package jalview.renderer.seqfeatures;
import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.datamodel.Range;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
+import java.util.List;
public class FeatureRenderer extends FeatureRendererModel
{
return null;
}
- SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
-
- if (sequenceFeatures == null || sequenceFeatures.length == 0)
- {
- return null;
- }
-
if (Comparison.isGap(seq.getCharAt(column)))
{
/*
* returning null allows the colour scheme to provide gap colour
- * - normally white, but can be customised otherwise
+ * - normally white, but can be customised
*/
return null;
}
/*
* simple case - just find the topmost rendered visible feature colour
*/
- renderedColour = findFeatureColour(seq, seq.findPosition(column));
+ renderedColour = findFeatureColour(seq, column);
}
else
{
final SequenceI seq, int start, int end, int y1,
boolean colourOnly)
{
- SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
- if (sequenceFeatures == null || sequenceFeatures.length == 0)
+ /*
+ * 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())
{
return null;
}
transparency));
}
- int startPos = seq.findPosition(start);
- int endPos = seq.findPosition(end);
-
- int sfSize = sequenceFeatures.length;
Color drawnColour = null;
/*
continue;
}
- // loop through all features in sequence to find
- // current feature to render
- for (int sfindex = 0; sfindex < sfSize; sfindex++)
+ FeatureColourI fc = getFeatureStyle(type);
+ List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
+ visiblePositions.getBegin(), visiblePositions.getEnd(), type);
+
+ filterFeaturesForDisplay(overlaps, fc);
+
+ for (SequenceFeature sf : overlaps)
{
- final SequenceFeature sequenceFeature = sequenceFeatures[sfindex];
- if (!sequenceFeature.type.equals(type))
+ Color featureColour = fc.getColor(sf);
+ if (featureColour == null)
{
+ // score feature outwith threshold for colouring
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(sequenceFeature))
+ int visibleStart = sf.getBegin();
+ if (visibleStart < visiblePositions.getBegin())
{
- continue;
+ visibleStart = sf.isContactFeature() ? sf.getEnd()
+ : visiblePositions.getBegin();
}
-
- /*
- * check feature overlaps the target range
- * TODO: efficient retrieval of features overlapping a range
- */
- if (sequenceFeature.getBegin() > endPos
- || sequenceFeature.getEnd() < startPos)
+ int visibleEnd = sf.getEnd();
+ if (visibleEnd > visiblePositions.getEnd())
{
- continue;
+ visibleEnd = sf.isContactFeature() ? sf.getBegin()
+ : visiblePositions.getEnd();
}
- Color featureColour = getColour(sequenceFeature);
- if (featureColour == null)
- {
- // score feature outwith threshold for colouring
- continue;
- }
+ int featureStartCol = seq.findIndex(visibleStart);
+ int featureEndCol = sf.begin == sf.end ? featureStartCol : seq
+ .findIndex(visibleEnd);
+
+ // Color featureColour = getColour(sequenceFeature);
- boolean isContactFeature = sequenceFeature.isContactFeature();
+ boolean isContactFeature = sf.isContactFeature();
if (isContactFeature)
{
- boolean drawn = renderFeature(g, seq,
- seq.findIndex(sequenceFeature.begin) - 1,
- seq.findIndex(sequenceFeature.begin) - 1, featureColour,
- start, end, y1, colourOnly);
- drawn |= renderFeature(g, seq,
- seq.findIndex(sequenceFeature.end) - 1,
- seq.findIndex(sequenceFeature.end) - 1, featureColour,
- start, end, y1, colourOnly);
+ boolean drawn = renderFeature(g, seq, featureStartCol - 1,
+ featureStartCol - 1, featureColour, start, end, y1,
+ colourOnly);
+ drawn |= renderFeature(g, seq, featureEndCol - 1,
+ featureEndCol - 1, featureColour, start, end, y1,
+ colourOnly);
if (drawn)
{
drawnColour = featureColour;
}
else
{
+ /*
+ * showing feature score by height of colour
+ * is not implemented as a selectable option
+ *
if (av.isShowSequenceFeaturesHeight()
&& !Float.isNaN(sequenceFeature.score))
{
}
else
{
+ */
boolean drawn = renderFeature(g, seq,
- seq.findIndex(sequenceFeature.begin) - 1,
- seq.findIndex(sequenceFeature.end) - 1, featureColour,
+ featureStartCol - 1,
+ featureEndCol - 1, featureColour,
start, end, y1, colourOnly);
if (drawn)
{
drawnColour = featureColour;
}
- }
+ /*}*/
}
}
}
}
/**
+<<<<<<< HEAD
+=======
* Answers true if the feature belongs to a feature group which is not
* currently displayed, else false
*
* @param sequenceFeature
* @return
*/
+ @Override
protected boolean featureGroupNotShown(
final SequenceFeature sequenceFeature)
{
}
/**
+>>>>>>> refs/heads/develop
* Called when alignment in associated view has new/modified features to
* discover and display.
*
}
/**
- * Returns the sequence feature colour rendered at the given sequence
- * 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.
+ * 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. 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
+ * if different behaviour is wanted.
*
* @param seq
- * @param pos
+ * @param column
+ * (1..)
* @return
*/
- Color findFeatureColour(SequenceI seq, int pos)
+ Color findFeatureColour(SequenceI seq, int column)
{
- SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
- if (sequenceFeatures == null || sequenceFeatures.length == 0)
- {
- return null;
- }
-
/*
* check for new feature added while processing
*/
continue;
}
- for (int sfindex = 0; sfindex < sequenceFeatures.length; sfindex++)
+ List<SequenceFeature> overlaps = seq.findFeatures(column, column,
+ type);
+ for (SequenceFeature sequenceFeature : overlaps)
{
- SequenceFeature sequenceFeature = sequenceFeatures[sfindex];
- if (!sequenceFeature.type.equals(type))
- {
- continue;
- }
-
- if (featureGroupNotShown(sequenceFeature))
+ if (!featureGroupNotShown(sequenceFeature))
{
- continue;
- }
-
- /*
- * check the column position is within the feature range
- * (or is one of the two contact positions for a contact feature)
- */
- boolean featureIsAtPosition = sequenceFeature.begin <= pos
- && sequenceFeature.end >= pos;
- if (sequenceFeature.isContactFeature())
- {
- featureIsAtPosition = sequenceFeature.begin == pos
- || sequenceFeature.end == pos;
- }
- if (featureIsAtPosition)
- {
- return getColour(sequenceFeature);
+ Color col = getColour(sequenceFeature);
+ if (col != null)
+ {
+ return col;
+ }
}
}
}
git://source.jalview.org / jalview.git / blobdiff