Package pal.datatype
Class AminoAcids
java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.AminoAcids
- All Implemented Interfaces:
Serializable
,DataType
- Direct Known Subclasses:
SpecificAminoAcids
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:
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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) description of data typeint
get number of unique statesprotected int
getStateImpl
(char c) For sub classes to implement main functionality of getState.static final String
getTLA
(int state) int
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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TERMINATE_CHARACTER
public static final char TERMINATE_CHARACTER- See Also:
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TERMINATE_STATE
public static final int TERMINATE_STATE- See Also:
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Constructor Details
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AminoAcids
public AminoAcids()
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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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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
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
- Returns:
- a three letter acronym for an AminoAcid, according to state
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