- Type Parameters:
S- each element of the alignment
Profileis of type S
C- each element of an
Compoundof type C
- All Known Implementing Classes:
public interface MatrixAligner<S extends Sequence<C>,C extends Compound> extends Aligner<S,C>Defines an
Alignerwhich builds a score matrix during computation.
- Mark Chapman
All Methods Instance Methods Abstract Methods Modifier and Type Method Description
getScoreMatrix()Returns the entire score matrix built during alignment.
getScoreMatrixAsString()Returns a depiction of the score matrix as a
Methods inherited from interface org.biojava.nbio.alignment.template.Aligner
int 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
- the score matrix
getScoreMatrixAsStringReturns 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.
- the score matrix as a character sequence