*
* Calculates the maximum width of the alignment, including gaps.
*
- * @return Greatest sequence length within alignment.
+ * @return Greatest sequence length within alignment, or -1 if no sequences
+ * present
*/
@Override
int getWidth();
* Used to set a particular index of the alignment with the given sequence.
*
* @param i
- * Index of sequence to be updated.
+ * Index of sequence to be updated. if i>length, sequence will be
+ * added to end, with no intervening positions.
* @param seq
- * New sequence to be inserted.
+ * New sequence to be inserted. The existing sequence at position i
+ * will be replaced.
+ * @return existing sequence (or null if i>current length)
*/
- void setSequenceAt(int i, SequenceI seq);
+ SequenceI replaceSequenceAt(int i, SequenceI seq);
/**
* Deletes a sequence from the alignment
* @return Alignment containing dataset sequences or null of this is a
* dataset.
*/
- Alignment getDataset();
+ AlignmentI getDataset();
/**
* Set the associated dataset for the alignment, or create one.
* @param dataset
* The dataset alignment or null to construct one.
*/
- void setDataset(Alignment dataset);
+ void setDataset(AlignmentI dataset);
/**
* pads sequences with gaps (to ensure the set looks like an alignment)
void addCodonFrame(AlignedCodonFrame codons);
/**
- * add a set of aligned codons mappings for this alignment, apart from any
- * duplicates which are ignored
- *
- * @param codons
- */
- void addCodonFrames(Iterable<AlignedCodonFrame> codons);
-
- /**
* remove a particular codon frame reference from this alignment
*
* @param codons