java.io.Serializable
public interface CodonTable
extends java.io.Serializable
Modifier and Type | Field | 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 | 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)