Uses of Class
org.biojava.utils.Unchangeable

Packages that use Unchangeable

Package	Description
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db.biofetch	Client for the OBDA BioFetch protocol.
org.biojava.bio.seq.db.flat	Support for OBDA flatfile databases.
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.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.ontology	A general-purpose API for ontologies.
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality The biojavax packages contain a number of extensions to the core biojava interfaces.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.

Uses of Unchangeable in org.biojava.bio.dist

Subclasses of Unchangeable in org.biojava.bio.dist

Modifier and Type	Class and Description
class	GapDistribution This distribution emits gap symbols.

Uses of Unchangeable in org.biojava.bio.dp

Subclasses of Unchangeable in org.biojava.bio.dp

Modifier and Type	Class and Description
class	SimpleStatePath A no-frills implementation of StatePath.

Uses of Unchangeable in org.biojava.bio.seq

Subclasses of Unchangeable in org.biojava.bio.seq

Modifier and Type	Class and Description
class	CircularView A circular view onto another Sequence object.
static class	FeatureHolder.EmptyFeatureHolder

Uses of Unchangeable in org.biojava.bio.seq.db.biofetch

Subclasses of Unchangeable in org.biojava.bio.seq.db.biofetch

Modifier and Type	Class and Description
class	BioFetchSequenceDB Simple SequenceDB implementation backed by a BioFetch (HTTP) server.

Uses of Unchangeable in org.biojava.bio.seq.db.flat

Subclasses of Unchangeable in org.biojava.bio.seq.db.flat

Modifier and Type	Class and Description
class	FlatSequenceDB FlatSequenceDB is an OBDA flatfile sequence databank implementation.

Uses of Unchangeable in org.biojava.bio.seq.homol

Subclasses of Unchangeable in org.biojava.bio.seq.homol

Modifier and Type	Class and Description
static class	SimilarityPairFeature.EmptyPairwiseAlignment EmptyPairwiseAlignment empty pairwise alignment which has labels to empty symbol lists.

Uses of Unchangeable in org.biojava.bio.seq.impl

Subclasses of Unchangeable in org.biojava.bio.seq.impl

Modifier and Type	Class and Description
class	ViewSequence A view onto another Sequence object.

Uses of Unchangeable in org.biojava.bio.seq.io

Subclasses of Unchangeable in org.biojava.bio.seq.io

Modifier and Type	Class and Description
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 Unchangeable in org.biojava.bio.symbol

Subclasses of Unchangeable in org.biojava.bio.symbol

Modifier and Type	Class and Description
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	IntegerAlphabet An efficient implementation of an Alphabet over the infinite set of integer values.
static class	IntegerAlphabet.IntegerSymbol A single int value.
class	RelabeledAlignment An alignment that relabels another alignment.
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 Unchangeable in org.biojava.ontology

Subclasses of Unchangeable in org.biojava.ontology

Modifier and Type	Class and Description
class	IntegerOntology
class	IntegerOntology.IntTerm
static class	Triple.Impl Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple

Uses of Unchangeable in org.biojavax

Subclasses of Unchangeable in org.biojavax

Modifier and Type	Class and Description
class	EmptyRichAnnotation A place holder for a RichAnnotation that prevents null having to be used
class	SimpleCrossRef A basic CrossRef implementation.
class	SimpleDocRefAuthor Represents an author of a documentary reference.

Uses of Unchangeable in org.biojavax.bio.seq

Subclasses of Unchangeable in org.biojavax.bio.seq

Modifier and Type	Class and Description
class	EmptyRichLocation An Empty implementation of RichLocation.