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.
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Uses of Annotatable in org.biojava.bio.dp
Subinterfaces of Annotatable in org.biojava.bio.dpModifier and TypeInterfaceDescriptioninterface
A Dot state.interface
A state in a markov process that has an emission spectrum.interface
A state that contains an entire sub-model.interface
A state in a markov process.Classes in org.biojava.bio.dp that implement AnnotatableModifier and TypeClassDescriptionfinal class
Start/end state for HMMs.class
A Dot state that you can make and use.class
class
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Uses of Annotatable in org.biojava.bio.molbio
Subinterfaces of Annotatable in org.biojava.bio.molbioModifier and TypeInterfaceDescriptioninterface
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.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 TypeClassDescriptionclass
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 -
Uses of Annotatable in org.biojava.bio.search
Subinterfaces of Annotatable in org.biojava.bio.searchModifier and TypeInterfaceDescriptioninterface
Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.interface
Objects of this type represent one particular result of a sequence similarity search.interface
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 AnnotatableModifier and TypeClassDescriptionclass
Deprecated.SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.class
Deprecated.SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.class
Deprecated.SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.class
SimpleSeqSimilaritySearchHit
objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.class
SimpleSeqSimilaritySearchResult
objects represent a result of a search of aSymbolList
against the sequences within aSequenceDB
object.class
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.seqModifier and TypeInterfaceDescriptioninterface
Feature which represents a component in an assembly (contig).interface
A feature within a sequence, or nested within another feature.static interface
A named collection of Types.static interface
A type of feature.interface
Title: FramedFeature.interface
Extension of GappedSymbolList which also projects features into the gapped coordinate system.interface
A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.interface
A biological sequence.interface
Adds the concept of 'strand' to features.Classes in org.biojava.bio.seq that implement AnnotatableModifier and TypeClassDescriptionclass
A circular view onto another Sequence object.static class
A simple implementation of a Repository.class
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.class
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.homolModifier and TypeInterfaceDescriptioninterface
interface
SimilarityPairFeature
describes 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 class
A Sequence implementation that has a name and URI but no features, and a zero length symbol list.class
A reverse complement view ontoSequence
interface.class
A no-frills implementation of a feature.class
Title: SimpleFramedFeature.class
Simple implementation of GappedSequence.class
class
A no-frills implementation of a remote feature.class
SimpleRestrictionSite
represents the recognition site of a restriction enzyme.class
A basic implementation of theSequence
interface.class
SimpleSimilarityPairFeature
represents a similarity between a query sequence and a subject sequence as produced by a search program.class
A no-frills implementation of StrandedFeature.class
View a sub-section of a given sequence object, including all the features intersecting that region.class
A view onto another Sequence object. -
Uses of Annotatable in org.biojava.bio.seq.io
Subinterfaces of Annotatable in org.biojava.bio.seq.ioModifier and TypeInterfaceDescriptioninterface
Encapsulate a mapping between BioJava Symbol objects and some string representation.Classes in org.biojava.bio.seq.io that implement AnnotatableModifier and TypeClassDescriptionclass
Implementation of SymbolTokenization which binds symbols to strings of characters.class
Implementation of SymbolTokenization which binds symbols to single unicode characters.class
Tokenization for cross-product alphabets.class
class
class
Simple implementation of SymbolTokenization which uses the `name' field of the symbols.class
class
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 AnnotatableModifier and TypeMethodDescriptionprotected 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 XMLprotected void
AgaveWriter.writeSequenceMap
(Annotatable seq) group sequence_map by getSource()protected void
AgaveWriter.writeSequenceMap2
(Annotatable f) Write SequenceMap XMLprotected void
AgaveWriter.writeTranscript
(Annotatable f) -
Uses of Annotatable in org.biojava.bio.seq.projection
Classes in org.biojava.bio.seq.projection that implement AnnotatableModifier and TypeClassDescriptionclass
Internal 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 TypeInterfaceDescriptioninterface
The set of AtomicSymbols which can be concatenated together to make a SymbolList.interface
A symbol that is not ambiguous.interface
A symbol that can be represented as a string of Symbols.interface
An alphabet over a finite set of Symbols.interface
A single symbol.Classes in org.biojava.bio.symbol that implement AnnotatableModifier and TypeClassDescriptionclass
An abstract implementation ofAlphabet
.class
The base-class for Symbol implementations.final class
An efficient implementation of an Alphabet over the infinite set of double values.static class
A range of double values.static class
A single double value.static class
A class to represent a contiguous range of double symbols.class
An atomic symbol consisting only of itself.final class
An efficient implementation of an Alphabet over the infinite set of integer values.static class
A single int value.static class
A class to represent a finite contiguous subset of the infinite IntegerAlphabetclass
A simple no-frills implementation of the FiniteAlphabet interface.class
A basic implementation of AtomicSymbol.class
An alphabet that contains a single atomic symbol.final class
Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.class
ThisSymbolTokenizer
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.taxaModifier and TypeInterfaceDescriptioninterface
Deprecated.replaced by classes inorg.biojavax.bio.taxa
Classes in org.biojava.bio.taxa that implement AnnotatableModifier and TypeClassDescriptionclass
Deprecated.replaced by classes inorg.biojavax.bio.taxa
class
Deprecated.replaced by classes inorg.biojavax.bio.taxa
class
Deprecated.replaced by classes inorg.biojavax.bio.taxa
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Uses of Annotatable in org.biojava.ontology
Subinterfaces of Annotatable in org.biojava.ontologyModifier and TypeInterfaceDescriptioninterface
A term in an ontology which identifies another ontology.interface
A term in another ontology.interface
A term in an ontology.interface
A triple in an ontology.interface
Classes in org.biojava.ontology that implement AnnotatableModifier and TypeClassDescriptionclass
Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.final class
static final class
Simple in-memory implementation of a remote ontology term.static final class
Simple in-memory implementation of a remote ontology term.static class
Simple in-memory implementation of an ontology term.static final class
Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriplestatic class
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Uses of Annotatable in org.biojavax
Subinterfaces of Annotatable in org.biojavaxModifier and TypeInterfaceDescriptioninterface
Represents a cross reference to another database.interface
Annotatable 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 TypeInterfaceDescriptioninterface
This class relates to the bioentry table in BioSQL.Classes in org.biojavax.bio that implement AnnotatableModifier and TypeClassDescriptionclass
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.seqModifier and TypeInterfaceDescriptioninterface
Represents a feature that can be given name and rank and be moved from one sequence to another.interface
Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.interface
A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.Classes in org.biojavax.bio.seq that implement AnnotatableModifier and TypeClassDescriptionclass
An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.class
An Empty implementation of RichLocation.class
An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.class
A simple implementation of RichFeature.class
A simple implementation of RichLocation.class
A simple implementation of RichSequence.class
A simple implementation of RichSequence. -
Uses of Annotatable in org.biojavax.ontology
Subinterfaces of Annotatable in org.biojavax.ontologyModifier and TypeInterfaceDescriptioninterface
Makes Term objects comparable properly and adds some extra features to them.interface
Comparable triples, obviously.Classes in org.biojavax.ontology that implement AnnotatableModifier and TypeClassDescriptionclass
A Term object that can be compared and thus sorted.class
Basic comparable triple, BioSQL style.