pal.datatype
Class Nucleotides

java.lang.Object
  pal.datatype.SimpleDataType
      pal.datatype.Nucleotides

All Implemented Interfaces:

java.io.Serializable, DataType, MolecularDataType

public class Nucleotides
extends SimpleDataType
implements 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:

Serialized Form

Nested Class Summary

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

MolecularDataType.Utils

Field Summary

static int	A_STATE
static int	C_STATE
static Nucleotides	DEFAULT_INSTANCE
static int	G_STATE
static int	UT_STATE

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

Constructor Summary

Nucleotides()

Nucleotides(boolean isRNA)
If isRNA is true than getChar(state) will return a U instead of a T

Method Summary

static 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 state
static int	getComplementState(int baseState) Obtain the complement state
java.lang.String	getDescription() description of data type
int[]	getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
int[]	getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
int	getNucleotideLength()
int[]	getNucleotideStates(int[] residueStates)
int	getNumStates() get number of unique states
int	getRelavantLength(int numberOfStates)
static 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	getTypeID() get numerical code describing the data type
boolean	isCreatesIUPACNuecleotides()
boolean	isTransitionByChar(char firstChar, char secondChar)
boolean	isTransitionByState(int firstState, int secondState)
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

A_STATE

public static final int A_STATE

See Also:

Constant Field Values

C_STATE

public static final int C_STATE

See Also:

Constant Field Values

G_STATE

public static final int G_STATE

See Also:

Constant Field Values

UT_STATE

public static final int UT_STATE

See Also:

Constant Field Values

DEFAULT_INSTANCE

public static final Nucleotides DEFAULT_INSTANCE

Constructor Detail

Nucleotides

public Nucleotides()

Nucleotides

public Nucleotides(boolean isRNA)

If isRNA is true than getChar(state) will return a U instead of a T

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

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

Returns:

true if this state is an unknown state

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 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:

a string describing the data type

getTypeID

public int getTypeID()

Description copied from interface: DataType

get numerical code describing the data type

Specified by:

getTypeID in interface DataType

Returns:

the unique 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!

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)

getNucleotideStates

public int[] getNucleotideStates(int[] residueStates)

Specified by:

getNucleotideStates in interface MolecularDataType

Parameters:

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

Returns:

a copy of the input

getRelavantLength

public int getRelavantLength(int numberOfStates)

Returns:

the input

getMolecularStatesFromSimpleNucleotides

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

Specified by:

getMolecularStatesFromSimpleNucleotides in interface MolecularDataType

Returns:

a copy of the input

getMolecularStatesFromIUPACNucleotides

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

Specified by:

getMolecularStatesFromIUPACNucleotides in interface MolecularDataType

Returns:

a copy of the input

isCreatesIUPACNuecleotides

public boolean isCreatesIUPACNuecleotides()

Specified by:

isCreatesIUPACNuecleotides in interface MolecularDataType

Returns:

false Nucleotide data will suffice

getNucleotideLength

public final int getNucleotideLength()

Specified by:

getNucleotideLength in interface MolecularDataType

Returns:

1

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

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

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)