*/
package jalview.api;
+import jalview.datamodel.MappedFeatures;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.util.matcher.KeyedMatcherSetI;
+import jalview.datamodel.features.FeatureMatcherSetI;
import java.awt.Color;
import java.awt.Graphics;
List<String> getGroups(boolean visible);
/**
- * change visibility for a range of groups
+ * Set visibility for a list of groups
*
* @param toset
* @param visible
void setGroupVisibility(List<String> toset, boolean visible);
/**
- * change visibiilty of given group
+ * Set visibility of the given feature group
*
* @param group
* @param visible
void setGroupVisibility(String group, boolean visible);
/**
- * Returns features at the specified aligned column on the given sequence.
- * Non-positional features are not included. If the column has a gap, then
- * enclosing features are included (but not contact features).
+ * Returns visible features at the specified aligned column on the given
+ * sequence. Non-positional features are not included. If the column has a gap,
+ * then enclosing features are included (but not contact features).
*
* @param sequence
* @param column
List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column);
/**
- * Returns features at the specified residue position on the given sequence.
- * Non-positional features are not included.
+ * Returns features at the specified residue positions on the given sequence.
+ * Non-positional features are not included. Features are returned in render
+ * order of their feature type (last is on top). Within feature type, ordering
+ * is undefined.
*
* @param sequence
- * @param resNo
- * residue position (start..)
+ * @param fromResNo
+ * @param toResNo
* @return
*/
- List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence, int resNo);
+ List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
+ int fromResNo, int toResNo);
/**
* get current displayed types, in ordering of rendering (on top last)
* @param featureType
* @return
*/
- KeyedMatcherSetI getFeatureFilter(String featureType);
+ FeatureMatcherSetI getFeatureFilter(String featureType);
/**
- * Answers a shallow copy of the feature filters map
+ * Answers the feature filters map
*
* @return
*/
- public Map<String, KeyedMatcherSetI> getFeatureFilters();
+ public Map<String, FeatureMatcherSetI> getFeatureFilters();
/**
* Sets the filters for the feature type, or removes them if a null or empty
* @param featureType
* @param filter
*/
- void setFeatureFilter(String featureType, KeyedMatcherSetI filter);
+ void setFeatureFilter(String featureType, FeatureMatcherSetI filter);
/**
* Replaces all feature filters with the given map
*
* @param filters
*/
- void setFeatureFilters(Map<String, KeyedMatcherSetI> filters);
+ void setFeatureFilters(Map<String, FeatureMatcherSetI> filters);
/**
* Returns the colour for a particular feature instance. This includes
* <p>
* Returns null if
* <ul>
- * <li>feature type is not visible, or</li>
* <li>feature group is not visible, or</li>
* <li>feature values lie outside any colour threshold, or</li>
* <li>feature is excluded by filter conditions</li>
* </ul>
+ * This method does not check feature type visibility.
*
* @param feature
* @return
*/
Color getColour(SequenceFeature feature);
+
+ /**
+ * Answers true if feature would be shown, else false. A feature is shown if
+ * <ul>
+ * <li>its feature type is set to visible</li>
+ * <li>its feature group is either null, or set to visible</li>
+ * <li>it is not excluded by a colour threshold on score or other numeric
+ * attribute</li>
+ * <li>it is not excluded by a filter condition</li>
+ * </ul>
+ *
+ * @param feature
+ * @return
+ */
+ boolean isVisible(SequenceFeature feature);
+
+ /**
+ * Answers a bean containing a mapping, and a list of visible features in this
+ * alignment at a position (or range) which is mappable from the given sequence
+ * residue position in a mapped alignment. Features are returned in render order
+ * of feature type (on top last), with order within feature type undefined. If
+ * no features or mapping are found, answers null.
+ *
+ * @param sequence
+ * @param pos
+ * @return
+ */
+ MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence, int pos);
+
+ /**
+ * Sends a message to let any registered parties know that something about
+ * feature rendering has changed
+ */
+ void notifyFeaturesChanged();
+
}