Package org.biojava.nbio.core.alignment

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

java.lang.Object

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

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

Type Parameters:

S - each element of an 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>, ProfilePair<S,C>

public class SimpleProfilePair<S extends Sequence<C>,C extends Compound>
extends SimpleProfile<S,C>
implements ProfilePair<S,C>

Implements a data structure for the results of the alignment of a pair of Profiles.

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
SimpleProfilePair(Profile<S,C> query, Profile<S,C> target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)	Creates a pair profile for the given profiles.

Method Summary

Modifier and Type	Method	Description
Profile<S,C>	getQuery()	Returns the first Profile of the pair.
Profile<S,C>	getTarget()	Returns the second Profile 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 Detail

SimpleProfilePair

public SimpleProfilePair(Profile<S,C> query,
                         Profile<S,C> target,
                         List<AlignedSequence.Step> sx,
                         List<AlignedSequence.Step> sy)

Creates a pair profile for the given profiles.

Parameters:

query - the first profile of the pair

target - the second profile of the pair

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

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

Throws:

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

Method Detail

getQuery

public Profile<S,C> getQuery()

Description copied from interface: ProfilePair

Returns the first Profile of the pair.

Specified by:

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

Returns:

the first Profile of the pair

getTarget

public Profile<S,C> getTarget()

Description copied from interface: ProfilePair

Returns the second Profile of the pair.

Specified by:

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

Returns:

the second Profile of the pair