import java.beans.PropertyChangeSupport;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
* @param type
* @return
*/
- protected boolean showFeatureOfType(String type)
+ public boolean showFeatureOfType(String type)
{
return type == null ? false : (av.getFeaturesDisplayed() == null ? true
: av.getFeaturesDisplayed().isVisible(type));
* 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;
@Override
public Map<String, FeatureMatcherSetI> getFeatureFilters()
{
- return new HashMap<>(featureFilters);
+ return featureFilters;
}
@Override
/**
* 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))
return filter == null ? true : filter.matches(sf);
}
+ /**
+ * Answers true unless the specified group is set to hidden. Defaults to true
+ * if group visibility is not set.
+ *
+ * @param group
+ * @return
+ */
+ public boolean isGroupVisible(String group)
+ {
+ if (!featureGroups.containsKey(group))
+ {
+ return true;
+ }
+ return featureGroups.get(group);
+ }
+
+ /**
+ * Orders features in render precedence (last in order is last to render, so
+ * displayed on top of other features)
+ *
+ * @param order
+ */
+ public void orderFeatures(Comparator<String> order)
+ {
+ Arrays.sort(renderOrder, order);
+ }
}