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- Type Parameters:
S
- each element of the alignmentProfile
is of type SC
- each element of anAlignedSequence
is aCompound
of type C
- 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 anAligner
which builds a score matrix during computation.- Author:
- Mark Chapman
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Method Summary
All Methods Instance Methods Abstract Methods 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 aString
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Methods inherited from interface org.biojava.nbio.alignment.template.Aligner
getComputationTime, getProfile
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Methods inherited from interface org.biojava.nbio.alignment.template.Scorer
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
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Method Detail
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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 eachSequence
.- Returns:
- the score matrix
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getScoreMatrixAsString
String getScoreMatrixAsString()
Returns a depiction of the score matrix as aString
. 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
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