public class SpecificAminoAcids extends AminoAcids implements MolecularDataType
MolecularDataType.Utils
DEFAULT_INSTANCE, TERMINATE_CHARACTER, TERMINATE_STATE
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 and Description |
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SpecificAminoAcids()
Creates with Universal Codon Table
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SpecificAminoAcids(CodonTable translationTable) |
SpecificAminoAcids(int organismTypeID) |
Modifier and Type | Method and Description |
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int[] |
getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates,
int startingIndex) |
int[] |
getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates,
int startingIndex) |
int |
getNucleotideLength() |
int[] |
getNucleotideStates(int[] residueStates) |
int |
getOrganismTypeID() |
boolean |
isCreatesIUPACNuecleotides() |
getCharImpl, getDescription, getNumStates, getStateImpl, getTLA, getTypeID, isUnknownStateImpl
getAmbiguousVersion, getChar, getPreferredChar, getPreferredCharImpl, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState, toString
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
getAmbiguousVersion, getChar, getDescription, getNumStates, getPreferredChar, getRecommendedGapState, getRecommendedUnknownState, getState, getTypeID, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState
public SpecificAminoAcids()
public SpecificAminoAcids(CodonTable translationTable)
public SpecificAminoAcids(int organismTypeID)
public int getOrganismTypeID()
public int[] getNucleotideStates(int[] residueStates)
getNucleotideStates
in interface MolecularDataType
residueStates
- an array of states corresponding to states of public final int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
getMolecularStatesFromIUPACNucleotides
in interface MolecularDataType
public final int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
getMolecularStatesFromSimpleNucleotides
in interface MolecularDataType
public boolean isCreatesIUPACNuecleotides()
isCreatesIUPACNuecleotides
in interface MolecularDataType
public final int getNucleotideLength()
getNucleotideLength
in interface MolecularDataType