public int findPosition(int i);
/**
- * Returns the range of sequence positions included in the given alignment
- * position range. If no positions are included (the range is entirely gaps),
- * then returns null.
- *
- * <pre>
- * Example:
- * >Seq/8-13
- * ABC--DE-F
- * findPositions(1, 4) returns Range(9, 9) // B only
- * findPositions(3, 4) returns null // all gaps
- * findPositions(2, 6) returns Range(10, 12) // CDE
- * findPositions(3, 7) returns Range(11,12) // DE
- * </pre>
- *
- * @param fromCol
- * first aligned column position (base 0, inclusive)
- * @param toCol
- * last aligned column position (base 0, inclusive)
- *
- * @return
- */
- public Range findPositions(int fromCol, int toCol);
-
- /**
* Returns an int array where indices correspond to each residue in the
* sequence and the element value gives its position in the alignment
*
public List<DBRefEntry> getPrimaryDBRefs();
/**
- * Returns a (possibly empty) list of sequence features that overlap the range
- * from-to (inclusive), optionally restricted to one or more specified feature
- * types
+ * Returns a (possibly empty) list of sequence features that overlap the given
+ * alignment column range, optionally restricted to one or more specified
+ * feature types. If the range is all gaps, then features which enclose it are
+ * included (but not contact features).
*
- * @param from
- * @param to
+ * @param fromCol
+ * start column of range inclusive (1..)
+ * @param toCol
+ * end column of range inclusive (1..)
* @param types
+ * optional feature types to restrict results to
* @return
*/
- List<SequenceFeature> findFeatures(int from, int to, String... types);
+ List<SequenceFeature> findFeatures(int fromCol, int toCol, String... types);
/**
*