Package org.biojava.nbio.core.alignment

Class SimpleSequencePair<S extends Sequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.core.alignment.SimpleProfile<S,C>

org.biojava.nbio.core.alignment.SimpleSequencePair<S,C>

Type Parameters:

S - each element of the alignment Profile is of type S

C - each element of an AlignedSequence is a Compound of type C

All Implemented Interfaces:

Serializable, Iterable<AlignedSequence<S,C>>, Profile<S,C>, SequencePair<S,C>

public class SimpleSequencePair<S extends Sequence<C>,C extends Compound>
extends SimpleProfile<S,C>
implements SequencePair<S,C>

Implements a data structure for the results of pairwise sequence alignment.

Author:

Mark Chapman, Paolo Pavan

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.core.alignment.template.Profile

Profile.StringFormat

Field Summary

Fields inherited from class org.biojava.nbio.core.alignment.SimpleProfile

matrix

Constructor Summary

Constructors

Constructor	Description
SimpleSequencePair(AlignedSequence<S,C> query, AlignedSequence<S,C> target)	Creates a pair profile for the given already aligned sequences.
SimpleSequencePair(S query, S target, List<AlignedSequence.Step> sx, int xb, int xa, List<AlignedSequence.Step> sy, int yb, int ya)	Creates a pair profile for the given sequences with a local alignment.
SimpleSequencePair(S query, S target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)	Creates a pair profile for the given sequences with a global alignment.

Method Summary

Modifier and Type	Method	Description
C	getCompoundInQueryAt(int alignmentIndex)	Returns the Compound in query sequence at given column index in alignment.
C	getCompoundInTargetAt(int alignmentIndex)	Returns the Compound in target sequence at given column index in alignment.
int	getIndexInQueryAt(int alignmentIndex)	Returns the query index corresponding to a given alignment column.
int	getIndexInQueryForTargetAt(int targetIndex)	Returns the query index corresponding to a given target index.
int	getIndexInTargetAt(int alignmentIndex)	Returns the target index corresponding to a given alignment column.
int	getIndexInTargetForQueryAt(int queryIndex)	Returns the target index corresponding to a given query index.
int	getNumIdenticals()	Returns the number of indices for which both the query and target sequences have an identical Compound.
int	getNumSimilars()	Returns the number of indices for which both the query and target sequences have a similar Compound.
double	getPercentageOfIdentity(boolean countGaps)	Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.
AlignedSequence<S,C>	getQuery()	Returns the first AlignedSequence of the pair.
AlignedSequence<S,C>	getTarget()	Returns the second AlignedSequence of the pair.

Methods inherited from class org.biojava.nbio.core.alignment.SimpleProfile

getAlignedSequence, getAlignedSequence, getAlignedSequences, getAlignedSequences, getAlignedSequences, getCompoundAt, getCompoundAt, getCompoundCountsAt, getCompoundCountsAt, getCompoundsAt, getCompoundSet, getCompoundWeightsAt, getCompoundWeightsAt, getIndexOf, getIndicesAt, getLastIndexOf, getLength, getOriginalSequences, getSize, getSubProfile, hasGap, isCircular, iterator, toString, toString, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, iterator, spliterator

Methods inherited from interface org.biojava.nbio.core.alignment.template.Profile

getAlignedSequence, getAlignedSequence, getAlignedSequences, getAlignedSequences, getAlignedSequences, getCompoundAt, getCompoundAt, getCompoundCountsAt, getCompoundCountsAt, getCompoundsAt, getCompoundSet, getCompoundWeightsAt, getCompoundWeightsAt, getIndexOf, getIndicesAt, getLastIndexOf, getLength, getOriginalSequences, getSize, getSubProfile, hasGap, isCircular, toString, toString, toString

Constructor Details

SimpleSequencePair

public SimpleSequencePair(AlignedSequence<S,C> query,
 AlignedSequence<S,C> target)

Creates a pair profile for the given already aligned sequences.

Parameters:

query - the first sequence of the pair

target - the second sequence of the pair

Throws:

IllegalArgumentException - if sequences differ in size

SimpleSequencePair

public SimpleSequencePair(S query,
 S target,
 List<AlignedSequence.Step> sx,
 List<AlignedSequence.Step> sy)

Creates a pair profile for the given sequences with a global alignment.

Parameters:

query - the first sequence of the pair

target - the second sequence of the pair

sx - lists whether the query sequence aligns a Compound or gap at each index of the alignment

sy - lists whether the target sequence aligns a Compound or gap at each index of the alignment

Throws:

IllegalArgumentException - if alignments differ in size or given sequences do not fit in alignments

SimpleSequencePair

public SimpleSequencePair(S query,
 S target,
 List<AlignedSequence.Step> sx,
 int xb,
 int xa,
 List<AlignedSequence.Step> sy,
 int yb,
 int ya)

Creates a pair profile for the given sequences with a local alignment.

