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public interface CodonTable
Describes a device for translating Nucleotide triplets or codon indices into amino acid codes. Codon Indexes (or states) are defined as in GeneralizedCodons
Field Summary | |
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static int |
ALTERNATIVE_YEAST
TypeID for Alternative Yeast |
static int |
ASCIDIAN_MITOCHONDRIAL
TypeID for Ascidian Mitochondrial |
static int |
BACTERIAL
TypeID for Bacterial |
static int |
BLEPHARISMA_NUCLEAR
TypeID for Blepharisma Nuclear |
static int |
CILATE
TypeID for Cilate |
static int |
ECHINODERM_MITOCHONDRIAL
TypeID for Echinoderm Mitochondrial |
static int |
EUPLOTID_NUCLEAR
TypeID for Euplotid Nuclear |
static int |
FLATWORM_MITOCHONDRIAL
TypeID for Flatworm Mitochondrial |
static int |
INVERTEBRATE_MITOCHONDRIAL
TypeID for Invertebrate Mitochondrial |
static int |
MOLD_PROTOZOAN_MITOCHONDRIAL
TypeID for Mold Protozoan Mitochondrial |
static int |
MYCOPLASMA
TypeID for Mycoplasma |
static java.lang.String[] |
ORGANISM_TYPE_NAMES
A textual version of an organism type - type is index into array |
static int |
UNIVERSAL
TypeID for Universal |
static int |
VERTEBRATE_MITOCHONDRIAL
TypeID for Vertebrate Mitochondrial |
static int |
YEAST
TypeID for Yeast |
Method Summary | |
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char |
getAminoAcidChar(char[] codon)
Returns the char associated with AminoAcid represented by 'codon' |
char |
getAminoAcidCharFromCodonIndex(int codonIndex)
Returns the amino acid char at the corresponding codonIndex |
int |
getAminoAcidState(char[] codon)
Returns the state associated with AminoAcid represented by 'codon' |
int |
getAminoAcidStateFromCodonIndex(int codonIndex)
Returns the amino acid state at the corresponding codonIndex |
int |
getAminoAcidStateFromStates(int[] states)
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char[][] |
getCodonsFromAminoAcidChar(char aminoAcidChar)
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char[][] |
getCodonsFromAminoAcidState(int aminoAcidState)
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int[] |
getIUPACStatesFromAminoAcidState(int aminoAcid)
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int |
getNumberOfTerminatorIndexes()
Returns the number of terminator amino acids. |
int |
getOrganismTypeID()
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int[] |
getStatesFromAminoAcidState(int aminoAcid)
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int[] |
getTerminatorIndexes()
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boolean |
isSynonymous(int codonIndexOne,
int codonIndexTwo)
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Field Detail |
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static final int UNIVERSAL
static final int VERTEBRATE_MITOCHONDRIAL
static final int YEAST
static final int MOLD_PROTOZOAN_MITOCHONDRIAL
static final int MYCOPLASMA
static final int INVERTEBRATE_MITOCHONDRIAL
static final int CILATE
static final int ECHINODERM_MITOCHONDRIAL
static final int EUPLOTID_NUCLEAR
static final int ASCIDIAN_MITOCHONDRIAL
static final int FLATWORM_MITOCHONDRIAL
static final int BLEPHARISMA_NUCLEAR
static final int BACTERIAL
static final int ALTERNATIVE_YEAST
static final java.lang.String[] ORGANISM_TYPE_NAMES
Method Detail |
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char getAminoAcidChar(char[] codon)
AminoAcids
int getAminoAcidState(char[] codon)
AminoAcids
char[][] getCodonsFromAminoAcidState(int aminoAcidState)
char[][] getCodonsFromAminoAcidChar(char aminoAcidChar)
char getAminoAcidCharFromCodonIndex(int codonIndex)
int getAminoAcidStateFromCodonIndex(int codonIndex)
int[] getIUPACStatesFromAminoAcidState(int aminoAcid)
int[] getStatesFromAminoAcidState(int aminoAcid)
int getAminoAcidStateFromStates(int[] states)
int[] getTerminatorIndexes()
int getNumberOfTerminatorIndexes()
int getOrganismTypeID()
boolean isSynonymous(int codonIndexOne, int codonIndexTwo)
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