org.nmdp.ngs.align

Class ParallelBiojavaPairwiseAlignment

java.lang.Object

org.nmdp.ngs.align.ParallelBiojavaPairwiseAlignment

All Implemented Interfaces:

PairwiseAlignment

public final class ParallelBiojavaPairwiseAlignment
extends Object

Parallel implementation of PairwiseAlignment based on Biojava.

Field Summary

Fields inherited from interface org.nmdp.ngs.align.PairwiseAlignment

DEFAULT_GLOBAL_GAP_PENALTIES, DEFAULT_LOCAL_GAP_PENALTIES

Method Summary

Methods

Modifier and Type	Method and Description
static PairwiseAlignment	create() Create and return a new pairwise alignment implementation configured with a cached thread pool and the default substitution matrix (NUC.4.4.txt).
static PairwiseAlignment	create(int threads) Create and return a new pairwise alignment implementation configured with a fixed thread pool and the default substitution matrix (NUC.4.4.txt).
static PairwiseAlignment	create(int threads, org.biojava.bio.alignment.SubstitutionMatrix substitutionMatrix) Create and return a new pairwise alignment implementation configured with a fixed thread pool and the specified substitution matrix.
static PairwiseAlignment	create(org.biojava.bio.alignment.SubstitutionMatrix substitutionMatrix) Create and return a new pairwise alignment implementation configured with a cached thread pool and the specified substitution matrix.
org.biojava.bio.alignment.SubstitutionMatrix	getSubstitutionMatrix() Return the substitution matrix for this pairwise alignment.
Iterable<org.biojava.bio.alignment.AlignmentPair>	global(List<org.biojava.bio.seq.Sequence> queries, List<org.biojava.bio.seq.Sequence> subjects) Return the alignment pairs from global alignment of the query and subject DNA sequences with the default global alignment gap penalties.
Iterable<org.biojava.bio.alignment.AlignmentPair>	global(List<org.biojava.bio.seq.Sequence> queries, List<org.biojava.bio.seq.Sequence> subjects, GapPenalties gapPenalties) Return the alignment pairs from global alignment of the query and subject DNA sequences with the specified gap penalties.
Iterable<org.biojava.bio.alignment.AlignmentPair>	global(org.biojava.bio.seq.Sequence query, List<org.biojava.bio.seq.Sequence> subjects) Return the alignment pairs from global alignment of the query and subject DNA sequences with the default global alignment gap penalties.
Iterable<org.biojava.bio.alignment.AlignmentPair>	global(org.biojava.bio.seq.Sequence query, List<org.biojava.bio.seq.Sequence> subjects, GapPenalties gapPenalties) Return the alignment pairs from global alignment of the query and subject DNA sequences with the specified gap penalties.
Iterable<org.biojava.bio.alignment.AlignmentPair>	global(org.biojava.bio.seq.Sequence query, org.biojava.bio.seq.Sequence subject) Return the alignment pairs from global alignment of the query and subject DNA sequences with the default global alignment gap penalties.
Iterable<org.biojava.bio.alignment.AlignmentPair>	global(org.biojava.bio.seq.Sequence query, org.biojava.bio.seq.Sequence subject, GapPenalties gapPenalties) Return the alignment pairs from global alignment of the query and subject DNA sequences with the specified gap penalties.
Iterable<org.biojava.bio.alignment.AlignmentPair>	local(List<org.biojava.bio.seq.Sequence> queries, List<org.biojava.bio.seq.Sequence> subjects) Return the alignment pairs from local alignment of the query and subject DNA sequences with the default local alignment gap penalties.
Iterable<org.biojava.bio.alignment.AlignmentPair>	local(List<org.biojava.bio.seq.Sequence> queries, List<org.biojava.bio.seq.Sequence> subjects, GapPenalties gapPenalties) Return the alignment pairs from local alignment of the query and subject DNA sequences with the specified gap penalties.
Iterable<org.biojava.bio.alignment.AlignmentPair>	local(org.biojava.bio.seq.Sequence query, List<org.biojava.bio.seq.Sequence> subjects) Return the alignment pairs from local alignment of the query and subject DNA sequences with the default local alignment gap penalties.
Iterable<org.biojava.bio.alignment.AlignmentPair>	local(org.biojava.bio.seq.Sequence query, List<org.biojava.bio.seq.Sequence> subjects, GapPenalties gapPenalties) Return the alignment pairs from local alignment of the query and subject DNA sequences with the specified gap penalties.
Iterable<org.biojava.bio.alignment.AlignmentPair>	local(org.biojava.bio.seq.Sequence query, org.biojava.bio.seq.Sequence subject) Return the alignment pairs from local alignment of the query and subject DNA sequences with the default local alignment gap penalties.
Iterable<org.biojava.bio.alignment.AlignmentPair>	local(org.biojava.bio.seq.Sequence query, org.biojava.bio.seq.Sequence subject, GapPenalties gapPenalties) Return the alignment pairs from local alignment of the query and subject DNA sequences with the specified gap penalties.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

local

public Iterable<org.biojava.bio.alignment.AlignmentPair> local(List<org.biojava.bio.seq.Sequence> queries,
                                                      List<org.biojava.bio.seq.Sequence> subjects,
                                                      GapPenalties gapPenalties)

Description copied from interface: PairwiseAlignment

Return the alignment pairs from local alignment of the query and subject DNA sequences with the specified gap penalties.

