Package pal.datatype
Class NumericDataType
- java.lang.Object
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- pal.datatype.SimpleDataType
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- pal.datatype.NumericDataType
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.datatype.DataType
DataType.Utils
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Field Summary
Fields Modifier and Type Field Description static DataType
DEFAULT_INSTANCE
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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
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Constructor Summary
Constructors Constructor Description NumericDataType()
NumericDataType(int numberOfStates)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected char
getCharImpl(int state)
Get character corresponding to a given statejava.lang.String
getDescription()
String describing the data typechar
getNumericCharFromNumericIndex(int index)
Returns a unique ascii character for any given numeric sizeint
getNumericIndexFromNumericChar(char c)
Returns numeric index (size) from a unique ascii characterint
getNumStates()
get number of unique statesprotected int
getStateImpl(char c)
get state corresponding to a characterint
getTypeID()
Get numerical code describing the data typeprotected 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
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Field Detail
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DEFAULT_INSTANCE
public static final DataType DEFAULT_INSTANCE
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Method Detail
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getNumStates
public int getNumStates()
Description copied from interface:DataType
get number of unique states- Returns:
- number of unique states
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isUnknownStateImpl
protected boolean isUnknownStateImpl(int state)
Description copied from class:SimpleDataType
For subclasses to handle, without regard for gaps- Specified by:
isUnknownStateImpl
in classSimpleDataType
- Returns:
- true if this state is an unknown state
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getStateImpl
protected int getStateImpl(char c)
get state corresponding to a character- Specified by:
getStateImpl
in classSimpleDataType
- Parameters:
c
- character- Returns:
- state
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getCharImpl
protected char getCharImpl(int state)
Get character corresponding to a given state- Specified by:
getCharImpl
in classSimpleDataType
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getNumericCharFromNumericIndex
public final char getNumericCharFromNumericIndex(int index)
Returns a unique ascii character for any given numeric size
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getNumericIndexFromNumericChar
public final int getNumericIndexFromNumericChar(char c)
Returns numeric index (size) from a unique ascii character
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getDescription
public java.lang.String getDescription()
String describing the data type- Returns:
- string describing the data type
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getTypeID
public int getTypeID()
Get numerical code describing the data type- Returns:
- numerical code
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