MatrixAligner

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 Details
- 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