Parameters:

query - the first sequence of the pair

target - the second sequence of the pair

sx - lists whether the query sequence aligns a Compound or gap at each index of the alignment

xb - number of Compounds skipped in the query sequence before the aligned region

xa - number of Compounds skipped in the query sequence after the aligned region

sy - lists whether the target sequence aligns a Compound or gap at each index of the alignment

yb - number of Compounds skipped in the target sequence before the aligned region

ya - number of Compounds skipped in the target sequence after the aligned region

Throws:

IllegalArgumentException - if alignments differ in size or given sequences do not fit in alignments

Method Details

getCompoundInQueryAt

public C getCompoundInQueryAt(int alignmentIndex)

Description copied from interface: SequencePair

Returns the Compound in query sequence at given column index in alignment.

Specified by:

getCompoundInQueryAt in interface SequencePair<S extends Sequence<C>,C extends Compound>

Parameters:

alignmentIndex - column index in alignment

Returns:

the query sequence element

getCompoundInTargetAt

public C getCompoundInTargetAt(int alignmentIndex)

Description copied from interface: SequencePair

Returns the Compound in target sequence at given column index in alignment.

Specified by:

getCompoundInTargetAt in interface SequencePair<S extends Sequence<C>,C extends Compound>

Parameters:

alignmentIndex - column index in alignment

Returns:

the target sequence element

getIndexInQueryAt

public int getIndexInQueryAt(int alignmentIndex)

Description copied from interface: SequencePair

Returns the query index corresponding to a given alignment column.

Specified by:

getIndexInQueryAt in interface SequencePair<S extends Sequence<C>,C extends Compound>

Parameters:

alignmentIndex - column index in alignment

Returns:

index in query Sequence

getIndexInQueryForTargetAt

public int getIndexInQueryForTargetAt(int targetIndex)

Description copied from interface: SequencePair

Returns the query index corresponding to a given target index.

Specified by:

getIndexInQueryForTargetAt in interface SequencePair<S extends Sequence<C>,C extends Compound>

Parameters:

targetIndex - index in target Sequence

Returns:

index in query Sequence

getIndexInTargetAt

public int getIndexInTargetAt(int alignmentIndex)

Description copied from interface: SequencePair

Returns the target index corresponding to a given alignment column.

Specified by:

getIndexInTargetAt in interface SequencePair<S extends Sequence<C>,C extends Compound>

Parameters:

alignmentIndex - column index in alignment

Returns:

index in target Sequence

getIndexInTargetForQueryAt

public int getIndexInTargetForQueryAt(int queryIndex)

Description copied from interface: SequencePair

Returns the target index corresponding to a given query index.

Specified by:

getIndexInTargetForQueryAt in interface SequencePair<S extends Sequence<C>,C extends Compound>

Parameters:

queryIndex - index in query Sequence

Returns:

index in target Sequence

getNumIdenticals

public int getNumIdenticals()

Description copied from interface: SequencePair

Returns the number of indices for which both the query and target sequences have an identical Compound.

Specified by:

getNumIdenticals in interface SequencePair<S extends Sequence<C>,C extends Compound>

Returns:

the number of identical indices

getNumSimilars

public int getNumSimilars()

Description copied from interface: SequencePair

Returns the number of indices for which both the query and target sequences have a similar Compound.

Specified by:

getNumSimilars in interface SequencePair<S extends Sequence<C>,C extends Compound>

Returns:

the number of similar indices

getQuery

public AlignedSequence<S,C> getQuery()

Description copied from interface: SequencePair

Returns the first AlignedSequence of the pair.

Specified by:

getQuery in interface SequencePair<S extends Sequence<C>,C extends Compound>

Returns:

the first AlignedSequence of the pair

getTarget

public AlignedSequence<S,C> getTarget()

Description copied from interface: SequencePair

Returns the second AlignedSequence of the pair.

Specified by:

getTarget in interface SequencePair<S extends Sequence<C>,C extends Compound>

Returns:

the second AlignedSequence of the pair

getPercentageOfIdentity

public double getPercentageOfIdentity(boolean countGaps)

Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.

Specified by:

getPercentageOfIdentity in interface SequencePair<S extends Sequence<C>,C extends Compound>

Parameters:

countGaps - If true, gap positions are counted as mismatches, i.e., the percentage is normalized by the alignment length. If false, gap positions are not counted, i.e. the percentage is normalized by the number of aligned residue pairs. See May (2004). "Percent sequence identity: the need to be explicit."

Returns:

the percentage of sequence identity as a fraction in [0,1]