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

Packages that use Profile

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

Uses of Profile in org.biojava.nbio.alignment

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

Modifier and Type	Method and Description
static <S extends Sequence<C>,C extends Compound> Profile<S,C>	Alignments.getMultipleSequenceAlignment(List<S> sequences, Object... settings) Factory method which computes a multiple sequence alignment for the given List of Sequences.
Profile<S,C>	FractionalSimilarityInProfileScorer.getProfile()
Profile<S,C>	GuideTree.Node.getProfile()
Profile<S,C>	FractionalIdentityInProfileScorer.getProfile()
Profile<S,C>	StandardRescoreRefiner.getProfile()
static <S extends Sequence<C>,C extends Compound> Profile<S,C>	Alignments.getProgressiveAlignment(GuideTree<S,C> tree, Alignments.ProfileProfileAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Factory method to run the profile-profile alignments of a progressive multiple sequence alignment concurrently.

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

Modifier and Type	Method and Description
void	GuideTree.Node.setProfile(Profile<S,C> profile)

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

Constructor and Description
FractionalIdentityInProfileScorer(Profile<S,C> profile, int query, int target) Creates a fractional identity scorer for an aligned pair of sequences in the given alignment profile.
FractionalSimilarityInProfileScorer(Profile<S,C> profile, int query, int target) Creates a fractional similarity scorer for an aligned pair of sequences in the given alignment profile.
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.
SimpleProfileProfileAligner(Profile<S,C> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Prepares for a profile-profile alignment.
SimpleProfileProfileAligner(Profile<S,C> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Prepares for a profile-profile alignment.

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

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

Modifier and Type	Field and Description
protected Profile<S,C>	AbstractMatrixAligner.profile

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

Modifier and Type	Method and Description
Profile<S,C>	AbstractMatrixAligner.getProfile()
Profile<S,C>	Aligner.getProfile() Returns the alignment Profile produced by this alignment algorithm.
Profile<S,C>	PairInProfileScorer.getProfile() Returns the Profile from which the aligned pair originated.
Profile<S,C>	GuideTreeNode.getProfile() Returns the profile stored at this node.
Profile<S,C>	AbstractProfileProfileAligner.getQuery()
Profile<S,C>	ProfileProfileScorer.getQuery() Returns the first profile of the pair.
Profile<S,C>	AbstractProfileProfileAligner.getTarget()
Profile<S,C>	ProfileProfileScorer.getTarget() Returns the second profile of the pair.

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

Modifier and Type	Method and Description
void	GuideTreeNode.setProfile(Profile<S,C> profile) Stores the given profile.
void	AbstractProfileProfileAligner.setQuery(Profile<S,C> query) Sets the query Profile.
void	AbstractProfileProfileAligner.setTarget(Profile<S,C> target) Sets the target Profile.

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

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

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.