Package pal.datatype
Class AminoAcids
- java.lang.Object
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- pal.datatype.SimpleDataType
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- pal.datatype.AminoAcids
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- All Implemented Interfaces:
java.io.Serializable
,DataType
- Direct Known Subclasses:
SpecificAminoAcids
public class AminoAcids extends SimpleDataType
implements DataType for amino acids- Version:
- $Id: AminoAcids.java,v 1.19 2003/03/23 00:04:23 matt Exp $
- Author:
- Korbinian Strimmer, Alexei Drummond, Matthew Goode
- 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 AminoAcids
DEFAULT_INSTANCE
static char
TERMINATE_CHARACTER
static int
TERMINATE_STATE
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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 AminoAcids()
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Method Summary
All Methods Static 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 statesprotected int
getStateImpl(char c)
For sub classes to implement main functionality of getState.static java.lang.String
getTLA(int state)
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 AminoAcids DEFAULT_INSTANCE
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TERMINATE_CHARACTER
public static final char TERMINATE_CHARACTER
- See Also:
- Constant Field Values
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TERMINATE_STATE
public static final int TERMINATE_STATE
- See Also:
- Constant Field Values
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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
protected 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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getCharImpl
protected char getCharImpl(int state)
- Specified by:
getCharImpl
in classSimpleDataType
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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
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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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getTLA
public static final java.lang.String getTLA(int state)
- Returns:
- a three letter acronym for an AminoAcid, according to state
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