Uses of Interface
org.biojava.bio.Annotatable

Packages that use Annotatable

Package	Description
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program.gff3	Support for reading and writing GFF3.
org.biojava.bio.program.hmmer	Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.unigene	Objects for representing Unigene clusters.
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.homol	The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.io.agave	Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.seq.projection	Code for projecting Feature objects and systematically altering their properties.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.bio.taxa	Taxonomy object for representing species information.
org.biojava.ontology	A general-purpose API for ontologies.
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality The biojavax packages contain a number of extensions to the core biojava interfaces.
org.biojavax.bio	Classes to represent biological entities and their relationships.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.ontology	Extensions to the biojava ontology model that represent BioSQL ontology.

Uses of Annotatable in org.biojava.bio.dp

Subinterfaces of Annotatable in org.biojava.bio.dp

Modifier and Type	Interface and Description
interface	DotState A Dot state.
interface	EmissionState A state in a markov process that has an emission spectrum.
interface	ModelInState A state that contains an entire sub-model.
interface	State A state in a markov process.

Classes in org.biojava.bio.dp that implement Annotatable

Modifier and Type	Class and Description
class	MagicalState Start/end state for HMMs.
class	SimpleDotState A Dot state that you can make and use.
class	SimpleEmissionState
class	SimpleModelInState

Uses of Annotatable in org.biojava.bio.molbio

Subinterfaces of Annotatable in org.biojava.bio.molbio

Modifier and Type	Interface and Description
interface	RestrictionSite RestrictionSite represents the recognition site of a restriction enzyme.

Uses of Annotatable in org.biojava.bio.program.gff3

Subinterfaces of Annotatable in org.biojava.bio.program.gff3

Modifier and Type	Interface and Description
interface	GFF3Record A record in a GFF3 formatted file.

Classes in org.biojava.bio.program.gff3 that implement Annotatable

Modifier and Type	Class and Description
static class	GFF3Record.Impl

Uses of Annotatable in org.biojava.bio.program.hmmer

Classes in org.biojava.bio.program.hmmer that implement Annotatable

Modifier and Type	Class and Description
class	ProfileEmissionState A state in a HMMer model.

Uses of Annotatable in org.biojava.bio.program.phred

Classes in org.biojava.bio.program.phred that implement Annotatable

Modifier and Type	Class and Description
class	PhredSequence PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.

Uses of Annotatable in org.biojava.bio.program.unigene

Subinterfaces of Annotatable in org.biojava.bio.program.unigene

Modifier and Type	Interface and Description
interface	UnigeneCluster A single unigene cluster.

Uses of Annotatable in org.biojava.bio.search

Subinterfaces of Annotatable in org.biojava.bio.search

Modifier and Type	Interface and Description
interface	SeqSimilaritySearchHit Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.
interface	SeqSimilaritySearchResult Objects of this type represent one particular result of a sequence similarity search.
interface	SeqSimilaritySearchSubHit Objects of this type represent one particular sub-hit (one concrete sequence stretch within a sequence and associated information) from a sequence similarity search hit.

Classes in org.biojava.bio.search that implement Annotatable

Modifier and Type	Class and Description
class	SequenceDBSearchHit Deprecated. SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.
class	SequenceDBSearchResult Deprecated. SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.
class	SequenceDBSearchSubHit Deprecated. SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.
class	SimpleSeqSimilaritySearchHit SimpleSeqSimilaritySearchHit objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.
class	SimpleSeqSimilaritySearchResult SimpleSeqSimilaritySearchResult objects represent a result of a search of a SymbolList against the sequences within a SequenceDB object.
class	SimpleSeqSimilaritySearchSubHit SimpleSeqSimilaritySearchSubHit objects represent sub-hits which make up a hit.

Uses of Annotatable in org.biojava.bio.seq

Subinterfaces of Annotatable in org.biojava.bio.seq

Modifier and Type	Interface and Description
interface	ComponentFeature Feature which represents a component in an assembly (contig).
interface	Feature A feature within a sequence, or nested within another feature.
static interface	FeatureTypes.Repository A named collection of Types.
static interface	FeatureTypes.Type A type of feature.
interface	FramedFeature Title: FramedFeature.
interface	GappedSequence Extension of GappedSymbolList which also projects features into the gapped coordinate system.
interface	RemoteFeature A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.
interface	Sequence A biological sequence.
interface	StrandedFeature Adds the concept of 'strand' to features.

Classes in org.biojava.bio.seq that implement Annotatable

Modifier and Type	Class and Description
class	CircularView A circular view onto another Sequence object.
static class	FeatureTypes.RepositoryImpl A simple implementation of a Repository.
class	NewSimpleAssembly A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
class	SimpleAssembly A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.

