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.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 into alternate coordinate systems. 
org.biojava.bio.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. 
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. 
 

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.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.
 class DummySequence
           
static class FeatureTypes.RepositoryImpl
          A simple implementation of a Repository.
 class SimpleAssembly
          A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
 class SimpleGappedSequence
          Simple implementation of GappedSequence.
 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.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 RevCompSequence
          A reverse complement view onto Sequence interface.
 class SimpleFeature
          A no-frills implementation of a feature.
 class SimpleFramedFeature
          Title: SimpleFramedFeature.
 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.
 

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 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.writeContig(Annotatable seq)
           
protected  void AgaveWriter.writeAssembly(Annotatable seq)
           
protected  void AgaveWriter.writeBioSequence(Annotatable seq)
           
protected  void AgaveWriter.writeSequenceMap(Annotatable seq)
          group sequence_map by getSource()
protected  void AgaveWriter.writeClassification(Annotatable seq)
           
protected  void AgaveWriter.writeSequenceMap2(Annotatable f)
          Write SequenceMap XML
protected  void AgaveWriter.writeGene(Annotatable f)
           
protected  void AgaveWriter.writeTranscript(Annotatable f)
           
protected  void AgaveWriter.writeSeqFeature(Annotatable f)
          Write SeqFeature XML
protected  void AgaveWriter.writeCompResult(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.
 class ProjectedStrandedFeature
          Internal class used by ProjectedFeatureHolder to wrap StrandedFeatures.
 

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

Classes in org.biojava.bio.seq.ragbag that implement Annotatable
(package private)  class org.biojava.bio.seq.ragbag.RagbagAbstractSequence
          object that instantiates a sequence in Ragbag.
 class RagbagAssembly
          object that instantiates a sequence when given a Ragbag directory.
 

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.
(package private)  class org.biojava.bio.symbol.SimpleBasisSymbol
          A basic implementation of BasisSymbol.
(package private)  class org.biojava.bio.symbol.SimpleSymbol
          A basic implementation of Symbol.
 class SingletonAlphabet
          An alphabet that contains a single atomic symbol.
 

Uses of Annotatable in org.biojava.bio.taxa
 

Subinterfaces of Annotatable in org.biojava.bio.taxa
 interface Taxon
          A taxon within a classification.
 

Classes in org.biojava.bio.taxa that implement Annotatable
 class AbstractTaxon
          An abstract implementation of Taxon.
 class SimpleTaxon
          A no-frills implementatation of Taxon.
 class WeakTaxon
          An implementation of Taxon that keeps only weak references to children, but full references to parents.