pal.datatype
Class NumericDataType

java.lang.Object
  extended by pal.datatype.SimpleDataType
      extended by 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