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Packages that use Annotatable | |
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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 |
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Subinterfaces of Annotatable in org.biojava.bio.dp | |
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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 | |
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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 |
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Subinterfaces of Annotatable in org.biojava.bio.molbio | |
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interface |
RestrictionSite
RestrictionSite represents the recognition site of a
restriction enzyme. |
Uses of Annotatable in org.biojava.bio.program.gff3 |
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Subinterfaces of Annotatable in org.biojava.bio.program.gff3 | |
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interface |
GFF3Record
A record in a GFF3 formatted file. |
Classes in org.biojava.bio.program.gff3 that implement Annotatable | |
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static class |
GFF3Record.Impl
|
Uses of Annotatable in org.biojava.bio.program.hmmer |
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Classes in org.biojava.bio.program.hmmer that implement Annotatable | |
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class |
ProfileEmissionState
A state in a HMMer model. |
Uses of Annotatable in org.biojava.bio.program.phred |
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Classes in org.biojava.bio.program.phred that implement Annotatable | |
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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 |
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Subinterfaces of Annotatable in org.biojava.bio.program.unigene | |
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interface |
UnigeneCluster
A single unigene cluster. |
Uses of Annotatable in org.biojava.bio.search |
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Subinterfaces of Annotatable in org.biojava.bio.search | |
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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 | |
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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 |
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Subinterfaces of Annotatable in org.biojava.bio.seq | |
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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 | |
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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 |
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Subinterfaces of Annotatable in org.biojava.bio.seq.homol | |
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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 |
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Classes in org.biojava.bio.seq.impl that implement Annotatable | |
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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 |
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Subinterfaces of Annotatable in org.biojava.bio.seq.io | |
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interface |
SymbolTokenization
Encapsulate a mapping between BioJava Symbol objects and some string representation. |
Classes in org.biojava.bio.seq.io that implement Annotatable | |
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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 |
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Methods in org.biojava.bio.seq.io.agave with parameters of type Annotatable | |
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protected void |
AgaveWriter.writeAssembly(Annotatable seq)
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protected void |
AgaveWriter.writeBioSequence(Annotatable seq)
|
protected void |
AgaveWriter.writeClassification(Annotatable seq)
|
protected void |
AgaveWriter.writeCompResult(Annotatable f)
|
protected void |
AgaveWriter.writeContig(Annotatable seq)
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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 |
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Classes in org.biojava.bio.seq.projection that implement Annotatable | |
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class |
ProjectedFeature
Internal class used by ProjectionEngine to wrap Feature objects. |
Uses of Annotatable in org.biojava.bio.symbol |
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Subinterfaces of Annotatable in org.biojava.bio.symbol | |
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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 | |
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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 |
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Subinterfaces of Annotatable in org.biojava.bio.taxa | |
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interface |
Taxon
Deprecated. replaced by classes in org.biojavax.bio.taxa |
Classes in org.biojava.bio.taxa that implement Annotatable | |
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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 |
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Subinterfaces of Annotatable in org.biojava.ontology | |
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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 | |
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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 |
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Subinterfaces of Annotatable in org.biojavax | |
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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 | |
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class |
SimpleCrossRef
A basic CrossRef implementation. |
Uses of Annotatable in org.biojavax.bio |
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Subinterfaces of Annotatable in org.biojavax.bio | |
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interface |
BioEntry
This class relates to the bioentry table in BioSQL. |
Classes in org.biojavax.bio that implement Annotatable | |
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class |
SimpleBioEntry
Reference implementation of a BioEntry object which has no features or sequence. |
Uses of Annotatable in org.biojavax.bio.seq |
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Subinterfaces of Annotatable in org.biojavax.bio.seq | |
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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 | |
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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 |
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Subinterfaces of Annotatable in org.biojavax.ontology | |
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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 | |
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class |
SimpleComparableTerm
A Term object that can be compared and thus sorted. |
class |
SimpleComparableTriple
Basic comparable triple, BioSQL style. |
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