Uses of Interface
org.biojava.bio.Annotatable
Packages that use Annotatable
Package
Description
HMM and Dynamic Programming Algorithms.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
Support for reading and writing GFF3.
Tools for working with profile Hidden Markov Models from the HMMer package.
Parser for Phred output
Objects for representing Unigene clusters.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence and
Feature.Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Code for projecting Feature objects and systematically altering their
properties.
Representation of the Symbols that make up a sequence, and locations within
them.
Taxonomy object for representing species information.
A general-purpose API for ontologies.
The Biojava extensions packages, classes that extend the core biojava
functionality
Classes to represent biological entities and their relationships.
Rich implementations of Sequences, Locations and Features.
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.dpModifier and TypeInterfaceDescriptioninterfaceA Dot state.interfaceA state in a markov process that has an emission spectrum.interfaceA state that contains an entire sub-model.interfaceA state in a markov process.Classes in org.biojava.bio.dp that implement AnnotatableModifier and TypeClassDescriptionfinal classStart/end state for HMMs.classA Dot state that you can make and use.classclass -
Uses of Annotatable in org.biojava.bio.molbio
Subinterfaces of Annotatable in org.biojava.bio.molbioModifier and TypeInterfaceDescriptioninterfaceRestrictionSiterepresents the recognition site of a restriction enzyme. -
Uses of Annotatable in org.biojava.bio.program.gff3
Subinterfaces of Annotatable in org.biojava.bio.program.gff3Classes in org.biojava.bio.program.gff3 that implement Annotatable -
Uses of Annotatable in org.biojava.bio.program.hmmer
Classes in org.biojava.bio.program.hmmer that implement Annotatable -
Uses of Annotatable in org.biojava.bio.program.phred
Classes in org.biojava.bio.program.phred that implement AnnotatableModifier and TypeClassDescriptionclassPhredSequence 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 -
Uses of Annotatable in org.biojava.bio.search
Subinterfaces of Annotatable in org.biojava.bio.searchModifier and TypeInterfaceDescriptioninterfaceObjects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.interfaceObjects of this type represent one particular result of a sequence similarity search.interfaceObjects 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 AnnotatableModifier and TypeClassDescriptionclassDeprecated.SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.classDeprecated.SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.classDeprecated.SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.classSimpleSeqSimilaritySearchHitobjects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.classSimpleSeqSimilaritySearchResultobjects represent a result of a search of aSymbolListagainst the sequences within aSequenceDBobject.classSimpleSeqSimilaritySearchSubHitobjects represent sub-hits which make up a hit. -
Uses of Annotatable in org.biojava.bio.seq
Subinterfaces of Annotatable in org.biojava.bio.seqModifier and TypeInterfaceDescriptioninterfaceFeature which represents a component in an assembly (contig).interfaceA feature within a sequence, or nested within another feature.static interfaceA named collection of Types.static interfaceA type of feature.interfaceTitle: FramedFeature.interfaceExtension of GappedSymbolList which also projects features into the gapped coordinate system.interfaceA feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.interfaceA biological sequence.interfaceAdds the concept of 'strand' to features.Classes in org.biojava.bio.seq that implement AnnotatableModifier and TypeClassDescriptionclassA circular view onto another Sequence object.static classA simple implementation of a Repository.classA Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.classA 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.homolModifier and TypeInterfaceDescriptioninterfaceinterfaceSimilarityPairFeaturedescribes a pairwise similarity between two nucleotide sequences (as it extendsStrandedFeature). -
Uses of Annotatable in org.biojava.bio.seq.impl
Classes in org.biojava.bio.seq.impl that implement AnnotatableModifier and TypeClassDescriptionfinal classA Sequence implementation that has a name and URI but no features, and a zero length symbol list.classA reverse complement view ontoSequenceinterface.classA no-frills implementation of a feature.classTitle: SimpleFramedFeature.classSimple implementation of GappedSequence.classclassA no-frills implementation of a remote feature.classSimpleRestrictionSiterepresents the recognition site of a restriction enzyme.classA basic implementation of theSequenceinterface.classSimpleSimilarityPairFeaturerepresents a similarity between a query sequence and a subject sequence as produced by a search program.classA no-frills implementation of StrandedFeature.classView a sub-section of a given sequence object, including all the features intersecting that region.classA view onto another Sequence object. -
Uses of Annotatable in org.biojava.bio.seq.io
