public interface CodonTable
extends java.io.Serializable
Modifier and Type | Field and Description |
---|---|
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
|
Modifier and Type | Method and Description |
---|---|
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) |
char[][] |
getCodonsFromAminoAcidChar(char aminoAcidChar) |
char[][] |
getCodonsFromAminoAcidState(int aminoAcidState) |
int[] |
getIUPACStatesFromAminoAcidState(int aminoAcid) |
int |
getNumberOfTerminatorIndexes()
Returns the number of terminator amino acids.
|
int |
getOrganismTypeID() |
int[] |
getStatesFromAminoAcidState(int aminoAcid) |
int[] |
getTerminatorIndexes() |
boolean |
isSynonymous(int codonIndexOne,
int codonIndexTwo) |
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
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)