Parameters:

queries - list of query DNA sequences, must not be null

subjects - list of subject DNA sequences, must not be null

gapPenalties - gap penalties, must not be null

Returns:

zero or more alignment pairs from local alignment of the query and subject DNA sequences with the default local alignment gap penalties

global

public Iterable<org.biojava.bio.alignment.AlignmentPair> global(List<org.biojava.bio.seq.Sequence> queries,
                                                       List<org.biojava.bio.seq.Sequence> subjects,
                                                       GapPenalties gapPenalties)

Description copied from interface: PairwiseAlignment

Return the alignment pairs from global alignment of the query and subject DNA sequences with the specified gap penalties.

Parameters:

queries - list of query DNA sequences, must not be null

subjects - list of subject DNA sequences, must not be null

gapPenalties - gap penalties, must not be null

Returns:

zero or more alignment pairs from global alignment of the query and subject DNA sequences with the default global alignment gap penalties

create

public static PairwiseAlignment create()

Create and return a new pairwise alignment implementation configured with a cached thread pool and the default substitution matrix (NUC.4.4.txt).

Returns:

a new pairwise alignment implementation configured with a cached thread pool and the default substitution matrix (NUC.4.4.txt)

create

public static PairwiseAlignment create(int threads)

Create and return a new pairwise alignment implementation configured with a fixed thread pool and the default substitution matrix (NUC.4.4.txt).

Parameters:

threads - number of threads, must be >= 0

Returns:

a new pairwise alignment implementation configured with a fixed thread pool and the default substitution matrix (NUC.4.4.txt)

create

public static PairwiseAlignment create(org.biojava.bio.alignment.SubstitutionMatrix substitutionMatrix)

Create and return a new pairwise alignment implementation configured with a cached thread pool and the specified substitution matrix.

Parameters:

substitutionMatrix - substitution matrix, must not be null

Returns:

a new pairwise alignment implementation configured with a cached thread pool and the specified substitution matrix

create

public static PairwiseAlignment create(int threads,
                       org.biojava.bio.alignment.SubstitutionMatrix substitutionMatrix)

Create and return a new pairwise alignment implementation configured with a fixed thread pool and the specified substitution matrix.

Parameters:

threads - number of threads, must be >= 0

substitutionMatrix - substitution matrix, must not be null

Returns:

a new pairwise alignment implementation configured with a fixed thread pool and the specified substitution matrix

getSubstitutionMatrix

public final org.biojava.bio.alignment.SubstitutionMatrix getSubstitutionMatrix()

Return the substitution matrix for this pairwise alignment.

Returns:

the substitution matrix for this pairwise alignment

local

public Iterable<org.biojava.bio.alignment.AlignmentPair> local(org.biojava.bio.seq.Sequence query,
                                                      org.biojava.bio.seq.Sequence subject)

Description copied from interface: PairwiseAlignment

Return the alignment pairs from local alignment of the query and subject DNA sequences with the default local alignment gap penalties.

Specified by:

local in interface PairwiseAlignment

Parameters:

query - query DNA sequence, must not be null

subject - subject DNA sequence, must not be null

Returns:

zero or more alignment pairs from local alignment of the query and subject DNA sequences with the default local alignment gap penalties

See Also:

PairwiseAlignment.DEFAULT_LOCAL_GAP_PENALTIES

local

public Iterable<org.biojava.bio.alignment.AlignmentPair> local(org.biojava.bio.seq.Sequence query,
                                                      org.biojava.bio.seq.Sequence subject,
                                                      GapPenalties gapPenalties)

Description copied from interface: PairwiseAlignment

Return the alignment pairs from local alignment of the query and subject DNA sequences with the specified gap penalties.

Specified by:

local in interface PairwiseAlignment

Parameters:

query - query DNA sequence, must not be null

subject - subject DNA sequence, must not be null

gapPenalties - gap penalties, must not be null

Returns:

zero or more alignment pairs from local alignment of the query and subject DNA sequences with the default local alignment gap penalties

local

public Iterable<org.biojava.bio.alignment.AlignmentPair> local(org.biojava.bio.seq.Sequence query,
                                                      List<org.biojava.bio.seq.Sequence> subjects)

Description copied from interface: PairwiseAlignment

Return the alignment pairs from local alignment of the query and subject DNA sequences with the default local alignment gap penalties.

