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

Nested Class Summary

Nested classes/interfaces inherited from interface pal.datatype.MolecularDataType

MolecularDataType.Utils

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

Constructor Summary

Constructors

Constructor and Description
SpecificAminoAcids() Creates with Universal Codon Table
SpecificAminoAcids(CodonTable translationTable)
SpecificAminoAcids(int organismTypeID)

Method Summary

Methods

Modifier and Type	Method and Description
int[]	getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
int[]	getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
int	getNucleotideLength()
int[]	getNucleotideStates(int[] residueStates)
int	getOrganismTypeID()
boolean	isCreatesIUPACNuecleotides()

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

Constructor Detail

SpecificAminoAcids

public SpecificAminoAcids()

Creates with Universal Codon Table

SpecificAminoAcids

public SpecificAminoAcids(CodonTable translationTable)

SpecificAminoAcids

public SpecificAminoAcids(int organismTypeID)

Method Detail

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