MutableProfile

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:: MutableProfilePair<S,C>, MutableSequencePair<S,C>

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

Defines a mutable (editable) data structure for a Profile. Returned Lists are modifiable.

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

setSequences(List<AlignedSequence<S,C>> sequences)

Sets entirely new set of AlignedSequences.

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 Details
- setSequences
  
  void setSequences(List<AlignedSequence<S,C>> sequences)
  
  Sets entirely new set of AlignedSequences.
  
  Parameters:
  
  sequences - new set of sequences
  
  Throws:
  
  IllegalArgumentException - if sequences have different lengths