Package org.biojava.nbio.alignment.template

Interface MatrixAligner<S extends Sequence<C>,C extends Compound>

Type Parameters:

S - each element of the alignment Profile is of type S

C - 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

Method Summary

Modifier and Type	Method	Description
int[][][]	getScoreMatrix()	Returns the entire score matrix built during alignment.
String	getScoreMatrixAsString()	Returns a depiction of the score matrix as a String.

Methods inherited from interface org.biojava.nbio.alignment.template.Aligner

getComputationTime, getProfile

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer

getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity

Method Detail

getScoreMatrix

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 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