Package pal.datatype
Interface CodonTable
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- All Superinterfaces:
java.io.Serializable
public interface CodonTable extends java.io.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
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Field Summary
Fields Modifier and Type Field Description static int
ALTERNATIVE_YEAST
TypeID for Alternative Yeaststatic int
ASCIDIAN_MITOCHONDRIAL
TypeID for Ascidian Mitochondrialstatic int
BACTERIAL
TypeID for Bacterialstatic int
BLEPHARISMA_NUCLEAR
TypeID for Blepharisma Nuclearstatic int
CILATE
TypeID for Cilatestatic int
ECHINODERM_MITOCHONDRIAL
TypeID for Echinoderm Mitochondrialstatic int
EUPLOTID_NUCLEAR
TypeID for Euplotid Nuclearstatic int
FLATWORM_MITOCHONDRIAL
TypeID for Flatworm Mitochondrialstatic int
INVERTEBRATE_MITOCHONDRIAL
TypeID for Invertebrate Mitochondrialstatic int
MOLD_PROTOZOAN_MITOCHONDRIAL
TypeID for Mold Protozoan Mitochondrialstatic int
MYCOPLASMA
TypeID for Mycoplasmastatic java.lang.String[]
ORGANISM_TYPE_NAMES
A textual version of an organism type - type is index into arraystatic int
UNIVERSAL
TypeID for Universalstatic int
VERTEBRATE_MITOCHONDRIAL
TypeID for Vertebrate Mitochondrialstatic int
YEAST
TypeID for Yeast
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Method Summary
All Methods Instance Methods Abstract Methods 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 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
getNumberOfTerminatorIndexes()
Returns the number of terminator amino acids.int
getOrganismTypeID()
int[]
getStatesFromAminoAcidState(int aminoAcid)
int[]
getTerminatorIndexes()
boolean
isSynonymous(int codonIndexOne, int codonIndexTwo)
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Field Detail
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UNIVERSAL
static final int UNIVERSAL
TypeID for Universal- See Also:
- Constant Field Values
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VERTEBRATE_MITOCHONDRIAL
static final int VERTEBRATE_MITOCHONDRIAL
TypeID for Vertebrate Mitochondrial- See Also:
- Constant Field Values
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YEAST
static final int YEAST
TypeID for Yeast- See Also:
- Constant Field Values
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MOLD_PROTOZOAN_MITOCHONDRIAL
static final int MOLD_PROTOZOAN_MITOCHONDRIAL
TypeID for Mold Protozoan Mitochondrial- See Also:
- Constant Field Values
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MYCOPLASMA
static final int MYCOPLASMA
TypeID for Mycoplasma- See Also:
- Constant Field Values
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INVERTEBRATE_MITOCHONDRIAL
static final int INVERTEBRATE_MITOCHONDRIAL
TypeID for Invertebrate Mitochondrial- See Also:
- Constant Field Values
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CILATE
static final int CILATE
TypeID for Cilate- See Also:
- Constant Field Values
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ECHINODERM_MITOCHONDRIAL
static final int ECHINODERM_MITOCHONDRIAL
TypeID for Echinoderm Mitochondrial- See Also:
- Constant Field Values
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EUPLOTID_NUCLEAR
static final int EUPLOTID_NUCLEAR
TypeID for Euplotid Nuclear- See Also:
- Constant Field Values
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ASCIDIAN_MITOCHONDRIAL
static final int ASCIDIAN_MITOCHONDRIAL
TypeID for Ascidian Mitochondrial- See Also:
- Constant Field Values
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FLATWORM_MITOCHONDRIAL
static final int FLATWORM_MITOCHONDRIAL
TypeID for Flatworm Mitochondrial- See Also:
- Constant Field Values
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BLEPHARISMA_NUCLEAR
static final int BLEPHARISMA_NUCLEAR
TypeID for Blepharisma Nuclear- See Also:
- Constant Field Values
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BACTERIAL
static final int BACTERIAL
TypeID for Bacterial- See Also:
- Constant Field Values
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ALTERNATIVE_YEAST
static final int ALTERNATIVE_YEAST
TypeID for Alternative Yeast- See Also:
- Constant Field Values
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ORGANISM_TYPE_NAMES
static final java.lang.String[] ORGANISM_TYPE_NAMES
A textual version of an organism type - type is index into array
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Method Detail
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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:
AminoAcids
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getAminoAcidState
int getAminoAcidState(char[] codon)
Returns the state associated with AminoAcid represented by 'codon'- Returns:
- '?' if codon unknown or wrong length
- See Also:
AminoAcids
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getCodonsFromAminoAcidState
char[][] getCodonsFromAminoAcidState(int aminoAcidState)
- Returns:
- all the possible codons for a given amino acid
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getCodonsFromAminoAcidChar
char[][] getCodonsFromAminoAcidChar(char aminoAcidChar)
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getAminoAcidCharFromCodonIndex
char getAminoAcidCharFromCodonIndex(int codonIndex)
Returns the amino acid char at the corresponding codonIndex
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getAminoAcidStateFromCodonIndex
int getAminoAcidStateFromCodonIndex(int codonIndex)
Returns the amino acid state at the corresponding codonIndex
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getIUPACStatesFromAminoAcidState
int[] getIUPACStatesFromAminoAcidState(int aminoAcid)
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getStatesFromAminoAcidState
int[] getStatesFromAminoAcidState(int aminoAcid)
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getAminoAcidStateFromStates
int getAminoAcidStateFromStates(int[] states)
- Returns:
- The AminoAcid states given the nucleotides states (array should be of size 3)
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getTerminatorIndexes
int[] getTerminatorIndexes()
- Returns:
- the codon states of terminator amino acids.
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getNumberOfTerminatorIndexes
int getNumberOfTerminatorIndexes()
Returns the number of terminator amino acids.
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getOrganismTypeID
int getOrganismTypeID()
- Returns:
- the type of this organism (see defined type constants)
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isSynonymous
boolean isSynonymous(int codonIndexOne, int codonIndexTwo)
- Returns:
- true if the amino acids that map to two codons are the same (synonymous). False otherwise
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