*
* @param sequence
* @param column
+ * aligned column position (1..)
* @param g
* @return
*/
void setGroupVisibility(String group, boolean visible);
/**
- * Returns features at the specified position on the given sequence.
+ * 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).
+ *
+ * @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();
+
}