Uses of Annotatable in org.biojava.bio.seq.homol

Subinterfaces of Annotatable in org.biojava.bio.seq.homol

Modifier and Type	Interface and Description
interface	HomologyFeature
interface	SimilarityPairFeature SimilarityPairFeature describes a pairwise similarity between two nucleotide sequences (as it extends StrandedFeature).

Uses of Annotatable in org.biojava.bio.seq.impl

Classes in org.biojava.bio.seq.impl that implement Annotatable

Modifier and Type	Class and Description
class	DummySequence A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
class	RevCompSequence A reverse complement view onto Sequence interface.
class	SimpleFeature A no-frills implementation of a feature.
class	SimpleFramedFeature Title: SimpleFramedFeature.
class	SimpleGappedSequence Simple implementation of GappedSequence.
class	SimpleHomologyFeature
class	SimpleRemoteFeature A no-frills implementation of a remote feature.
class	SimpleRestrictionSite SimpleRestrictionSite represents the recognition site of a restriction enzyme.
class	SimpleSequence A basic implementation of the Sequence interface.
class	SimpleSimilarityPairFeature SimpleSimilarityPairFeature represents a similarity between a query sequence and a subject sequence as produced by a search program.
class	SimpleStrandedFeature A no-frills implementation of StrandedFeature.
class	SubSequence View a sub-section of a given sequence object, including all the features intersecting that region.
class	ViewSequence A view onto another Sequence object.

Uses of Annotatable in org.biojava.bio.seq.io

Subinterfaces of Annotatable in org.biojava.bio.seq.io

Modifier and Type	Interface and Description
interface	SymbolTokenization Encapsulate a mapping between BioJava Symbol objects and some string representation.

Classes in org.biojava.bio.seq.io that implement Annotatable

Modifier and Type	Class and Description
class	AlternateTokenization Implementation of SymbolTokenization which binds symbols to strings of characters.
class	CharacterTokenization Implementation of SymbolTokenization which binds symbols to single unicode characters.
class	CrossProductTokenization Tokenization for cross-product alphabets.
class	DoubleTokenization
class	IntegerTokenization
class	NameTokenization Simple implementation of SymbolTokenization which uses the `name' field of the symbols.
class	SubIntegerTokenization
class	WordTokenization Base class for tokenizations which accept whitespace-separated `words'.

Uses of Annotatable in org.biojava.bio.seq.io.agave

Methods in org.biojava.bio.seq.io.agave with parameters of type Annotatable

Modifier and Type	Method and Description
protected void	AgaveWriter.writeAssembly(Annotatable seq)
protected void	AgaveWriter.writeBioSequence(Annotatable seq)
protected void	AgaveWriter.writeClassification(Annotatable seq)
protected void	AgaveWriter.writeCompResult(Annotatable f)
protected void	AgaveWriter.writeContig(Annotatable seq)
protected void	AgaveWriter.writeGene(Annotatable f)
protected void	AgaveWriter.writeSeqFeature(Annotatable f) Write SeqFeature XML
protected void	AgaveWriter.writeSequenceMap(Annotatable seq) group sequence_map by getSource()
protected void	AgaveWriter.writeSequenceMap2(Annotatable f) Write SequenceMap XML
protected void	AgaveWriter.writeTranscript(Annotatable f)

Uses of Annotatable in org.biojava.bio.seq.projection

Classes in org.biojava.bio.seq.projection that implement Annotatable

Modifier and Type	Class and Description
class	ProjectedFeature Internal class used by ProjectionEngine to wrap Feature objects.

Uses of Annotatable in org.biojava.bio.symbol

Subinterfaces of Annotatable in org.biojava.bio.symbol

Modifier and Type	Interface and Description
interface	Alphabet The set of AtomicSymbols which can be concatenated together to make a SymbolList.
interface	AtomicSymbol A symbol that is not ambiguous.
interface	BasisSymbol A symbol that can be represented as a string of Symbols.
interface	FiniteAlphabet An alphabet over a finite set of Symbols.
interface	Symbol A single symbol.

