Package pal.datatype
Interface CodonTable
- All Superinterfaces:
Serializable
Describes a device for translating Nucleotide triplets
or codon indices into amino acid codes.
Codon Indexes (or states) are defined as in GeneralizedCodons
- Version:
- $Id: CodonTable.java,v 1.10 2003/09/04 03:22:34 matt Exp $
- Author:
- Matthew Goode, Alexei Drummond
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
TypeID for Alternative Yeaststatic final int
TypeID for Ascidian Mitochondrialstatic final int
TypeID for Bacterialstatic final int
TypeID for Blepharisma Nuclearstatic final int
TypeID for Cilatestatic final int
TypeID for Echinoderm Mitochondrialstatic final int
TypeID for Euplotid Nuclearstatic final int
TypeID for Flatworm Mitochondrialstatic final int
TypeID for Invertebrate Mitochondrialstatic final int
TypeID for Mold Protozoan Mitochondrialstatic final int
TypeID for Mycoplasmastatic final String[]
A textual version of an organism type - type is index into arraystatic final int
TypeID for Universalstatic final int
TypeID for Vertebrate Mitochondrialstatic final int
TypeID for Yeast -
Method Summary
Modifier and TypeMethodDescriptionchar
getAminoAcidChar
(char[] codon) Returns the char associated with AminoAcid represented by 'codon'char
getAminoAcidCharFromCodonIndex
(int codonIndex) Returns the amino acid char at the corresponding codonIndexint
getAminoAcidState
(char[] codon) Returns the state associated with AminoAcid represented by 'codon'int
getAminoAcidStateFromCodonIndex
(int codonIndex) Returns the amino acid state at the corresponding codonIndexint
getAminoAcidStateFromStates
(int[] states) char[][]
getCodonsFromAminoAcidChar
(char aminoAcidChar) char[][]
getCodonsFromAminoAcidState
(int aminoAcidState) int[]
getIUPACStatesFromAminoAcidState
(int aminoAcid) int
Returns the number of terminator amino acids.int
int[]
getStatesFromAminoAcidState
(int aminoAcid) int[]
boolean
isSynonymous
(int codonIndexOne, int codonIndexTwo)
-
Field Details
-
UNIVERSAL
static final int UNIVERSALTypeID for Universal- See Also:
-
VERTEBRATE_MITOCHONDRIAL
static final int VERTEBRATE_MITOCHONDRIALTypeID for Vertebrate Mitochondrial- See Also:
-
YEAST
static final int YEASTTypeID for Yeast- See Also:
-
MOLD_PROTOZOAN_MITOCHONDRIAL
static final int MOLD_PROTOZOAN_MITOCHONDRIALTypeID for Mold Protozoan Mitochondrial- See Also:
-
MYCOPLASMA
static final int MYCOPLASMATypeID for Mycoplasma- See Also:
-
INVERTEBRATE_MITOCHONDRIAL
static final int INVERTEBRATE_MITOCHONDRIALTypeID for Invertebrate Mitochondrial- See Also:
-
CILATE
static final int CILATETypeID for Cilate- See Also:
-
ECHINODERM_MITOCHONDRIAL
static final int ECHINODERM_MITOCHONDRIALTypeID for Echinoderm Mitochondrial- See Also:
-
EUPLOTID_NUCLEAR
static final int EUPLOTID_NUCLEARTypeID for Euplotid Nuclear- See Also:
-
ASCIDIAN_MITOCHONDRIAL
static final int ASCIDIAN_MITOCHONDRIALTypeID for Ascidian Mitochondrial- See Also:
-
FLATWORM_MITOCHONDRIAL
static final int FLATWORM_MITOCHONDRIALTypeID for Flatworm Mitochondrial- See Also:
-
BLEPHARISMA_NUCLEAR
static final int BLEPHARISMA_NUCLEARTypeID for Blepharisma Nuclear- See Also:
-
BACTERIAL
static final int BACTERIALTypeID for Bacterial- See Also:
-
ALTERNATIVE_YEAST
static final int ALTERNATIVE_YEASTTypeID for Alternative Yeast- See Also:
-
ORGANISM_TYPE_NAMES
A textual version of an organism type - type is index into array
-
-
Method Details
-
getAminoAcidChar
char getAminoAcidChar(char[] codon) Returns the char associated with AminoAcid represented by 'codon'- Returns:
- state for '?' if codon unknown or wrong length
- See Also:
-
getAminoAcidState
int getAminoAcidState(char[] codon) Returns the state associated with AminoAcid represented by 'codon'- Returns:
- '?' if codon unknown or wrong length
- See Also:
-
getCodonsFromAminoAcidState
char[][] getCodonsFromAminoAcidState(int aminoAcidState) - Returns:
- all the possible codons for a given amino acid
-
getCodonsFromAminoAcidChar
char[][] getCodonsFromAminoAcidChar(char aminoAcidChar) -
getAminoAcidCharFromCodonIndex
char getAminoAcidCharFromCodonIndex(int codonIndex) Returns the amino acid char at the corresponding codonIndex -
getAminoAcidStateFromCodonIndex
int getAminoAcidStateFromCodonIndex(int codonIndex) Returns the amino acid state at the corresponding codonIndex -
getIUPACStatesFromAminoAcidState
int[] getIUPACStatesFromAminoAcidState(int aminoAcid) -
getStatesFromAminoAcidState
int[] getStatesFromAminoAcidState(int aminoAcid) -
getAminoAcidStateFromStates
int getAminoAcidStateFromStates(int[] states) - Returns:
- The AminoAcid states given the nucleotides states (array should be of size 3)
-
getTerminatorIndexes
int[] getTerminatorIndexes()- Returns:
- the codon states of terminator amino acids.
-
getNumberOfTerminatorIndexes
int getNumberOfTerminatorIndexes()Returns the number of terminator amino acids. -
getOrganismTypeID
int getOrganismTypeID()- Returns:
- the type of this organism (see defined type constants)
-
isSynonymous
boolean isSynonymous(int codonIndexOne, int codonIndexTwo) - Returns:
- true if the amino acids that map to two codons are the same (synonymous). False otherwise
-