Package org.biojava.nbio.alignment.template

Interface Aligner<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:
Scorer
All Known Subinterfaces:
MatrixAligner<S,C>, PairwiseSequenceAligner<S,C>, PartitionRefiner<S,C>, ProfileProfileAligner<S,C>, RescoreRefiner<S,C>
All Known Implementing Classes:
AbstractMatrixAligner, AbstractPairwiseSequenceAligner, AbstractProfileProfileAligner, AnchoredPairwiseSequenceAligner, GuanUberbacher, NeedlemanWunsch, SimpleProfileProfileAligner, SmithWaterman, StandardRescoreRefiner
public interface Aligner<S extends Sequence<C>,C extends Compound> extends Scorer
Defines an algorithm which computes an alignment Profile from a list of Sequences.
Author:
Mark Chapman

  • Method Details

    • getComputationTime

      long getComputationTime()
      Returns the computation time needed for an alignment computed in nanoseconds.
      Returns:
      the computation time in nanoseconds

    • getProfile

      Profile<S,C> getProfile()
      Returns the alignment Profile produced by this alignment algorithm.
      Returns:
      the alignment profile