pal.datatype

Class Codons

java.lang.Object

pal.datatype.SimpleDataType

pal.datatype.Codons

All Implemented Interfaces:

java.io.Serializable, DataType, MolecularDataType

public class Codons
extends SimpleDataType
implements MolecularDataType

implements DataType for all Codons (including terminators). Characters are defined as 'A-Z' followed by 'a-z' followed by '0-9' followed by '@' and '%' Now incorporates the ungeneral code from GeneralizedCodons (which has died due to it's limited use)

Version:

$Id: Codons.java,v 1.21 2004/03/10 04:42:54 matt Exp $

Author:

Matthew Goode, Alexei Drummond

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.datatype.MolecularDataType

MolecularDataType.Utils

Field Summary

Fields

Modifier and Type	Field and Description
static Codons	DEFAULT_INSTANCE

Fields inherited from interface pal.datatype.DataType

AMINO_ACID_DESCRIPTION, AMINOACIDS, CODON_DESCRIPTION, CODONS, GAP_BALANCED, GAP_BALANCED_DESCRIPTION, IUPAC_NUCELOTIDES_DESCRIPTION, IUPACNUCLEOTIDES, NUCLEOTIDE_DESCRIPTION, NUMERIC, PRIMARY_SUGGESTED_GAP_CHARACTER, SUGGESTED_GAP_CHARACTERS, SUGGESTED_GAP_STATE, SUGGESTED_UNKNOWN_STATE, TWO_STATE_DESCRIPTION, TWOSTATES, UNKNOWN, UNKNOWN_CHARACTER, UNKNOWN_TLA

Constructor Summary

Constructors

Constructor and Description
Codons()

Method Summary

Methods

Modifier and Type	Method and Description
protected char	getCharImpl(int state) Get character corresponding to a given state
static int	getCodonIndexFromIUPACNucleotideStates(int[] codon) The codon index is a number between 0 and 64 assigned to each different codon type
static int	getCodonIndexFromIUPACNucleotideStates(int[] codon, int startingPosition) The codon index is a number between 0 and 64 assigned to each different codon type
static int	getCodonIndexFromNucleotides(char[] codon) The codon index is a number between 0 and 64 assigned to each different codon type
static int	getCodonIndexFromNucleotideStates(int[] codon) The codon index is a number between 0 and 64 assigned to each different codon type
static int	getCodonIndexFromNucleotideStates(int[] codon, int startingPosition) The codon index is a number between 0 and 64 assigned to each different codon type
java.lang.String	getDescription() description of data type
static double[]	getF1X4CodonFrequencies(double[] nucleotideFrequencies)
static double[]	getF3X4CodonFrequencies(double[][] nucleotideTripletFrequencies)
int[]	getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
int[]	getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
int	getNucleotideLength()
static char[]	getNucleotidesFromCodonIndex(int index) Translates an index into a codon
int[]	getNucleotideStates(int[] residueStates)
static int[]	getNucleotideStatesFromCodonIndex(int codonIndex) Translates an index into a codon
int	getNumStates() get number of unique states
int	getStateImpl(char c) For sub classes to implement main functionality of getState.
static java.lang.String	getTLA(int state)
int	getTypeID() get numerical code describing the data type
boolean	isCreatesIUPACNuecleotides()
protected boolean	isUnknownStateImpl(int state) For subclasses to handle, without regard for gaps

Methods inherited from class pal.datatype.SimpleDataType

getAmbiguousVersion, getChar, getPreferredChar, getPreferredCharImpl, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface pal.datatype.DataType

getAmbiguousVersion, getChar, getPreferredChar, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState

Field Detail

DEFAULT_INSTANCE

public static final Codons DEFAULT_INSTANCE

Constructor Detail

Codons

public Codons()

Method Detail

getNumStates

public int getNumStates()

Description copied from interface: DataType

get number of unique states

Specified by:

getNumStates in interface DataType

Returns:

number of unique states

getStateImpl

public int getStateImpl(char c)

Description copied from class: SimpleDataType

For sub classes to implement main functionality of getState. Gaps do not need to be considered

Specified by:

getStateImpl in class SimpleDataType

getCharImpl

protected char getCharImpl(int state)

Get character corresponding to a given state

Specified by:

getCharImpl in class SimpleDataType

getDescription

public java.lang.String getDescription()

