pal.datatype
Class SpecificAminoAcids
java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.AminoAcids
pal.datatype.SpecificAminoAcids
- 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
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 |
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 |
SpecificAminoAcids
public SpecificAminoAcids()
- Creates with Universal Codon Table
SpecificAminoAcids
public SpecificAminoAcids(CodonTable translationTable)
SpecificAminoAcids
public SpecificAminoAcids(int organismTypeID)
getOrganismTypeID
public int getOrganismTypeID()
- Returns:
- Organism TypeID as for CodonTable
getNucleotideStates
public int[] getNucleotideStates(int[] residueStates)
- Specified by:
getNucleotideStates
in interface MolecularDataType
- Parameters:
residueStates
- an array of states corresponding to states of this datatype
- Returns:
- the corresponding IUPAC states
getMolecularStatesFromIUPACNucleotides
public final int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates,
int startingIndex)
- Specified by:
getMolecularStatesFromIUPACNucleotides
in interface MolecularDataType
getMolecularStatesFromSimpleNucleotides
public final int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates,
int startingIndex)
- Specified by:
getMolecularStatesFromSimpleNucleotides
in interface MolecularDataType
isCreatesIUPACNuecleotides
public boolean isCreatesIUPACNuecleotides()
- Specified by:
isCreatesIUPACNuecleotides
in interface MolecularDataType
- Returns:
- false
getNucleotideLength
public final int getNucleotideLength()
- Specified by:
getNucleotideLength
in interface MolecularDataType
- Returns:
- 3