import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
import java.awt.Color;
import java.awt.Graphics;
{
/**
- * Returns the combined feature colour for a given sequence and column
- * position, taking into account feature colour schemes, ordering, feature and
- * feature group visibility, and transparency. Returns null if there is no
- * visible feature at the position.
+ * Computes the feature colour for a given sequence and column position,
+ * taking into account sequence feature locations, feature colour schemes,
+ * render ordering, feature and feature group visibility, and transparency.
* <p>
- * The Graphics argument is optional and may be null if no transparency is
- * applied. With feature transparency, visible features are written to the
- * graphics context and the composite colour can be read off.
+ * The graphics argument should be provided if transparency is applied
+ * (getTransparency() < 1). With feature transparency, visible features are
+ * written to the graphics context and the composite colour may be read off
+ * from it. In this case, the returned feature colour is not the composite
+ * colour but that of the last feature drawn.
* <p>
- * This is provided for use by Structure Viewers and the Overview Window to
- * get the feature colour of the rendered sequence.
+ * If no transparency applies, then the graphics argument may be null, and the
+ * returned colour is the one that would be drawn for the feature.
+ * <p>
+ * Returns null if there is no visible feature at the position.
+ * <p>
+ * This is provided to support rendering of feature colours other than on the
+ * sequence alignment, including by structure viewers and the overview window.
+ * Note this method takes no account of whether the sequence or column is
+ * hidden.
*
* @param sequence
* @param column
+ * aligned column position (1..)
* @param g
* @return
*/
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 position on the given sequence.
+ * 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
+ * aligned column position (1..)
+ * @return
+ */
+ List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column);
+
+ /**
+ * Returns features at the specified residue position on the given sequence.
* Non-positional features are not included.
*
* @param sequence
- * @param res
+ * @param resNo
+ * residue position (start..)
* @return
*/
- List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res);
+ List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence, int resNo);
/**
* get current displayed types, in ordering of rendering (on top last)
List<String> getDisplayedFeatureTypes();
/**
- * get current displayed groups
+ * Returns a (possibly empty) list of currently visible feature groups
*
- * @return a (possibly empty) list of feature groups
+ * @return
*/
List<String> getDisplayedFeatureGroups();
* @return
*/
float getTransparency();
+
+ /**
+ * Answers the filters applied to the given feature type, or null if none is
+ * set
+ *
+ * @param featureType
+ * @return
+ */
+ FeatureMatcherSetI getFeatureFilter(String featureType);
+
+ /**
+ * Answers the feature filters map
+ *
+ * @return
+ */
+ public Map<String, FeatureMatcherSetI> getFeatureFilters();
+
+ /**
+ * Sets the filters for the feature type, or removes them if a null or empty
+ * filter is passed
+ *
+ * @param featureType
+ * @param filter
+ */
+ void setFeatureFilter(String featureType, FeatureMatcherSetI filter);
+
+ /**
+ * Replaces all feature filters with the given map
+ *
+ * @param filters
+ */
+ void setFeatureFilters(Map<String, FeatureMatcherSetI> filters);
+
+ /**
+ * Returns the colour for a particular feature instance. This includes
+ * calculation of 'colour by label', or of a graduated score colour, if
+ * applicable.
+ * <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>
+ *
+ * @param feature
+ * @return
+ */
+ Color getColour(SequenceFeature feature);
}