public class Alignments
extends java.lang.Object
ConcurrencyTools
utility, ConcurrencyTools.shutdown()
or
ConcurrencyTools.shutdownAndAwaitTermination()
must be called.Modifier and Type | Class | Description |
---|---|---|
static class |
Alignments.PairInProfileScorerType |
List of implemented sequence pair in a profile scoring routines.
|
static class |
Alignments.PairwiseSequenceAlignerType |
List of implemented pairwise sequence alignment routines.
|
static class |
Alignments.PairwiseSequenceScorerType |
List of implemented pairwise sequence scoring routines.
|
static class |
Alignments.ProfileProfileAlignerType |
List of implemented profile-profile alignment routines.
|
static class |
Alignments.RefinerType |
List of implemented profile refinement routines.
|
Modifier and Type | Method | Description |
---|---|---|
static <S extends Sequence<C>,C extends Compound> |
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 . |
static <S extends Sequence<C>,C extends Compound> |
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 . |
static <S extends Sequence<C>,C extends Compound> |
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 . |
static <S extends Sequence<C>,C extends Compound> |
getMultipleSequenceAlignment(java.util.List<S> sequences,
java.lang.Object... settings) |
Factory method which computes a multiple sequence alignment for the given
List of Sequence s. |
static <S extends Sequence<C>,C extends Compound> |
getPairwiseAligner(S query,
S target,
Alignments.PairwiseSequenceAlignerType type,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix) |
Factory method which constructs a pairwise sequence aligner.
|
static <S extends Sequence<C>,C extends Compound> |
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. |
static <S extends Sequence<C>,C extends Compound> |
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.
|
static <S extends Sequence<C>,C extends Compound> |
runPairwiseScorers(java.util.List<PairwiseSequenceScorer<S,C>> scorers) |
Factory method to run a list of scorers concurrently.
|
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)
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.S
- each Sequence
of an alignment pair is of type SC
- each element of an AlignedSequence
is a Compound
of type Csequences
- the List
of Sequence
s to aligntype
- chosen type from list of pairwise sequence alignment routinesgapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentpublic static <S extends Sequence<C>,C extends Compound> Profile<S,C> getMultipleSequenceAlignment(java.util.List<S> sequences, java.lang.Object... settings)
List
of Sequence
s.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)
Sequence
pair.S
- each Sequence
of the pair is of type SC
- each element of an AlignedSequence
is a Compound
of type Cquery
- the first Sequence
s to aligntarget
- the second Sequence
s to aligntype
- chosen type from list of pairwise sequence alignment routinesgapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentpublic 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)
Sequence
pairs in the given List
.S
- each Sequence
of a pair is of type SC
- each element of a Sequence
is a Compound
of type Csequences
- the List
of Sequence
s to aligntype
- chosen type from list of pairwise sequence scoring routinesgapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentpublic static <S extends Sequence<C>,C extends Compound> double[] getAllPairsScores(java.util.List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
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.S
- each Sequence
of a pair is of type SC
- each element of a Sequence
is a Compound
of type Csequences
- the List
of Sequence
s to aligntype
- chosen type from list of pairwise sequence scoring routinesgapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentpublic static <S extends Sequence<C>,C extends Compound> PairwiseSequenceAligner<S,C> getPairwiseAligner(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
S
- each Sequence
of an alignment pair is of type SC
- each element of an AlignedSequence
is a Compound
of type Cquery
- the first Sequence
to aligntarget
- the second Sequence
to aligntype
- chosen type from list of pairwise sequence alignment routinesgapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentpublic static <S extends Sequence<C>,C extends Compound> Profile<S,C> getProgressiveAlignment(GuideTree<S,C> tree, Alignments.ProfileProfileAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
ConcurrencyTools
utility.S
- each Sequence
of the Profile
pair is of type SC
- each element of an AlignedSequence
is a Compound
of type Ctree
- guide tree to follow aligning profiles from leaves to roottype
- chosen type from list of profile-profile alignment routinesgapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentpublic static <S extends Sequence<C>,C extends Compound> double[] runPairwiseScorers(java.util.List<PairwiseSequenceScorer<S,C>> scorers)
ConcurrencyTools
utility.