IUPACNucleotides

java.lang.Object
- pal.datatype.SimpleDataType
- - pal.datatype.IUPACNucleotides

All Implemented Interfaces:

java.io.Serializable, AmbiguousDataType, DataType, MolecularDataType
```
public class IUPACNucleotides
extends SimpleDataType
implements MolecularDataType, AmbiguousDataType
```
implements DataType for nucleotides with ambiguous characters

Version:

$Id: IUPACNucleotides.java,v 1.19 2004/09/13 05:20:47 matt Exp $

Author:

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 IUPACNucleotides DEFAULT_INSTANCE

static IUPACNucleotides DNA_INSTANCE

static IUPACNucleotides RNA_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, NUCLEOTIDES, NUMERIC, PRIMARY_SUGGESTED_GAP_CHARACTER, SUGGESTED_GAP_CHARACTERS, SUGGESTED_GAP_STATE, SUGGESTED_UNKNOWN_STATE, TWO_STATE_DESCRIPTION, TWOSTATES, UNKNOWN, UNKNOWN_CHARACTER, UNKNOWN_TLA

Fields
Modifier and Type	Field and Description
`static IUPACNucleotides`	`DEFAULT_INSTANCE`
`static IUPACNucleotides`	`DNA_INSTANCE`
`static IUPACNucleotides`	`RNA_INSTANCE`

Constructor Summary

Constructors
Constructor and Description

IUPACNucleotides()

IUPACNucleotides(boolean isRNA)

Constructors
Constructor and Description
`IUPACNucleotides()`
`IUPACNucleotides(boolean isRNA)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`getAmbiguity(int ambiguousState, boolean[] specificInclusion)` Attempts to "resolve" the ambiguity in a state with regard to the specific data type.
`void`	`getAmbiguity(int ambiguousState, double[] specificInclusion)` A more accurate attempt to "resolve" the ambiguity in a state with regard to the specific data type.
`AmbiguousDataType`	`getAmbiguousVersion()`
`protected char`	`getCharImpl(int state)`
`java.lang.String`	`getDescription()` description of data type
`static int`	`getIUPACState(boolean maybeA, boolean maybeC, boolean maybeG, boolean maybeT)`
`static int`	`getIUPACState(int inclusion)`
`int[]`	`getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)`
`int[]`	`getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)`
`int`	`getNucleotideLength()`
`int[]`	`getNucleotideStates(int[] residueStates)`
`int`	`getNumStates()` Get number of states.
`int`	`getRecommendedUnknownState()`
`static int`	`getSimpleState(int state)` Converts an IUPAC State to either a A,T,G,C state (eg.
`static int[]`	`getSimpleStates(int[] states)` Converts an IUPAC State array to either a A,T,G,C state (eg.
`static int[]`	`getSimpleStates(int[] states, int startingIndex)` Converts an IUPAC State array to either a A,T,G,C state (eg.
`DataType`	`getSpecificDataType()`
`int[]`	`getSpecificStates(int state)` returns an array containing the non-ambiguous states that this state represents.
`protected int`	`getStateImpl(char c)` For sub classes to implement main functionality of getState.
`int`	`getTypeID()` get numerical code describing the data type
`boolean`	`isAmbiguous()`
`boolean`	`isCreatesIUPACNuecleotides()`
`static boolean`	`isNucleotideState(int iupacState, int nucleotideState)`
`protected boolean`	`isUnknownStateImpl(int state)` For subclasses to handle, without regard for gaps
`java.lang.String`	`toString()`

Methods inherited from class pal.datatype.SimpleDataType
getChar, getPreferredChar, getPreferredCharImpl, getRecommendedGapState, getState, hasGap, isGapChar, isGapState, isUnknownChar, isUnknownState

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface pal.datatype.DataType
getChar, getPreferredChar, getRecommendedGapState, getState, hasGap, isGapChar, isGapState, isUnknownChar, isUnknownState

- Field Detail
  - DEFAULT_INSTANCE
```
public static final IUPACNucleotides DEFAULT_INSTANCE
```
  - DNA_INSTANCE
```
public static final IUPACNucleotides DNA_INSTANCE
```
  - RNA_INSTANCE
```
public static final IUPACNucleotides RNA_INSTANCE
```
- Constructor Detail
  - IUPACNucleotides
```
public IUPACNucleotides()
```
  - IUPACNucleotides
```
public IUPACNucleotides(boolean isRNA)
```
- Method Detail
  - getNumStates
```
public int getNumStates()
```
    Get number of states.
    
