Uses of Interface
org.biojava.bio.symbol.BasisSymbol

Packages that use BasisSymbol

Package	Description
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.program.hmmer	Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.

Uses of BasisSymbol in org.biojava.bio.dp

Subinterfaces of BasisSymbol in org.biojava.bio.dp

Modifier and Type	Interface and Description
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 BasisSymbol

Modifier and Type	Class and Description
class	MagicalState Start/end state for HMMs.
class	SimpleDotState A Dot state that you can make and use.
class	SimpleEmissionState
class	SimpleModelInState

Uses of BasisSymbol in org.biojava.bio.program.hmmer

Classes in org.biojava.bio.program.hmmer that implement BasisSymbol

Modifier and Type	Class and Description
class	ProfileEmissionState A state in a HMMer model.

Uses of BasisSymbol in org.biojava.bio.symbol

Subinterfaces of BasisSymbol in org.biojava.bio.symbol

Modifier and Type	Interface and Description
interface	AtomicSymbol A symbol that is not ambiguous.

Classes in org.biojava.bio.symbol that implement BasisSymbol

Modifier and Type	Class and Description
static class	DoubleAlphabet.DoubleRange A range of double values.
static class	DoubleAlphabet.DoubleSymbol A single double value.
class	FundamentalAtomicSymbol An atomic symbol consisting only of itself.
static class	IntegerAlphabet.IntegerSymbol A single int value.
class	SimpleAtomicSymbol A basic implementation of AtomicSymbol.

Methods in org.biojava.bio.symbol with parameters of type BasisSymbol

Modifier and Type	Method and Description
boolean	SoftMaskedAlphabet.isMasked(BasisSymbol s) Determines if a Symbol is masked.