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

Packages that use Profile

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

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

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

Modifier and Type	Class and Description
class	SimpleProfile<S extends Sequence<C>,C extends Compound> Implements a data structure for the results of sequence alignment.
class	SimpleProfilePair<S extends Sequence<C>,C extends Compound> Implements a data structure for the results of the alignment of a pair of Profiles.
class	SimpleSequencePair<S extends Sequence<C>,C extends Compound> Implements a data structure for the results of pairwise sequence alignment.

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

Modifier and Type	Method and Description
Profile<S,C>	SimpleProfilePair.getQuery()
Profile<S,C>	SimpleProfilePair.getTarget()

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

Constructor and Description
SimpleProfile(Profile<S,C> query, Profile<S,C> target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Creates a pair profile for the given profiles.
SimpleProfile(Profile<S,C> query, Profile<S,C> target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Creates a pair profile for the given profiles.
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.
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.

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

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

Modifier and Type	Interface and Description
interface	MutableProfile<S extends Sequence<C>,C extends Compound> Defines a mutable (editable) data structure for a Profile.
interface	MutableProfilePair<S extends Sequence<C>,C extends Compound> Defines a mutable (editable) data structure for a ProfilePair.
interface	MutableSequencePair<S extends Sequence<C>,C extends Compound> Defines a mutable (editable) data structure for the results of pairwise sequence alignment.
interface	ProfilePair<S extends Sequence<C>,C extends Compound> Defines a data structure for the results of the alignment of a pair of Profiles.
interface	ProfileView<S extends Sequence<C>,C extends Compound> Defines a data structure for a view of sequence alignment.
interface	SequencePair<S extends Sequence<C>,C extends Compound> Defines a data structure for the results of pairwise sequence alignment.

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

Modifier and Type	Method and Description
Profile<S,C>	ProfilePair.getQuery() Returns the first Profile of the pair.
Profile<S,C>	ProfilePair.getTarget() Returns the second Profile of the pair.
Profile<S,C>	ProfileView.getViewedProfile() Returns the entire Profile being viewed

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

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