Subinterfaces of Annotatable in org.biojava.bio.seq.ioModifier and TypeInterfaceDescriptioninterfaceEncapsulate a mapping between BioJava Symbol objects and some string representation.Classes in org.biojava.bio.seq.io that implement AnnotatableModifier and TypeClassDescriptionclassImplementation of SymbolTokenization which binds symbols to strings of characters.classImplementation of SymbolTokenization which binds symbols to single unicode characters.classTokenization for cross-product alphabets.classclassclassSimple implementation of SymbolTokenization which uses the `name' field of the symbols.classclassBase 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 AnnotatableModifier and TypeMethodDescriptionprotected voidAgaveWriter.writeAssembly(Annotatable seq) protected voidAgaveWriter.writeBioSequence(Annotatable seq) protected voidAgaveWriter.writeClassification(Annotatable seq) protected voidAgaveWriter.writeCompResult(Annotatable f) protected voidAgaveWriter.writeContig(Annotatable seq) protected voidAgaveWriter.writeGene(Annotatable f) protected voidAgaveWriter.writeSeqFeature(Annotatable f) Write SeqFeature XMLprotected voidAgaveWriter.writeSequenceMap(Annotatable seq) group sequence_map by getSource()protected voidAgaveWriter.writeSequenceMap2(Annotatable f) Write SequenceMap XMLprotected voidAgaveWriter.writeTranscript(Annotatable f) -
Uses of Annotatable in org.biojava.bio.seq.projection
Classes in org.biojava.bio.seq.projection that implement AnnotatableModifier and TypeClassDescriptionclassInternal class used by ProjectionEngine to wrap Feature objects. -
Uses of Annotatable in org.biojava.bio.symbol
Subinterfaces of Annotatable in org.biojava.bio.symbolModifier and TypeInterfaceDescriptioninterfaceThe set of AtomicSymbols which can be concatenated together to make a SymbolList.interfaceA symbol that is not ambiguous.interfaceA symbol that can be represented as a string of Symbols.interfaceAn alphabet over a finite set of Symbols.interfaceA single symbol.Classes in org.biojava.bio.symbol that implement AnnotatableModifier and TypeClassDescriptionclassAn abstract implementation ofAlphabet.classThe base-class for Symbol implementations.final classAn efficient implementation of an Alphabet over the infinite set of double values.static classA range of double values.static classA single double value.static classA class to represent a contiguous range of double symbols.classAn atomic symbol consisting only of itself.final classAn efficient implementation of an Alphabet over the infinite set of integer values.static classA single int value.static classA class to represent a finite contiguous subset of the infinite IntegerAlphabetclassA simple no-frills implementation of the FiniteAlphabet interface.classA basic implementation of AtomicSymbol.classAn alphabet that contains a single atomic symbol.final classSoft masking is usually displayed by making the masked regions somehow different from the non masked regions.classThisSymbolTokenizerworks with a delegate to softmask symbol tokenization as appropriate. -
Uses of Annotatable in org.biojava.bio.taxa
Subinterfaces of Annotatable in org.biojava.bio.taxaModifier and TypeInterfaceDescriptioninterfaceDeprecated.replaced by classes inorg.biojavax.bio.taxaClasses in org.biojava.bio.taxa that implement AnnotatableModifier and TypeClassDescriptionclassDeprecated.replaced by classes inorg.biojavax.bio.taxaclassDeprecated.replaced by classes inorg.biojavax.bio.taxaclassDeprecated.replaced by classes inorg.biojavax.bio.taxa -
Uses of Annotatable in org.biojava.ontology
Subinterfaces of Annotatable in org.biojava.ontologyModifier and TypeInterfaceDescriptioninterfaceA term in an ontology which identifies another ontology.interfaceA term in another ontology.interfaceA term in an ontology.interfaceA triple in an ontology.interfaceClasses in org.biojava.ontology that implement AnnotatableModifier and TypeClassDescriptionclassAbstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.final classstatic final classSimple in-memory implementation of a remote ontology term.static final classSimple in-memory implementation of a remote ontology term.static classSimple in-memory implementation of an ontology term.static final classBasic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriplestatic class -
Uses of Annotatable in org.biojavax
Subinterfaces of Annotatable in org.biojavaxModifier and TypeInterfaceDescriptioninterfaceRepresents a cross reference to another database.interfaceAnnotatable objects that can have rich annotations.Classes in org.biojavax that implement Annotatable -
Uses of Annotatable in org.biojavax.bio
Subinterfaces of Annotatable in org.biojavax.bioModifier and TypeInterfaceDescriptioninterfaceThis class relates to the bioentry table in BioSQL.Classes in org.biojavax.bio that implement AnnotatableModifier and TypeClassDescriptionclassReference 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.seqModifier and TypeInterfaceDescriptioninterfaceRepresents a feature that can be given name and rank and be moved from one sequence to another.interfaceDescribes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.interfaceA rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.Classes in org.biojavax.bio.seq that implement AnnotatableModifier and TypeClassDescriptionclassAn implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.classAn Empty implementation of RichLocation.classAn implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.classA simple implementation of RichFeature.classA simple implementation of RichLocation.classA simple implementation of RichSequence.classA simple implementation of RichSequence. -
Uses of Annotatable in org.biojavax.ontology
Subinterfaces of Annotatable in org.biojavax.ontologyModifier and TypeInterfaceDescriptioninterfaceMakes Term objects comparable properly and adds some extra features to them.interfaceComparable triples, obviously.Classes in org.biojavax.ontology that implement AnnotatableModifier and TypeClassDescriptionclassA Term object that can be compared and thus sorted.classBasic comparable triple, BioSQL style.