Uses of Class
jebl.evolution.sequences.NucleotideState

Packages that use NucleotideState
jebl.evolution.sequences   
 

Uses of NucleotideState in jebl.evolution.sequences
 

Fields in jebl.evolution.sequences declared as NucleotideState
static NucleotideState Nucleotides.A_STATE
           
static NucleotideState Nucleotides.B_STATE
           
static NucleotideState Nucleotides.C_STATE
           
static NucleotideState[] Nucleotides.CANONICAL_STATES
          Deprecated. 
static NucleotideState[] Nucleotides.COMPLEMENTARY_STATES
          Deprecated. 
static NucleotideState Nucleotides.D_STATE
           
static NucleotideState Nucleotides.G_STATE
           
static NucleotideState Nucleotides.GAP_STATE
           
static NucleotideState Nucleotides.H_STATE
           
static NucleotideState Nucleotides.K_STATE
           
static NucleotideState Nucleotides.M_STATE
           
static NucleotideState Nucleotides.N_STATE
           
static NucleotideState Nucleotides.R_STATE
           
static NucleotideState Nucleotides.S_STATE
           
static NucleotideState[] Nucleotides.STATES
          Deprecated. 
static NucleotideState Nucleotides.T_STATE
           
static NucleotideState Nucleotides.UNKNOWN_STATE
           
static NucleotideState Nucleotides.V_STATE
           
static NucleotideState Nucleotides.W_STATE
           
static NucleotideState Nucleotides.Y_STATE
           
 

Methods in jebl.evolution.sequences that return NucleotideState
static NucleotideState[] Utils.complement(NucleotideState[] sequence)
           
static NucleotideState Nucleotides.getComplementaryState(NucleotideState state)
           
static NucleotideState Nucleotides.getGapState()
           
static NucleotideState Nucleotides.getState(char code)
           
static NucleotideState Nucleotides.getState(int index)
           
static NucleotideState Nucleotides.getState(java.lang.String code)
           
static NucleotideState Nucleotides.getUnknownState()
           
static NucleotideState[] Utils.reverseComplement(NucleotideState[] sequence)
           
static NucleotideState[] Codons.toNucleotides(CodonState state)
           
static NucleotideState[] Nucleotides.toStateArray(byte[] indexArray)
           
static NucleotideState[] Nucleotides.toStateArray(java.lang.String sequenceString)
           
 

Methods in jebl.evolution.sequences that return types with arguments of type NucleotideState
static java.util.List<NucleotideState> Nucleotides.getCanonicalStates()
           
 

Methods in jebl.evolution.sequences with parameters of type NucleotideState
static NucleotideState[] Utils.complement(NucleotideState[] sequence)
           
static NucleotideState Nucleotides.getComplementaryState(NucleotideState state)
           
static CodonState Codons.getState(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
           
 AminoAcidState GeneticCode.getTranslation(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
          Returns the state associated with AminoAcid represented by the three nucleotides.
static boolean Nucleotides.isGap(NucleotideState state)
           
static boolean Nucleotides.isUnknown(NucleotideState state)
           
static NucleotideState[] Utils.reverseComplement(NucleotideState[] sequence)
           
 



http://code.google.com/p/jebl2/