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

Packages that use ProfilePair

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

Uses of ProfilePair in org.biojava.nbio.alignment

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

Modifier and Type	Method	Description
Future<ProfilePair<S,C>>	GuideTree.Node.getProfileFuture()

Method parameters in org.biojava.nbio.alignment with type arguments of type ProfilePair

Modifier and Type	Method	Description
void	GuideTree.Node.setProfileFuture(Future<ProfilePair<S,C>> profileFuture)

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

Modifier	Constructor	Description
	SimpleProfileProfileAligner(Future<ProfilePair<S,C>> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
	SimpleProfileProfileAligner(Future<ProfilePair<S,C>> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
	SimpleProfileProfileAligner(Profile<S,C> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.

Uses of ProfilePair in org.biojava.nbio.alignment.template

Fields in org.biojava.nbio.alignment.template declared as ProfilePair

Modifier and Type	Field	Description
protected ProfilePair<S,C>	AbstractProfileProfileAligner.pair

Methods in org.biojava.nbio.alignment.template that return ProfilePair

Modifier and Type	Method	Description
ProfilePair<S,C>	CallableProfileProfileAligner.call()
ProfilePair<S,C>	AbstractProfileProfileAligner.getPair()
ProfilePair<S,C>	ProfileProfileAligner.getPair()	Returns alignment profile pair.

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

Modifier and Type	Method	Description
Future<ProfilePair<S,C>>	GuideTreeNode.getProfileFuture()	Returns the profile future stored at this node, but does not force the calculation, yet.

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

Modifier and Type	Method	Description
void	GuideTreeNode.setProfileFuture(Future<ProfilePair<S,C>> profileFuture)	Stores the given profile future.

Constructor parameters in org.biojava.nbio.alignment.template with type arguments of type ProfilePair

Modifier	Constructor	Description
protected	AbstractProfileProfileAligner(Future<ProfilePair<S,C>> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
protected	AbstractProfileProfileAligner(Future<ProfilePair<S,C>> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
protected	AbstractProfileProfileAligner(Profile<S,C> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.

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

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

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

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

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

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