Class Alignments

    • Method Detail

      • getAllPairsAlignments

        public static <S extends Sequence<C>,​C extends Compound> java.util.List<SequencePair<S,​C>> getAllPairsAlignments​(java.util.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 CompoundProfile<S,​C> getMultipleSequenceAlignment​(java.util.List<S> sequences,
                                                                                                                       java.lang.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 CompoundSequencePair<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> java.util.List<PairwiseSequenceScorer<S,​C>> getAllPairsScorers​(java.util.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​(java.util.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 CompoundPairwiseSequenceAligner<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 CompoundProfile<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​(java.util.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