/**
*
- * Calculates the maximum width of the alignment, including gaps.
+ * Answers the width of the alignment, including gaps, that is, the length of
+ * the longest sequence, or -1 if there are no sequences. Avoid calling this
+ * method repeatedly where possible, as it has to perform a calculation. Note
+ * that this width includes any hidden columns.
*
- * @return Greatest sequence length within alignment, or -1 if no sequences
- * present
+ * @return
+ * @see AlignmentI#getVisibleWidth()
*/
@Override
int getWidth();
/**
+ *
+ * Answers the visible width of the alignment, including gaps, that is, the
+ * length of the longest sequence, excluding any hidden columns. Answers -1 if
+ * there are no sequences. Avoid calling this method repeatedly where
+ * possible, as it has to perform a calculation.
+ *
+ * @return
+ */
+ int getVisibleWidth();
+
+ /**
* Calculates if this set of sequences (visible and invisible) are all the
* same length
*
public HiddenColumns propagateInsertions(SequenceI profileseq,
AlignmentView input);
+ /**
+ * resolve a contact list instance (if any) associated with the annotation row
+ * and column position
+ *
+ * @param _aa
+ * @param column
+ * @return
+ */
+ ContactListI getContactListFor(AlignmentAnnotation _aa, int column);
+
+ AlignmentAnnotation addContactList(ContactMatrixI cm);
}