*
* 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
int findIndex(SequenceI s);
/**
- * Finds group that given sequence is part of.
+ * Returns the first group (in the order in which groups were added) that
+ * includes the given sequence and aligned position (base 0), or null if none
+ * found
*
- * @param s
- * Sequence in alignment.
+ * @param seq
+ * @param position
*
- * @return First group found for sequence. WARNING : Sequences may be members
- * of several groups. This method is incomplete.
+ * @return
*/
- SequenceGroup findGroup(SequenceI s);
+ SequenceGroup findGroup(SequenceI seq, int position);
/**
* Finds all groups that a given sequence is part of.
boolean hasRNAStructure();
/**
- * Set alignment to be a nucleotide sequence
- *
- */
- void setNucleotide(boolean b);
-
- /**
* Get the associated dataset for 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)
* @param results
* @return -1 or index of sequence in alignment
*/
- int findIndex(SearchResults results);
+ int findIndex(SearchResultsI results);
/**
* append sequences and annotation from another alignment object to this one.