Package org.biojava.nbio.alignment

Class Alignments

java.lang.Object
org.biojava.nbio.alignment.Alignments
public class Alignments extends Object
Static utility to easily run alignment routines. To exit cleanly after running any parallel method that mentions use of the ConcurrencyTools utility, ConcurrencyTools.shutdown() or ConcurrencyTools.shutdownAndAwaitTermination() must be called.
Author:
Mark Chapman

  • Method Details

    • getAllPairsAlignments

      public static <S extends Sequence<C>, C extends Compound> List<SequencePair<S,C>> getAllPairsAlignments(List<S> sequences, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
      Factory method which computes a sequence alignment for all Sequence pairs in the given List. This method runs the alignments in parallel by submitting all of the alignments to the shared thread pool of the ConcurrencyTools utility.
      Type Parameters:
      S - each Sequence of an alignment pair is of type S
      C - each element of an AlignedSequence is a Compound of type C
      Parameters:
      sequences - the List of Sequences to align
      type - chosen type from list of pairwise sequence alignment routines
      gapPenalty - the gap penalties used during alignment
      subMatrix - the set of substitution scores used during alignment
      Returns:
      list of sequence alignment pairs

    • getMultipleSequenceAlignment

      public static <S extends Sequence<C>, C extends Compound> Profile<S,C> getMultipleSequenceAlignment(List<S> sequences, Object... settings)
      Factory method which computes a multiple sequence alignment for the given List of Sequences.
      Type Parameters:
      S - each Sequence of the List is of type S
      C - each element of a Sequence is a Compound of type C
      Parameters:
      sequences - the List of Sequences to align
      settings - optional settings that adjust the alignment
      Returns:
      multiple sequence alignment Profile

    • getPairwiseAlignment

      public static <S extends Sequence<C>, C extends Compound> SequencePair<S,C> getPairwiseAlignment(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
      Factory method which computes a sequence alignment for the given Sequence pair.
      Type Parameters:
      S - each Sequence of the pair is of type S
      C - each element of an AlignedSequence is a Compound of type C
      Parameters:
      query - the first Sequences to align
      target - the second Sequences to align
      type - chosen type from list of pairwise sequence alignment routines
      gapPenalty - the gap penalties used during alignment
      subMatrix - the set of substitution scores used during alignment
      Returns:
      sequence alignment pair

    • getAllPairsScorers

      public static <S extends Sequence<C>, C extends Compound> List<PairwiseSequenceScorer<S,C>> getAllPairsScorers(List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
      Factory method which sets up a sequence pair scorer for all Sequence pairs in the given List.
      Type Parameters:
      S - each Sequence of a pair is of type S
      C - each element of a Sequence is a Compound of type C
      Parameters:
      sequences - the List of Sequences to align
      type - chosen type from list of pairwise sequence scoring routines
      gapPenalty - the gap penalties used during alignment
      subMatrix - the set of substitution scores used during alignment
      Returns:
      list of sequence pair scorers

    • getAllPairsScores

      public static <S extends Sequence<C>, C extends Compound> double[] getAllPairsScores(List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
      Factory method which computes a sequence pair score for all Sequence pairs in the given List. This method runs the scorings in parallel by submitting all of the scorings to the shared thread pool of the ConcurrencyTools utility.
      Type Parameters:
      S - each Sequence of a pair is of type S
      C - each element of a Sequence is a Compound of type C
      Parameters:
      sequences - the List of Sequences to align
      type - chosen type from list of pairwise sequence scoring routines
      gapPenalty - the gap penalties used during alignment
      subMatrix - the set of substitution scores used during alignment
      Returns:
      list of sequence pair scores

    • getPairwiseAligner

      public static <S extends Sequence<C>, C extends Compound> PairwiseSequenceAligner<S,C> getPairwiseAligner(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
      Factory method which constructs a pairwise sequence aligner.
      Type Parameters:
      S - each Sequence of an alignment pair is of type S
      C - each element of an AlignedSequence is a Compound of type C
      Parameters:
      query - the first Sequence to align
      target - the second Sequence to align
      type - chosen type from list of pairwise sequence alignment routines
      gapPenalty - the gap penalties used during alignment
      subMatrix - the set of substitution scores used during alignment
      Returns:
      pairwise sequence aligner

    • getProgressiveAlignment

      public static <S extends Sequence<C>, C extends Compound> Profile<S,C> getProgressiveAlignment(GuideTree<S,C> tree, Alignments.ProfileProfileAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
      Factory method to run the profile-profile alignments of a progressive multiple sequence alignment concurrently. This method runs the alignments in parallel by submitting all of the alignment tasks to the shared thread pool of the ConcurrencyTools utility.
      Type Parameters:
      S - each Sequence of the Profile pair is of type S
      C - each element of an AlignedSequence is a Compound of type C
      Parameters:
      tree - guide tree to follow aligning profiles from leaves to root
      type - chosen type from list of profile-profile alignment routines
      gapPenalty - the gap penalties used during alignment
      subMatrix - the set of substitution scores used during alignment
      Returns:
      multiple sequence alignment

    • runPairwiseScorers

      public static <S extends Sequence<C>, C extends Compound> double[] runPairwiseScorers(List<PairwiseSequenceScorer<S,C>> scorers)
      Factory method to run a list of scorers concurrently. This method runs the scorers in parallel by submitting all of the scoring tasks to the shared thread pool of the ConcurrencyTools utility.
      Type Parameters:
      S - each Sequence of an alignment pair is of type S
      C - each element of an AlignedSequence is a Compound of type C
      Parameters:
      scorers - list of scorers to run
      Returns:
      list of score results from running scorers