Uses of Interface
org.biojava.bio.Annotatable

Packages that use Annotatable
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 
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
 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
 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
 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
 interface GFF3Record
          A record in a GFF3 formatted file.
 

Classes in org.biojava.bio.program.gff3 that implement Annotatable
static class GFF3Record.Impl
           
 

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

Classes in org.biojava.bio.program.hmmer that implement Annotatable
 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
 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
 interface UnigeneCluster
           A single unigene cluster.
 

Uses of Annotatable in org.biojava.bio.search
 

Subinterfaces of Annotatable in org.biojava.bio.search
 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
 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
 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
 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
 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
 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
 interface SymbolTokenization
          Encapsulate a mapping between BioJava Symbol objects and some string representation.
 

Classes in org.biojava.bio.seq.io that implement Annotatable
 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
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
 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
 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
 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
 interface Taxon
          Deprecated. replaced by classes in org.biojavax.bio.taxa
 

Classes in org.biojava.bio.taxa that implement Annotatable
 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
 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
 class AbstractTerm
          Abstract implementation of term
 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
static class Variable.Impl
           
 

Uses of Annotatable in org.biojavax
 

Subinterfaces of Annotatable in org.biojavax
 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
 class SimpleCrossRef
          A basic CrossRef implementation.
 

Uses of Annotatable in org.biojavax.bio
 

Subinterfaces of Annotatable in org.biojavax.bio
 interface BioEntry
          This class relates to the bioentry table in BioSQL.
 

Classes in org.biojavax.bio that implement Annotatable
 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
 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
 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
 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
 class SimpleComparableTerm
          A Term object that can be compared and thus sorted.
 class SimpleComparableTriple
          Basic comparable triple, BioSQL style.