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	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	Description
Profile<S,C>	SimpleProfilePair.getQuery()
Profile<S,C>	SimpleProfilePair.getTarget()

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

Constructor	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.
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	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	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	Description
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.