Package pal.datatype
Class SpecificAminoAcids
java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.AminoAcids
pal.datatype.SpecificAminoAcids
- All Implemented Interfaces:
Serializable
,DataType
,MolecularDataType
implements a MolecularDataType for amino acids, where we specifiy the Codon Table basis of amino acid by
supplying the CodonTable which is/was used for converting Nucleotide sequences to Amino Acids.
We need this table to do conversion between Nucleotides and Amino Acids (and vice versa)
- Version:
- $Id: SpecificAminoAcids.java,v 1.8 2004/10/29 01:13:37 matt Exp $
- Author:
- Matthew Goode
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.datatype.DataType
DataType.Utils
Nested classes/interfaces inherited from interface pal.datatype.MolecularDataType
MolecularDataType.Utils
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Field Summary
Fields inherited from class pal.datatype.AminoAcids
DEFAULT_INSTANCE, TERMINATE_CHARACTER, TERMINATE_STATE
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
ConstructorsConstructorDescriptionCreates with Universal Codon TableSpecificAminoAcids
(int organismTypeID) SpecificAminoAcids
(CodonTable translationTable) -
Method Summary
Modifier and TypeMethodDescriptionfinal int[]
getMolecularStatesFromIUPACNucleotides
(int[] nucleotideStates, int startingIndex) final int[]
getMolecularStatesFromSimpleNucleotides
(int[] nucleotideStates, int startingIndex) final int
int[]
getNucleotideStates
(int[] residueStates) int
boolean
Methods inherited from class pal.datatype.AminoAcids
getCharImpl, getDescription, getNumStates, getStateImpl, getTLA, getTypeID, isUnknownStateImpl
Methods inherited from class pal.datatype.SimpleDataType
getAmbiguousVersion, getChar, getPreferredChar, getPreferredCharImpl, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState, toString
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface pal.datatype.DataType
getAmbiguousVersion, getChar, getDescription, getNumStates, getPreferredChar, getRecommendedGapState, getRecommendedUnknownState, getState, getTypeID, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState
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Constructor Details
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SpecificAminoAcids
public SpecificAminoAcids()Creates with Universal Codon Table -
SpecificAminoAcids
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SpecificAminoAcids
public SpecificAminoAcids(int organismTypeID)
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Method Details
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getOrganismTypeID
public int getOrganismTypeID()- Returns:
- Organism TypeID as for CodonTable
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getNucleotideStates
public int[] getNucleotideStates(int[] residueStates) - Specified by:
getNucleotideStates
in interfaceMolecularDataType
- Parameters:
residueStates
- an array of states corresponding to states ofthis datatype- Returns:
- the corresponding IUPAC states
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getMolecularStatesFromIUPACNucleotides
public final int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex) - Specified by:
getMolecularStatesFromIUPACNucleotides
in interfaceMolecularDataType
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getMolecularStatesFromSimpleNucleotides
public final int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex) - Specified by:
getMolecularStatesFromSimpleNucleotides
in interfaceMolecularDataType
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isCreatesIUPACNuecleotides
public boolean isCreatesIUPACNuecleotides()- Specified by:
isCreatesIUPACNuecleotides
in interfaceMolecularDataType
- Returns:
- false
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getNucleotideLength
public final int getNucleotideLength()- Specified by:
getNucleotideLength
in interfaceMolecularDataType
- Returns:
- 3
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