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java.lang.Objectorg.biojava3.alignment.Alignments
public class Alignments
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.
Nested Class Summary | |
---|---|
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. |
Method Summary | ||
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static
|
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 . |
|
static
|
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 . |
|
static
|
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 . |
|
static
|
getMultipleSequenceAlignment(List<S> sequences,
Object... settings)
Factory method which computes a multiple sequence alignment for the given List of Sequence s. |
|
static
|
getPairwiseAligner(S query,
S target,
Alignments.PairwiseSequenceAlignerType type,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix)
Factory method which constructs a pairwise sequence aligner. |
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static
|
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
|
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
|
runPairwiseScorers(List<PairwiseSequenceScorer<S,C>> scorers)
Factory method to run a list of scorers concurrently. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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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)
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 alignment
public static <S extends Sequence<C>,C extends Compound> Profile<S,C> getMultipleSequenceAlignment(List<S> sequences, Object... settings)
List
of Sequence
s.
S
- each Sequence
of the List
is of type SC
- each element of a Sequence
is a Compound
of type Csequences
- the List
of Sequence
s to alignsettings
- optional settings that adjust the alignment
Profile
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 alignment
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)
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 alignment
public static <S extends Sequence<C>,C extends Compound> int[] getAllPairsScores(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 alignment
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)
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 alignment
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)
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 alignment
public static <S extends Sequence<C>,C extends Compound> int[] runPairwiseScorers(List<PairwiseSequenceScorer<S,C>> scorers)
ConcurrencyTools
utility.
S
- each Sequence
of an alignment pair is of type SC
- each element of an AlignedSequence
is a Compound
of type Cscorers
- list of scorers to run
|
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