* Removes from the list of features any that duplicate the location of a
* feature of the same type. Should be used only for features of the same,
* simple, feature colour (which normally implies the same feature type). Does
- * not check visibility settings for feature type or feature group.
+ * not check visibility settings for feature type or feature group. No
+ * filtering is done if transparency, or any feature filters, are in force.
*
* @param features
*/
public void filterFeaturesForDisplay(List<SequenceFeature> features)
{
- if (features.isEmpty())
+ /*
+ * don't remove 'redundant' features if
+ * - transparency is applied (feature count affects depth of feature colour)
+ * - filters are applied (not all features may be displayable)
+ */
+ if (features.isEmpty() || transparency != 1f
+ || !featureFilters.isEmpty())
{
return;
}
+
SequenceFeatures.sortFeatures(features, true);
SequenceFeature lastFeature = null;
/**
* Answers the colour for the feature, or null if the feature is excluded by
- * feature type or group visibility, by filters, or by colour threshold
- * settings
+ * feature group visibility, by filters, or by colour threshold settings. This
+ * method does not take feature visibility into account.
*
* @param sf
* @param fc
public Color getColor(SequenceFeature sf, FeatureColourI fc)
{
/*
- * is the feature type displayed?
- */
- if (!showFeatureOfType(sf.getType()))
- {
- return null;
- }
-
- /*
* is the feature group displayed?
*/
if (featureGroupNotShown(sf))