Specified by:

local in interface PairwiseAlignment

Parameters:

query - query DNA sequence, must not be null

subjects - list of subject DNA sequences, must not be null

Returns:

zero or more alignment pairs from local alignment of the query and subject DNA sequences with the default local alignment gap penalties

See Also:

PairwiseAlignment.DEFAULT_LOCAL_GAP_PENALTIES

local

public Iterable<org.biojava.bio.alignment.AlignmentPair> local(org.biojava.bio.seq.Sequence query,
                                                      List<org.biojava.bio.seq.Sequence> subjects,
                                                      GapPenalties gapPenalties)

Description copied from interface: PairwiseAlignment

Return the alignment pairs from local alignment of the query and subject DNA sequences with the specified gap penalties.

Specified by:

local in interface PairwiseAlignment

Parameters:

query - query DNA sequence, must not be null

subjects - list of subject DNA sequences, must not be null

gapPenalties - gap penalties, must not be null

Returns:

zero or more alignment pairs from local alignment of the query and subject DNA sequences with the default local alignment gap penalties

local

public Iterable<org.biojava.bio.alignment.AlignmentPair> local(List<org.biojava.bio.seq.Sequence> queries,
                                                      List<org.biojava.bio.seq.Sequence> subjects)

Description copied from interface: PairwiseAlignment

Return the alignment pairs from local alignment of the query and subject DNA sequences with the default local alignment gap penalties.

Specified by:

local in interface PairwiseAlignment

Parameters:

queries - list of query DNA sequences, must not be null

subjects - list of subject DNA sequences, must not be null

Returns:

zero or more alignment pairs from local alignment of the query and subject DNA sequences with the default local alignment gap penalties

See Also:

PairwiseAlignment.DEFAULT_LOCAL_GAP_PENALTIES

global

public Iterable<org.biojava.bio.alignment.AlignmentPair> global(org.biojava.bio.seq.Sequence query,
                                                       org.biojava.bio.seq.Sequence subject)

Description copied from interface: PairwiseAlignment

Return the alignment pairs from global alignment of the query and subject DNA sequences with the default global alignment gap penalties.

Specified by:

global in interface PairwiseAlignment

Parameters:

query - query DNA sequence, must not be null

subject - subject DNA sequence, must not be null

Returns:

zero or more alignment pairs from global alignment of the query and subject DNA sequences with the default global alignment gap penalties

See Also:

PairwiseAlignment.DEFAULT_LOCAL_GAP_PENALTIES

global

public Iterable<org.biojava.bio.alignment.AlignmentPair> global(org.biojava.bio.seq.Sequence query,
                                                       org.biojava.bio.seq.Sequence subject,
                                                       GapPenalties gapPenalties)

Description copied from interface: PairwiseAlignment

Return the alignment pairs from global alignment of the query and subject DNA sequences with the specified gap penalties.

Specified by:

global in interface PairwiseAlignment

Parameters:

query - query DNA sequence, must not be null

subject - subject DNA sequence, must not be null

gapPenalties - gap penalties, must not be null

Returns:

zero or more alignment pairs from global alignment of the query and subject DNA sequences with the default global alignment gap penalties

global

public Iterable<org.biojava.bio.alignment.AlignmentPair> global(org.biojava.bio.seq.Sequence query,
                                                       List<org.biojava.bio.seq.Sequence> subjects)

Description copied from interface: PairwiseAlignment

Return the alignment pairs from global alignment of the query and subject DNA sequences with the default global alignment gap penalties.

Specified by:

global in interface PairwiseAlignment

Parameters:

query - query DNA sequence, must not be null

subjects - list of subject DNA sequences, must not be null

Returns:

zero or more alignment pairs from global alignment of the query and subject DNA sequences with the default global alignment gap penalties

See Also:

PairwiseAlignment.DEFAULT_GLOBAL_GAP_PENALTIES

global

public Iterable<org.biojava.bio.alignment.AlignmentPair> global(org.biojava.bio.seq.Sequence query,
                                                       List<org.biojava.bio.seq.Sequence> subjects,
                                                       GapPenalties gapPenalties)

Description copied from interface: PairwiseAlignment

Return the alignment pairs from global alignment of the query and subject DNA sequences with the specified gap penalties.

Specified by:

global in interface PairwiseAlignment

Parameters:

query - query DNA sequence, must not be null

subjects - list of subject DNA sequences, must not be null

gapPenalties - gap penalties, must not be null

Returns:

zero or more alignment pairs from global alignment of the query and subject DNA sequences with the default global alignment gap penalties

global

public Iterable<org.biojava.bio.alignment.AlignmentPair> global(List<org.biojava.bio.seq.Sequence> queries,
                                                       List<org.biojava.bio.seq.Sequence> subjects)

Description copied from interface: PairwiseAlignment

Return the alignment pairs from global alignment of the query and subject DNA sequences with the default global alignment gap penalties.

Specified by:

global in interface PairwiseAlignment

Parameters:

queries - list of query DNA sequences, must not be null

subjects - list of subject DNA sequences, must not be null

Returns:

zero or more alignment pairs from global alignment of the query and subject DNA sequences with the default global alignment gap penalties

See Also:

PairwiseAlignment.DEFAULT_GLOBAL_GAP_PENALTIES