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 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
 short[][][] 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.biojava3.alignment.template.Aligner
getComputationTime, getProfile
 
Methods inherited from interface org.biojava3.alignment.template.Scorer
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
 

Method Detail

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