DataType
, java.io.Serializable
Codons
, GapBalanced
, IUPACNucleotides
, Nucleotides
, SpecificAminoAcids
public interface MolecularDataType extends DataType
Modifier and Type | Interface | Description |
---|---|---|
static class |
MolecularDataType.Utils |
Utilities relating to MolecularDataType stuff
|
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
Modifier and Type | Method | Description |
---|---|---|
int[] |
getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates,
int startingIndex) |
|
int[] |
getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates,
int startingIndex) |
|
int |
getNucleotideLength() |
|
int[] |
getNucleotideStates(int[] molecularStates) |
|
boolean |
isCreatesIUPACNuecleotides() |
getAmbiguousVersion, getChar, getDescription, getNumStates, getPreferredChar, getRecommendedGapState, getRecommendedUnknownState, getState, getTypeID, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState
int[] getNucleotideStates(int[] molecularStates)
molecularStates
- an array of states corresponding to states of int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
the
- IUPAC nucleotidestatesint[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
the
- Simple nucleotide states (eg 0,1,2,3 or A,C,G,T)boolean isCreatesIUPACNuecleotides()
int getNucleotideLength()