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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. |
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