Classes in org.biojava.bio.symbol that implement Annotatable

Modifier and Type	Class and Description
class	AbstractAlphabet An abstract implementation of Alphabet.
class	AbstractSymbol The base-class for Symbol implementations.
class	DoubleAlphabet An efficient implementation of an Alphabet over the infinite set of double values.
static class	DoubleAlphabet.DoubleRange A range of double values.
static class	DoubleAlphabet.DoubleSymbol A single double value.
static class	DoubleAlphabet.SubDoubleAlphabet A class to represent a contiguous range of double symbols.
class	FundamentalAtomicSymbol An atomic symbol consisting only of itself.
class	IntegerAlphabet An efficient implementation of an Alphabet over the infinite set of integer values.
static class	IntegerAlphabet.IntegerSymbol A single int value.
static class	IntegerAlphabet.SubIntegerAlphabet A class to represent a finite contiguous subset of the infinite IntegerAlphabet
class	SimpleAlphabet A simple no-frills implementation of the FiniteAlphabet interface.
class	SimpleAtomicSymbol A basic implementation of AtomicSymbol.
class	SingletonAlphabet An alphabet that contains a single atomic symbol.
class	SoftMaskedAlphabet Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.
class	SoftMaskedAlphabet.CaseSensitiveTokenization This SymbolTokenizer works with a delegate to softmask symbol tokenization as appropriate.

Uses of Annotatable in org.biojava.bio.taxa

Subinterfaces of Annotatable in org.biojava.bio.taxa

Modifier and Type	Interface and Description
interface	Taxon Deprecated. replaced by classes in org.biojavax.bio.taxa

Classes in org.biojava.bio.taxa that implement Annotatable

Modifier and Type	Class and Description
class	AbstractTaxon Deprecated. replaced by classes in org.biojavax.bio.taxa
class	SimpleTaxon Deprecated. replaced by classes in org.biojavax.bio.taxa
class	WeakTaxon Deprecated. replaced by classes in org.biojavax.bio.taxa

Uses of Annotatable in org.biojava.ontology

Subinterfaces of Annotatable in org.biojava.ontology

Modifier and Type	Interface and Description
interface	OntologyTerm A term in an ontology which identifies another ontology.
interface	RemoteTerm A term in another ontology.
interface	Term A term in an ontology.
interface	Triple A triple in an ontology.
interface	Variable

Classes in org.biojava.ontology that implement Annotatable

Modifier and Type	Class and Description
class	AbstractTerm Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
class	IntegerOntology.IntTerm
static class	OntologyTerm.Impl Simple in-memory implementation of a remote ontology term.
static class	RemoteTerm.Impl Simple in-memory implementation of a remote ontology term.
static class	Term.Impl Simple in-memory implementation of an ontology term.
static class	Triple.Impl Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple
static class	Variable.Impl

Uses of Annotatable in org.biojavax

Subinterfaces of Annotatable in org.biojavax

Modifier and Type	Interface and Description
interface	CrossRef Represents a cross reference to another database.
interface	RichAnnotatable Annotatable objects that can have rich annotations.

Classes in org.biojavax that implement Annotatable

Modifier and Type	Class and Description
class	SimpleCrossRef A basic CrossRef implementation.

Uses of Annotatable in org.biojavax.bio

Subinterfaces of Annotatable in org.biojavax.bio

Modifier and Type	Interface and Description
interface	BioEntry This class relates to the bioentry table in BioSQL.

Classes in org.biojavax.bio that implement Annotatable

Modifier and Type	Class and Description
class	SimpleBioEntry Reference implementation of a BioEntry object which has no features or sequence.

Uses of Annotatable in org.biojavax.bio.seq

Subinterfaces of Annotatable in org.biojavax.bio.seq

Modifier and Type	Interface and Description
interface	RichFeature Represents a feature that can be given name and rank and be moved from one sequence to another.
interface	RichLocation Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.
interface	RichSequence A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.

Classes in org.biojavax.bio.seq that implement Annotatable

Modifier and Type	Class and Description
class	CompoundRichLocation An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
class	EmptyRichLocation An Empty implementation of RichLocation.
class	MultiSourceCompoundRichLocation An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.
class	SimpleRichFeature A simple implementation of RichFeature.
class	SimpleRichLocation A simple implementation of RichLocation.
class	SimpleRichSequence A simple implementation of RichSequence.
class	ThinRichSequence A simple implementation of RichSequence.

Uses of Annotatable in org.biojavax.ontology

Subinterfaces of Annotatable in org.biojavax.ontology

Modifier and Type	Interface and Description
interface	ComparableTerm Makes Term objects comparable properly and adds some extra features to them.
interface	ComparableTriple Comparable triples, obviously.

Classes in org.biojavax.ontology that implement Annotatable

Modifier and Type	Class and Description
class	SimpleComparableTerm A Term object that can be compared and thus sorted.
class	SimpleComparableTriple Basic comparable triple, BioSQL style.