    Specified by:
    
    getNumStates in interface DataType
    
    Returns:
    
    number of unique states
  - isUnknownStateImpl
```
protected boolean isUnknownStateImpl(int state)
```
    Description copied from class: SimpleDataType
    
    For subclasses to handle, without regard for gaps
    
    Specified by:
    
    isUnknownStateImpl in class SimpleDataType
  - getStateImpl
```
protected final 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)
```
    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
  - 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
  - isNucleotideState
```
public static final boolean isNucleotideState(int iupacState,
                                              int nucleotideState)
```
    Returns:
    
    true if the iupacState is an state which includes the possibility of being of a nucleotide state
  - getRecommendedUnknownState
```
public int getRecommendedUnknownState()
```
    Specified by:
    
    getRecommendedUnknownState in interface DataType
    
    Overrides:
    
    getRecommendedUnknownState in class SimpleDataType
    
    Returns:
    
    -1 (not getNumStates())
  - getIUPACState
```
public static final int getIUPACState(int inclusion)
```
    Parameters:
    
    inclusion - should be a number constructed as follows 1. start at zero 2. if maybe A add 1 3. if maybe C add 2 4. if maybe G add 4 5. if maybe T add 8
  - getIUPACState
```
public static final int getIUPACState(boolean maybeA,
                                      boolean maybeC,
                                      boolean maybeG,
                                      boolean maybeT)
```
  - getSimpleState
```
public static final int getSimpleState(int state)
```
    Converts an IUPAC State to either a A,T,G,C state (eg. if state represents either C or G, state becomes C - an arbitary choice is made to take "lowest" letter)
  - getSimpleStates
```
public static final int[] getSimpleStates(int[] states)
```
    Converts an IUPAC State array to either a A,T,G,C state (eg. if state represents either C or G, state becomes C - an arbitary choice is made to take "lowest" letter)
    
    Returns:
    
    new array containing only simple states (orignal is not altered)
  - getSimpleStates
```
public static final int[] getSimpleStates(int[] states,
                                          int startingIndex)
```
    Converts an IUPAC State array to either a A,T,G,C state (eg. if state represents either C or G, state becomes C - an arbitary choice is made to take "lowest" letter)
    
    Parameters:
    
    staringIndex - amount to skip at beginning of input array
    
    Returns:
    
    new array containing only simple states (orignal is not altered)
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class SimpleDataType
  - 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
  - getMolecularStatesFromSimpleNucleotides
```
public int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates,
                                                     int startingIndex)
```
    Specified by:
    
    getMolecularStatesFromSimpleNucleotides in interface MolecularDataType
    
    Returns:
    
    a copy of the input
  - getMolecularStatesFromIUPACNucleotides
```
public final 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:
    
    true
  - getNucleotideLength
```
public final int getNucleotideLength()
```
    Specified by:
    
    getNucleotideLength in interface MolecularDataType
    
    Returns:
    
    1
  - getSpecificStates
```
public int[] getSpecificStates(int state)
```
    returns an array containing the non-ambiguous states that this state represents.
    
    Specified by:
    
    getSpecificStates in interface AmbiguousDataType
  - isAmbiguous
```
public boolean isAmbiguous()
```
    Specified by:
    
    isAmbiguous in interface DataType
    
    Overrides:
    
    isAmbiguous in class SimpleDataType
    
    Returns:
    
    true
  - getAmbiguousVersion
```
public AmbiguousDataType getAmbiguousVersion()
```
    Specified by:
    
    getAmbiguousVersion in interface DataType
    
    Overrides:
    
    getAmbiguousVersion in class SimpleDataType
    
    Returns:
    
    this!
  - getSpecificDataType
```
public DataType getSpecificDataType()
```
    Specified by:
    
    getSpecificDataType in interface AmbiguousDataType
    
    Returns:
    
    Nucleotides
  - getAmbiguity
```
public void getAmbiguity(int ambiguousState,
                         boolean[] specificInclusion)
```
    Attempts to "resolve" the ambiguity in a state with regard to the specific data type.
    
    Specified by:
    
    getAmbiguity in interface AmbiguousDataType
    
    Parameters:
    
    ambiguousState - the state of this data type (the ambiguous one!)
    
    specificInclusion - An array of length equal to or greater than the number of states of the specific DataType. Each state of the specific data type is represented by the corresponding element in this array. The result of this method will be to set the states that the ambiguous state cannot represent to false, and those states that the ambiguous state might represent to true.
  - getAmbiguity
```
public void getAmbiguity(int ambiguousState,
                         double[] specificInclusion)
```
    A more accurate attempt to "resolve" the ambiguity in a state with regard to the specific data type.
    
    Specified by:
    
    getAmbiguity in interface AmbiguousDataType
    
    Parameters:
    
    ambiguousState - the state of this data type (the ambiguous one!)
    
    specificInclusion - An array of length equal to or greater than the number of states of the specific DataType. Each state of the specific data type is represented by the corresponding element in this array. The result of this method will be to set the states that the ambiguous state cannot represent to zero, and those states that the ambiguous state might represent to a value representing the frequency that the ambiguous state is actually that specific state. In general this should be one for each specific state covered by the ambiguous state (result should be suitable for use in likelihood calculations).

Class IUPACNucleotides

Nested Class Summary

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

DEFAULT_INSTANCE

DNA_INSTANCE

RNA_INSTANCE

Constructor Detail

IUPACNucleotides

IUPACNucleotides

Method Detail

getNumStates

isUnknownStateImpl

getStateImpl

getCharImpl

getDescription

getTypeID

isNucleotideState

getRecommendedUnknownState

getIUPACState

getIUPACState

getSimpleState

getSimpleStates

getSimpleStates

toString

getNucleotideStates

getMolecularStatesFromSimpleNucleotides

getMolecularStatesFromIUPACNucleotides

isCreatesIUPACNuecleotides

getNucleotideLength

getSpecificStates

isAmbiguous

getAmbiguousVersion

getSpecificDataType

getAmbiguity

getAmbiguity