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 and 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 and 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 and 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

Constructor and 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.
SimpleProfile(AlignedSequence<S,C> query, AlignedSequence<S,C> target) Creates a pair profile for the given already aligned sequences.
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.
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

Constructor and 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 and 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 and 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 and 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 and Description
void	MutableSequencePair.setPair(AlignedSequence<S,C> query, AlignedSequence<S,C> target) Sets both AlignedSequences of the pair.
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 and Description
void	MutableProfile.setSequences(List<AlignedSequence<S,C>> sequences) Sets entirely new set of AlignedSequences.