Package pal.datatype
Class TwoStates
- java.lang.Object
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- pal.datatype.SimpleDataType
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- pal.datatype.TwoStates
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- All Implemented Interfaces:
java.io.Serializable
,DataType
public class TwoStates extends SimpleDataType
implements DataType for two-state data- Version:
- $Id: TwoStates.java,v 1.9 2003/03/23 00:04:23 matt Exp $
- Author:
- Korbinian Strimmer, Alexei Drummond
- 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 TwoStates
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 TwoStates()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected char
getCharImpl(int state)
java.lang.String
getDescription()
description of data typeint
getNumStates()
get number of unique statesint
getStateImpl(char c)
For sub classes to implement main functionality of getState.int
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 TwoStates 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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getStateImpl
public 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 classSimpleDataType
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isUnknownStateImpl
protected final boolean isUnknownStateImpl(int state)
Description copied from class:SimpleDataType
For subclasses to handle, without regard for gaps- Specified by:
isUnknownStateImpl
in classSimpleDataType
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getCharImpl
protected char getCharImpl(int state)
- Specified by:
getCharImpl
in classSimpleDataType
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getDescription
public java.lang.String getDescription()
Description copied from interface:DataType
description of data type- Returns:
- string describing the data type
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getTypeID
public int getTypeID()
Description copied from interface:DataType
get numerical code describing the data type- Returns:
- numerical code
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