Package pal.datatype
Class Codons
java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.Codons
- All Implemented Interfaces:
Serializable
,DataType
,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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.datatype.DataType
DataType.Utils
Nested classes/interfaces inherited from interface pal.datatype.MolecularDataType
MolecularDataType.Utils
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Field Summary
FieldsFields 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected char
getCharImpl
(int state) Get character corresponding to a given statestatic final int
getCodonIndexFromIUPACNucleotideStates
(int[] codon) The codon index is a number between 0 and 64 assigned to each different codon typestatic final int
getCodonIndexFromIUPACNucleotideStates
(int[] codon, int startingPosition) The codon index is a number between 0 and 64 assigned to each different codon typestatic final int
getCodonIndexFromNucleotides
(char[] codon) The codon index is a number between 0 and 64 assigned to each different codon typestatic final int
getCodonIndexFromNucleotideStates
(int[] codon) The codon index is a number between 0 and 64 assigned to each different codon typestatic final int
getCodonIndexFromNucleotideStates
(int[] codon, int startingPosition) The codon index is a number between 0 and 64 assigned to each different codon typedescription of data typestatic final double[]
getF1X4CodonFrequencies
(double[] nucleotideFrequencies) static final double[]
getF3X4CodonFrequencies
(double[][] nucleotideTripletFrequencies) final int[]
getMolecularStatesFromIUPACNucleotides
(int[] nucleotideStates, int startingIndex) final int[]
getMolecularStatesFromSimpleNucleotides
(int[] nucleotideStates, int startingIndex) final int
static final char[]
getNucleotidesFromCodonIndex
(int index) Translates an index into a codonint[]
getNucleotideStates
(int[] residueStates) static final int[]
getNucleotideStatesFromCodonIndex
(int codonIndex) Translates an index into a codonint
get number of unique statesint
getStateImpl
(char c) For sub classes to implement main functionality of getState.static final String
getTLA
(int state) int
get numerical code describing the data typeboolean
protected final boolean
isUnknownStateImpl
(int state) For subclasses to handle, without regard for gapsMethods 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
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Field Details
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DEFAULT_INSTANCE
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Constructor Details
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Codons
public Codons()
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Method Details
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getNumStates
public int getNumStates()Description copied from interface:DataType
get number of unique states- Specified by:
getNumStates
in interfaceDataType
- Returns:
- number of unique states
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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 classSimpleDataType
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getCharImpl
protected char getCharImpl(int state) Get character corresponding to a given state- Specified by:
getCharImpl
in classSimpleDataType
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getDescription
Description copied from interface:DataType
description of data type- Specified by:
getDescription
in interfaceDataType
- Returns:
- string describing the data type
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isUnknownStateImpl
protected final boolean isUnknownStateImpl(int state) Description copied from class:SimpleDataType
For subclasses to handle, without regard for gaps- Specified by:
isUnknownStateImpl
in classSimpleDataType
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getTypeID
public int getTypeID()Description copied from interface:DataType
get numerical code describing the data type -
getNucleotideStates
public int[] getNucleotideStates(int[] residueStates) - Specified by:
getNucleotideStates
in interfaceMolecularDataType
- Parameters:
residueStates
- an array of states corresponding to states ofthis datatyperesidue
- states an array of states corresponding to states ofthis datatype- Returns:
- the corresponding IUPAC states
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getMolecularStatesFromIUPACNucleotides
public final int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex) - Specified by:
getMolecularStatesFromIUPACNucleotides
in interfaceMolecularDataType
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getMolecularStatesFromSimpleNucleotides
public final int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex) - Specified by:
getMolecularStatesFromSimpleNucleotides
in interfaceMolecularDataType
- Returns:
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isCreatesIUPACNuecleotides
public boolean isCreatesIUPACNuecleotides()- Specified by:
isCreatesIUPACNuecleotides
in interfaceMolecularDataType
- Returns:
- false
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getNucleotideLength
public final int getNucleotideLength()- Specified by:
getNucleotideLength
in interfaceMolecularDataType
- Returns:
- 3
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getTLA
- Returns:
- a three letter acronym for an AminoAcid, according to state
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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
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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
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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 statesstartingPosition
- 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
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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 statesstartingPosition
- 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
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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 statesstartingPosition
- 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
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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
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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
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getF1X4CodonFrequencies
public static final double[] getF1X4CodonFrequencies(double[] nucleotideFrequencies) -
getF3X4CodonFrequencies
public static final double[] getF3X4CodonFrequencies(double[][] nucleotideTripletFrequencies)
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