org.biojava3.alignment.template
Interface MatrixAligner<S extends Sequence<C>,C extends Compound>
- Type Parameters:
S
- each element of the alignment Profile
is of type SC
- each element of an AlignedSequence
is a Compound
of type C
- All Superinterfaces:
- Aligner<S,C>, Scorer
- All Known Implementing Classes:
- AbstractMatrixAligner, AbstractPairwiseSequenceAligner, AbstractProfileProfileAligner, AnchoredPairwiseSequenceAligner, GuanUberbacher, NeedlemanWunsch, SimpleProfileProfileAligner, SmithWaterman
public interface MatrixAligner<S extends Sequence<C>,C extends Compound>
- extends Aligner<S,C>
Defines an Aligner
which builds a score matrix during computation.
- Author:
- Mark Chapman
getScoreMatrix
short[][][] getScoreMatrix()
- Returns the entire score matrix built during alignment. The first dimension has the length of the first (query)
sequence + 1; the second has the length of the second (target) sequence + 1; the third has length equal to the
number of scores stored per pairing of an element from each
Sequence
.
- Returns:
- the score matrix
getScoreMatrixAsString
String getScoreMatrixAsString()
- Returns a depiction of the score matrix as a
String
. This may include additional description such as
labels for each dimension: element from query sequence, element from target sequence, and meaning of each score.
- Returns:
- the score matrix as a character sequence