Uses of Interface
org.biojava.nbio.alignment.template.ProfileProfileScorer

Packages that use ProfileProfileScorer

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

Uses of ProfileProfileScorer in org.biojava.nbio.alignment

Classes in org.biojava.nbio.alignment that implement ProfileProfileScorer

Modifier and Type	Class	Description
class	SimpleProfileProfileAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Implements a simple (naive) Aligner for a pair of Profiles.

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

Subinterfaces of ProfileProfileScorer in org.biojava.nbio.alignment.template

Modifier and Type	Interface	Description
interface	PartitionRefiner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning.
interface	ProfileProfileAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Defines an Aligner for a pair of Profiles.

Classes in org.biojava.nbio.alignment.template that implement ProfileProfileScorer

Modifier and Type	Class	Description
class	AbstractProfileProfileAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Implements common code for an Aligner for a pair of Profiles.