+ return findAlignedSequence(seq, al, null);
+ }
+ /**
+ * Convenience method to return the first aligned sequence in the given
+ * alignment whose dataset has a mapping with the given (aligned or dataset)
+ * sequence, and optionally the mapping that relates them
+ *
+ * @param seq
+ * @param al
+ * @param map - list to add the mapping to
+ * @return sequence from al that maps to seq
+ */
+ public SequenceI findAlignedSequence(SequenceI seq, AlignmentI al,List<SequenceToSequenceMapping> map)
+ {