Package pal.datatype
Class NumericDataType
java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.NumericDataType
- All Implemented Interfaces:
Serializable
,DataType
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.datatype.DataType
DataType.Utils
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Field Summary
FieldsFields 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 -
Method Summary
Modifier and TypeMethodDescriptionprotected char
getCharImpl
(int state) Get character corresponding to a given stateString describing the data typefinal char
getNumericCharFromNumericIndex
(int index) Returns a unique ascii character for any given numeric sizefinal int
getNumericIndexFromNumericChar
(char c) Returns numeric index (size) from a unique ascii characterint
get number of unique statesprotected int
getStateImpl
(char c) get state corresponding to a characterint
Get numerical code describing the data typeprotected boolean
isUnknownStateImpl
(int state) For subclasses to handle, without regard for gapsMethods 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 Details
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DEFAULT_INSTANCE
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Constructor Details
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NumericDataType
public NumericDataType() -
NumericDataType
public NumericDataType(int numberOfStates)
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Method Details
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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 -
getNumericIndexFromNumericChar
public final int getNumericIndexFromNumericChar(char c) Returns numeric index (size) from a unique ascii character -
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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