Package pal.datatype
Class SpecificAminoAcids
- java.lang.Object
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- pal.datatype.SimpleDataType
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- pal.datatype.AminoAcids
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- pal.datatype.SpecificAminoAcids
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- All Implemented Interfaces:
java.io.Serializable
,DataType
,MolecularDataType
public class SpecificAminoAcids extends AminoAcids implements 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:
- 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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Nested classes/interfaces inherited from interface pal.datatype.MolecularDataType
MolecularDataType.Utils
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Field Summary
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Fields inherited from class pal.datatype.AminoAcids
DEFAULT_INSTANCE, TERMINATE_CHARACTER, 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 SpecificAminoAcids()
Creates with Universal Codon TableSpecificAminoAcids(int organismTypeID)
SpecificAminoAcids(CodonTable translationTable)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int[]
getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
int[]
getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
int
getNucleotideLength()
int[]
getNucleotideStates(int[] residueStates)
int
getOrganismTypeID()
boolean
isCreatesIUPACNuecleotides()
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Methods inherited from class pal.datatype.AminoAcids
getCharImpl, getDescription, getNumStates, getStateImpl, getTLA, getTypeID, isUnknownStateImpl
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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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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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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 Detail
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SpecificAminoAcids
public SpecificAminoAcids()
Creates with Universal Codon Table
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SpecificAminoAcids
public SpecificAminoAcids(CodonTable translationTable)
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SpecificAminoAcids
public SpecificAminoAcids(int organismTypeID)
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Method Detail
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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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