pal.datatype
Class NumericDataType

java.lang.Object
  pal.datatype.SimpleDataType
      pal.datatype.NumericDataType

All Implemented Interfaces:

java.io.Serializable, DataType

public class NumericDataType
extends SimpleDataType

This datatype stores numeric values. These can be any 2 byte integer between 0-65536. This can be used for SSR alleles or indel sizes.

Version:

$Id:

Author:

Ed Buckler

See Also:

Serialized Form

Nested Class Summary

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

DataType.Utils

Field Summary

static DataType

DEFAULT_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

Constructor Summary

NumericDataType()

NumericDataType(int numberOfStates)

Method Summary

protected char	getCharImpl(int state) Get character corresponding to a given state
java.lang.String	getDescription() String describing the data type
char	getNumericCharFromNumericIndex(int index) Returns a unique ascii character for any given numeric size
int	getNumericIndexFromNumericChar(char c) Returns numeric index (size) from a unique ascii character
int	getNumStates() get number of unique states
protected int	getStateImpl(char c) get state corresponding to a character
int	getTypeID() Get numerical code describing the data type
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

Field Detail

DEFAULT_INSTANCE

public static final DataType DEFAULT_INSTANCE

Constructor Detail

NumericDataType

public NumericDataType()

NumericDataType

public NumericDataType(int numberOfStates)

Method Detail

getNumStates

public int getNumStates()

Description copied from interface: DataType

get number of unique states

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

Returns:

true if this state is an unknown state

getStateImpl

protected int getStateImpl(char c)

get state corresponding to a character

Specified by:

getStateImpl in class SimpleDataType

Parameters:

c - character

Returns:

state

getCharImpl

protected char getCharImpl(int state)

Get character corresponding to a given state

Specified by:

getCharImpl in class SimpleDataType

getNumericCharFromNumericIndex

public final char getNumericCharFromNumericIndex(int index)

Returns a unique ascii character for any given numeric size

getNumericIndexFromNumericChar

public final int getNumericIndexFromNumericChar(char c)

Returns numeric index (size) from a unique ascii character

getDescription

public java.lang.String getDescription()

String describing the data type

Returns:

string describing the data type

getTypeID

public int getTypeID()

Get numerical code describing the data type

Returns:

numerical code