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

Packages that use BasisSymbol
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
 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
 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
 class ProfileEmissionState
          A state in a HMMer model.
 

Uses of BasisSymbol in org.biojava.bio.symbol
 

Subinterfaces of BasisSymbol in org.biojava.bio.symbol
 interface AtomicSymbol
           A symbol that is not ambiguous.
 

Classes in org.biojava.bio.symbol that implement BasisSymbol
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
 boolean SoftMaskedAlphabet.isMasked(BasisSymbol s)
          Determines if a Symbol is masked.