Package pal.datatype
Class Nucleotides
java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.Nucleotides
- All Implemented Interfaces:
Serializable
,DataType
,MolecularDataType
implements DataType for nucleotides
- Version:
- $Id: Nucleotides.java,v 1.20 2004/09/13 05:20:47 matt Exp $
- Author:
- Korbinian Strimmer, 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
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
static final Nucleotides
static final int
static final int
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, NUCLEOTIDES, 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
ConstructorsConstructorDescriptionNucleotides
(boolean isRNA) If isRNA is true than getChar(state) will return a U instead of a T -
Method Summary
Modifier and TypeMethodDescriptionstatic final void
complementSequence
(int[] sequence) Complement of a sequence of nucleotides (or IUPACNucleotides - but IUPAC ness is lost)protected char
getCharImpl
(int state) Get character corresponding to a given statestatic final int
getComplementState
(int baseState) Obtain the complement statedescription of data typeint[]
getMolecularStatesFromIUPACNucleotides
(int[] nucleotideStates, int startingIndex) int[]
getMolecularStatesFromSimpleNucleotides
(int[] nucleotideStates, int startingIndex) final int
int[]
getNucleotideStates
(int[] residueStates) int
get number of unique statesint
getRelavantLength
(int numberOfStates) static final int[]
getSequenceComplement
(int[] sequence) Obtain the complement of a sequence of nucleotides (or IUPACNucleotides - but IUPAC ness is lost)protected int
getStateImpl
(char c) Get state corresponding to character c
NOTE: IF YOU CHANGE THIS IT MAY STOP THE NUCLEOTIDE TRANSLATOR FROM WORKING! - It relies on the fact that all the states for 'ACGTU' are between [0, 3]int
get numerical code describing the data typeboolean
final boolean
isTransitionByChar
(char firstChar, char secondChar) final boolean
isTransitionByState
(int firstState, int secondState) 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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A_STATE
public static final int A_STATE- See Also:
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C_STATE
public static final int C_STATE- See Also:
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G_STATE
public static final int G_STATE- See Also:
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UT_STATE
public static final int UT_STATE- See Also:
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DEFAULT_INSTANCE
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Constructor Details
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Nucleotides
public Nucleotides() -
Nucleotides
public Nucleotides(boolean isRNA) If isRNA is true than getChar(state) will return a U instead of a T
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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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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
- Returns:
- true if this state is an unknown state
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getStateImpl
protected int getStateImpl(char c) Get state corresponding to character c
NOTE: IF YOU CHANGE THIS IT MAY STOP THE NUCLEOTIDE TRANSLATOR FROM WORKING! - It relies on the fact that all the states for 'ACGTU' are between [0, 3]- 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:
- a string describing the data type
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getTypeID
public int getTypeID()Description copied from interface:DataType
get numerical code describing the data type -
isTransitionByState
public final boolean isTransitionByState(int firstState, int secondState) - Returns:
- true if A->G, G->A, C->T, or T->C if firstState equals secondState returns FALSE!
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isTransitionByChar
public final boolean isTransitionByChar(char firstChar, char secondChar) - Returns:
- true if A->G, G->A, C->T, or T->C if firstState equals secondState returns FALSE! (I've renamed things to avoid confusion between java typing of ints and chars)
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getNucleotideStates
public int[] getNucleotideStates(int[] residueStates) - Specified by:
getNucleotideStates
in interfaceMolecularDataType
- Parameters:
residueStates
- an array of states corresponding to states ofthis datatype- Returns:
- a copy of the input
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getRelavantLength
public int getRelavantLength(int numberOfStates) - Returns:
- the input
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getMolecularStatesFromSimpleNucleotides
public int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex) - Specified by:
getMolecularStatesFromSimpleNucleotides
in interfaceMolecularDataType
- Returns:
- a copy of the input
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getMolecularStatesFromIUPACNucleotides
public int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex) - Specified by:
getMolecularStatesFromIUPACNucleotides
in interfaceMolecularDataType
- Returns:
- a copy of the input
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isCreatesIUPACNuecleotides
public boolean isCreatesIUPACNuecleotides()- Specified by:
isCreatesIUPACNuecleotides
in interfaceMolecularDataType
- Returns:
- false Nucleotide data will suffice
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getNucleotideLength
public final int getNucleotideLength()- Specified by:
getNucleotideLength
in interfaceMolecularDataType
- Returns:
- 1
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getComplementState
public static final int getComplementState(int baseState) Obtain the complement state- Parameters:
baseState
- the base state to complement (may be IUPAC but IUPACness is lost)- Returns:
- the complement state
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getSequenceComplement
public static final int[] getSequenceComplement(int[] sequence) Obtain the complement of a sequence of nucleotides (or IUPACNucleotides - but IUPAC ness is lost)- Parameters:
sequence
- the sequence (of nucleotide states)- Returns:
- the complement
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complementSequence
public static final void complementSequence(int[] sequence) Complement of a sequence of nucleotides (or IUPACNucleotides - but IUPAC ness is lost)- Parameters:
sequence
- the sequence (of nucleotide states) (is modified)
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