g.drawString(String.valueOf(s),
+ charOffset + (charWidth * (i - start)), pady);
}
return true;
}
g.setColor(Color.black);
int charOffset = (charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s), charOffset
- + (charWidth * (i - start)), pady);
+ g.drawString(String.valueOf(s),
+ charOffset + (charWidth * (i - start)), pady);
}
return true;
}
return null;
}
- if (Comparison.isGap(seq.getCharAt(column)))
+ // column is 'base 1' but getCharAt is an array index (ie from 0)
+ if (Comparison.isGap(seq.getCharAt(column - 1)))
{
- return Color.white;
+ /*
+ * returning null allows the colour scheme to provide gap colour
+ * - normally white, but can be customised
+ */
+ return null;
}
Color renderedColour = null;
final SequenceI seq, int start, int end, int y1,
boolean colourOnly)
{
- if (!seq.getFeatures().hasFeatures())
+ /*
+ * if columns are all gapped, or sequence has no features, nothing to do
+ */
+ 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++)
}
FeatureColourI fc = getFeatureStyle(type);
- List<SequenceFeature> overlaps = seq.findFeatures(start + 1, end + 1,
- type);
+ List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
+ visiblePositions.getBegin(), visiblePositions.getEnd(), type);
- filterFeaturesForDisplay(overlaps, fc);
+ if (overlaps.size() > 1 && fc.isSimpleColour())
+ {
+ filterFeaturesForDisplay(overlaps);
+ }
for (SequenceFeature sf : overlaps)
{
+ Color featureColour = getColor(sf, fc);
+ if (featureColour == null)
+ {
+ /*
+ * feature excluded by filters, or colour threshold
+ */
+ continue;
+ }
+
/*
- * a feature type may be flagged as shown but the group
- * an instance of it belongs to may be hidden
+ * if feature starts/ends outside the visible range,
+ * restrict to visible positions (or if a contact feature,
+ * to a single position)
*/
- if (featureGroupNotShown(sf))
+ int visibleStart = sf.getBegin();
+ if (visibleStart < visiblePositions.getBegin())
{
- continue;
+ visibleStart = sf.isContactFeature() ? sf.getEnd()
+ : visiblePositions.getBegin();
+ }
+ int visibleEnd = sf.getEnd();
+ if (visibleEnd > visiblePositions.getEnd())
+ {
+ visibleEnd = sf.isContactFeature() ? sf.getBegin()
+ : visiblePositions.getEnd();
}
- Color featureColour = fc.getColor(sf);
+ int featureStartCol = seq.findIndex(visibleStart);
+ int featureEndCol = sf.begin == sf.end ? featureStartCol
+ : seq.findIndex(visibleEnd);
+
+ // Color featureColour = getColour(sequenceFeature);
+
boolean isContactFeature = sf.isContactFeature();
- int featureStartCol = seq.findIndex(sf.begin);
- int featureEndCol = sf.begin == sf.end ? featureStartCol : seq
- .findIndex(sf.end);
if (isContactFeature)
{
boolean drawn = renderFeature(g, seq, featureStartCol - 1,
drawnColour = featureColour;
}
}
- else if (showFeature(sf))
+ else
{
/*
* showing feature score by height of colour
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;
+ }
/*}*/
}
}
}
+ /*
+ * draw 'complement' features above ours if configured to do so
+ */
+ if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop())
+ {
+ 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.
*
* Returns the sequence feature colour rendered at the given column position,
* or null if none found. The feature of highest render order (i.e. on top) is
* found, subject to both feature type and feature group being visible, and
- * its colour returned.
+ * its colour returned. This method is suitable when no feature transparency
+ * applied (only the topmost visible feature colour is rendered).
* <p>
* Note this method does not check for a gap in the column so would return the
* colour for features enclosing a gapped column. Check for gap before calling
updateFeatures();
/*
+ * show complement features on top (if configured to show them)
+ */
+ if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop())
+ {
+ Color col = findComplementFeatureColour(seq, column);
+ if (col != null)
+ {
+ return col;
+ }
+ }
+
+ /*
* inspect features in reverse renderOrder (the last in the array is
* displayed on top) until we find one that is rendered at the position
*/
- for (int renderIndex = renderOrder.length - 1; renderIndex >= 0; renderIndex--)
+ for (int renderIndex = renderOrder.length
+ - 1; renderIndex >= 0; renderIndex--)
{
String type = renderOrder[renderIndex];
if (!showFeatureOfType(type))
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))
{
- return getColour(sequenceFeature);
+ Color col = getColour(sequenceFeature);
+ if (col != null)
+ {
+ return col;
+ }
}
}
}
-
+
/*
- * 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