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.DataType
  DataType.Utils
- Nested classes/interfaces inherited from interface pal.datatype.MolecularDataType
  MolecularDataType.Utils

Field Summary

Fields
Modifier and Type Field Description

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

Constructors
Constructor Description

Nucleotides()

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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)

Modifier and Type	Field	Description
`static int`	`A_STATE`
`static int`	`C_STATE`
`static Nucleotides`	`DEFAULT_INSTANCE`
`static int`	`G_STATE`
`static int`	`UT_STATE`

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

Class Nucleotides

Nested Class Summary

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

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

Field Summary

Fields inherited from interface pal.datatype.DataType

Constructor Summary

Method Summary

Methods inherited from class pal.datatype.SimpleDataType

Methods inherited from class java.lang.Object

Methods inherited from interface pal.datatype.DataType

Field Detail

A_STATE

C_STATE

G_STATE

UT_STATE

DEFAULT_INSTANCE

Constructor Detail

Nucleotides

Nucleotides

Method Detail

getNumStates

isUnknownStateImpl

getStateImpl

getCharImpl

getDescription

getTypeID

isTransitionByState

isTransitionByChar

getNucleotideStates

getRelavantLength

getMolecularStatesFromSimpleNucleotides

getMolecularStatesFromIUPACNucleotides

isCreatesIUPACNuecleotides

getNucleotideLength

getComplementState

getSequenceComplement

complementSequence