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)
* <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);
}