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 alignmentProfileis of type SC- each element of anAlignedSequenceis aCompoundof 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:
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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
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Constructor Summary
ConstructorsConstructorDescriptionSimpleProfilePair(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
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, toStringMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitMethods inherited from interface java.lang.Iterable
forEach, iterator, spliteratorMethods 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
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Constructor Details
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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 pairtarget- the second profile of the pairsx- lists whether the query profile aligns aCompoundor gap at each index of the alignmentsy- lists whether the target profile aligns aCompoundor gap at each index of the alignment- Throws:
IllegalArgumentException- if alignments differ in size or given profiles do not fit in alignments
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Method Details
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getQuery
Description copied from interface:ProfilePairReturns the firstProfileof the pair. -
getTarget
Description copied from interface:ProfilePairReturns the secondProfileof the pair.
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