MutableSequencePair

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>>, MutableProfile<S,C>, Profile<S,C>, SequencePair<S,C>

public interface MutableSequencePair<S extends Sequence<C>,C extends Compound> extends MutableProfile<S,C>, SequencePair<S,C>

Defines a mutable (editable) 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

void

setPair(AlignedSequence<S,C> query, AlignedSequence<S,C> target)

Sets both AlignedSequences of the pair.

void

setQuery(AlignedSequence<S,C> query)

Sets the first AlignedSequence of the pair.

void

setTarget(AlignedSequence<S,C> target)

Sets 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.MutableProfile
setSequences

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

Methods inherited from interface org.biojava.nbio.core.alignment.template.SequencePair
getCompoundInQueryAt, getCompoundInTargetAt, getIndexInQueryAt, getIndexInQueryForTargetAt, getIndexInTargetAt, getIndexInTargetForQueryAt, getNumIdenticals, getNumSimilars, getQuery, getTarget

Method Details
- setPair
  
  void setPair(AlignedSequence<S,C> query, AlignedSequence<S,C> target)
  
  Sets both AlignedSequences of the pair.
  
  Parameters:
  
  query - becomes the first AlignedSequence of the pair
  
  target - becomes the second AlignedSequence of the pair
  
  Throws:
  
  IllegalArgumentException - if query and target are different lengths
- setQuery
  
  void setQuery(AlignedSequence<S,C> query)
  
  Sets the first AlignedSequence of the pair.
  
  Parameters:
  
  query - becomes the first AlignedSequence of the pair
  
  Throws:
  
  IllegalArgumentException - if (new) query and (old) target are different lengths
- setTarget
  
  void setTarget(AlignedSequence<S,C> target)
  
  Sets the second AlignedSequence of the pair.
  
  Parameters:
  
  target - becomes the second AlignedSequence of the pair
  
  Throws:
  
  IllegalArgumentException - if (old) query and (new) target are different lengths