Description copied from interface: DataType

description of data type

Specified by:

getDescription in interface DataType

Returns:

string describing the data type

isUnknownStateImpl

protected final boolean isUnknownStateImpl(int state)

Description copied from class: SimpleDataType

For subclasses to handle, without regard for gaps

Specified by:

isUnknownStateImpl in class SimpleDataType

getTypeID

public int getTypeID()

Description copied from interface: DataType

get numerical code describing the data type

Specified by:

getTypeID in interface DataType

Returns:

numerical code

getNucleotideStates

public int[] getNucleotideStates(int[] residueStates)

Specified by:

getNucleotideStates in interface MolecularDataType

Parameters:

residue - states an array of states corresponding to states of this datatype

Returns:

the corresponding IUPAC states

getMolecularStatesFromIUPACNucleotides

public final int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates,
                                           int startingIndex)

Specified by:

getMolecularStatesFromIUPACNucleotides in interface MolecularDataType

getMolecularStatesFromSimpleNucleotides

public final int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates,
                                            int startingIndex)

Specified by:

getMolecularStatesFromSimpleNucleotides in interface MolecularDataType

Returns:

isCreatesIUPACNuecleotides

public boolean isCreatesIUPACNuecleotides()

Specified by:

isCreatesIUPACNuecleotides in interface MolecularDataType

Returns:

false

getNucleotideLength

public final int getNucleotideLength()

Specified by:

getNucleotideLength in interface MolecularDataType

Returns:

3

getTLA

public static final java.lang.String getTLA(int state)

Returns:

a three letter acronym for an AminoAcid, according to state

getCodonIndexFromNucleotides

public static final int getCodonIndexFromNucleotides(char[] codon)

The codon index is a number between 0 and 64 assigned to each different codon type

Parameters:

codon - a 3 element array of characters which contain Nucleotide characters

Returns:

-1 if the codon has unknowns, or gaps in it, or is length is less than 3

getCodonIndexFromNucleotideStates

public static final int getCodonIndexFromNucleotideStates(int[] codon)

The codon index is a number between 0 and 64 assigned to each different codon type

Parameters:

codon - a 3 element array of characters which contain Nucleotide states

Returns:

-1 if the codon has unknowns, or gaps in it, or is length is less than 3

getCodonIndexFromNucleotideStates

public static final int getCodonIndexFromNucleotideStates(int[] codon,
                                    int startingPosition)

The codon index is a number between 0 and 64 assigned to each different codon type

Parameters:

codon - a 3 element array of characters which contain Nucleotide states

startingPosition - an offset into the array to start examining

Returns:

-1 if the codon has unknowns, or gaps in it, or is length is less than 3

getCodonIndexFromIUPACNucleotideStates

public static final int getCodonIndexFromIUPACNucleotideStates(int[] codon)

The codon index is a number between 0 and 64 assigned to each different codon type

Parameters:

codon - a 3 element array of characters which contain Nucleotide states

startingPosition - an offset into the array to start examining

Returns:

-1 if the codon has unknowns, or gaps in it, or is length is less than 3

getCodonIndexFromIUPACNucleotideStates

public static final int getCodonIndexFromIUPACNucleotideStates(int[] codon,
                                         int startingPosition)

The codon index is a number between 0 and 64 assigned to each different codon type

Parameters:

codon - a 3 element array of characters which contain Nucleotide states

startingPosition - an offset into the array to start examining

Returns:

-1 if the codon has unknowns, or gaps in it, or is length is less than 3

getNucleotidesFromCodonIndex

public static final char[] getNucleotidesFromCodonIndex(int index)

Translates an index into a codon

Parameters:

index - the codon index

Returns:

a char array contain 3 nucleotide characters

getNucleotideStatesFromCodonIndex

public static final int[] getNucleotideStatesFromCodonIndex(int codonIndex)

Translates an index into a codon

Parameters:

index - the codon index

Returns:

an int array contain 3 nucleotide states

getF1X4CodonFrequencies

public static final double[] getF1X4CodonFrequencies(double[] nucleotideFrequencies)

getF3X4CodonFrequencies

public static final double[] getF3X4CodonFrequencies(double[][] nucleotideTripletFrequencies)