pal.datatype
Interface MolecularDataType
- All Superinterfaces:
- DataType, java.io.Serializable
- All Known Implementing Classes:
- Codons, GapBalanced, IUPACNucleotides, Nucleotides, SpecificAminoAcids
public interface MolecularDataType
- extends DataType
An extension to the generic DataType class for DataTypes
related to genetic residues (by this it is meant Nucleotides,
AminoAcids, and Codons).
- Version:
- 1.1
- Author:
- Matthew Goode
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 interface pal.datatype.DataType |
getAmbiguousVersion, getChar, getDescription, getNumStates, getPreferredChar, getRecommendedGapState, getRecommendedUnknownState, getState, getTypeID, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState |
getNucleotideStates
int[] getNucleotideStates(int[] molecularStates)
- Parameters:
molecularStates
- an array of states corresponding to states of this datatype
- Returns:
- the corresponding IUPAC states
getMolecularStatesFromIUPACNucleotides
int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates,
int startingIndex)
- Parameters:
the
- IUPAC nucleotidestates
getMolecularStatesFromSimpleNucleotides
int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates,
int startingIndex)
- Parameters:
the
- Simple nucleotide states (eg 0,1,2,3 or A,C,G,T)
isCreatesIUPACNuecleotides
boolean isCreatesIUPACNuecleotides()
- Returns:
- true if this data type will create Nucleotide states using IUPAC states (for example if this
DataType is AminoAcid based, IUPAC states are needed to maintain information on different possible values for a state)
getNucleotideLength
int getNucleotideLength()
- Returns:
- the number of nucleotides required for a single character of this data typedata