Package org.biojava.nbio.core.alignment.template

Interface SequencePair<S extends Sequence<C>,C extends Compound>

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 Superinterfaces:

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

All Known Subinterfaces:

MutableSequencePair<S,C>

All Known Implementing Classes:

SimpleSequencePair

public interface SequencePair<S extends Sequence<C>,C extends Compound>
extends Profile<S,C>

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

Author:

Mark Chapman, Paolo Pavan

Nested Class Summary

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

Profile.StringFormat

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 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

Method Detail

getCompoundInQueryAt

C getCompoundInQueryAt(int alignmentIndex)

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

Parameters:

alignmentIndex - column index in alignment

Returns:

the query sequence element

Throws:

IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Profile.getLength()

getCompoundInTargetAt

C getCompoundInTargetAt(int alignmentIndex)

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

Parameters:

alignmentIndex - column index in alignment

Returns:

the target sequence element

Throws:

IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Profile.getLength()

getIndexInQueryAt

int getIndexInQueryAt(int alignmentIndex)

Returns the query index corresponding to a given alignment column.

Parameters:

alignmentIndex - column index in alignment

Returns:

index in query Sequence

Throws:

IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Profile.getLength()

getIndexInQueryForTargetAt

int getIndexInQueryForTargetAt(int targetIndex)

Returns the query index corresponding to a given target index.

Parameters:

targetIndex - index in target Sequence

Returns:

index in query Sequence

Throws:

IndexOutOfBoundsException - if targetIndex < 1 or targetIndex > getTarget().getLength()

getIndexInTargetAt

int getIndexInTargetAt(int alignmentIndex)

Returns the target index corresponding to a given alignment column.

Parameters:

alignmentIndex - column index in alignment

Returns:

index in target Sequence

Throws:

IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Profile.getLength()

getIndexInTargetForQueryAt

int getIndexInTargetForQueryAt(int queryIndex)

Returns the target index corresponding to a given query index.

Parameters:

queryIndex - index in query Sequence

Returns:

index in target Sequence

Throws:

IndexOutOfBoundsException - if queryIndex < 1 or queryIndex > getQuery().getLength()

getNumIdenticals

int getNumIdenticals()

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

Returns:

the number of identical indices

getPercentageOfIdentity

double getPercentageOfIdentity(boolean countGaps)

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

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]

getNumSimilars

int getNumSimilars()

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

Returns:

the number of similar indices

getQuery

AlignedSequence<S,C> getQuery()

Returns the first AlignedSequence of the pair.

Returns:

the first AlignedSequence of the pair

getTarget

AlignedSequence<S,C> getTarget()

Returns the second AlignedSequence of the pair.

Returns:

the second AlignedSequence of the pair