Uses of Interface
org.biojava.nbio.core.alignment.template.AlignedSequence

Packages that use AlignedSequence

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

Uses of AlignedSequence in org.biojava.nbio.core.alignment

Classes in org.biojava.nbio.core.alignment that implement AlignedSequence

Modifier and Type	Class	Description
class	SimpleAlignedSequence<S extends Sequence<C>,C extends Compound>	Implements a data structure for a Sequence within an alignment.

Methods in org.biojava.nbio.core.alignment that return AlignedSequence

Modifier and Type	Method	Description
AlignedSequence<S,C>	SimpleProfile.getAlignedSequence(int listIndex)
AlignedSequence<S,C>	SimpleProfile.getAlignedSequence(S sequence)
AlignedSequence<S,C>	SimpleSequencePair.getQuery()
AlignedSequence<S,C>	SimpleSequencePair.getTarget()

Methods in org.biojava.nbio.core.alignment that return types with arguments of type AlignedSequence

Modifier and Type	Method	Description
List<AlignedSequence<S,C>>	SimpleProfile.getAlignedSequences()
List<AlignedSequence<S,C>>	SimpleProfile.getAlignedSequences(int... listIndices)
List<AlignedSequence<S,C>>	SimpleProfile.getAlignedSequences(S... sequences)
Iterator<AlignedSequence<S,C>>	SimpleProfile.iterator()

Constructors in org.biojava.nbio.core.alignment with parameters of type AlignedSequence

Modifier	Constructor	Description
	SimpleAlignedSequence(AlignedSequence<S,C> prev, List<AlignedSequence.Step> steps)	Creates a new AlignedSequence for the given AlignedSequence in a global alignment.
	SimpleAlignedSequence(AlignedSequence<S,C> prev, List<AlignedSequence.Step> steps, int numBefore, int numAfter)	Creates a new AlignedSequence for the given AlignedSequence in a local alignment.
protected	SimpleProfile(AlignedSequence<S,C> query, AlignedSequence<S,C> target)	Creates a pair profile for the given already aligned sequences.
	SimpleSequencePair(AlignedSequence<S,C> query, AlignedSequence<S,C> target)	Creates a pair profile for the given already aligned sequences.

Constructor parameters in org.biojava.nbio.core.alignment with type arguments of type AlignedSequence

Modifier	Constructor	Description
	SimpleProfile(Collection<AlignedSequence<S,C>> alignedSequences)	Creates a profile for the already aligned sequences.

Uses of AlignedSequence in org.biojava.nbio.core.alignment.template

Subinterfaces of AlignedSequence in org.biojava.nbio.core.alignment.template

Modifier and Type	Interface	Description
interface	MutableAlignedSequence<S extends Sequence<C>,C extends Compound>	Defines a mutable (editable) data structure for an AlignedSequence.

Methods in org.biojava.nbio.core.alignment.template that return AlignedSequence

Modifier and Type	Method	Description
AlignedSequence<S,C>	Profile.getAlignedSequence(int listIndex)	Returns AlignedSequence at given index.
AlignedSequence<S,C>	Profile.getAlignedSequence(S sequence)	Searches for the given Sequence within this alignment profile.
AlignedSequence<S,C>	SequencePair.getQuery()	Returns the first AlignedSequence of the pair.
AlignedSequence<S,C>	SequencePair.getTarget()	Returns the second AlignedSequence of the pair.

Methods in org.biojava.nbio.core.alignment.template that return types with arguments of type AlignedSequence

Modifier and Type	Method	Description
List<AlignedSequence<S,C>>	Profile.getAlignedSequences()	Returns a List containing the individual AlignedSequences of this alignment.
List<AlignedSequence<S,C>>	Profile.getAlignedSequences(int... listIndices)	Returns a List containing some of the individual AlignedSequences of this alignment.
List<AlignedSequence<S,C>>	Profile.getAlignedSequences(S... sequences)	Returns a List containing some of the individual AlignedSequences of this alignment.

Methods in org.biojava.nbio.core.alignment.template with parameters of type AlignedSequence

Modifier and Type	Method	Description
void	MutableSequencePair.setPair(AlignedSequence<S,C> query, AlignedSequence<S,C> target)	Sets both AlignedSequences of the pair.
void	MutableSequencePair.setQuery(AlignedSequence<S,C> query)	Sets the first AlignedSequence of the pair.
void	MutableSequencePair.setTarget(AlignedSequence<S,C> target)	Sets the second AlignedSequence of the pair.

Method parameters in org.biojava.nbio.core.alignment.template with type arguments of type AlignedSequence

Modifier and Type	Method	Description
void	MutableProfile.setSequences(List<AlignedSequence<S,C>> sequences)	Sets entirely new set of AlignedSequences.