Uses of Interface pal.datatype.MolecularDataType

Packages that use MolecularDataType
Package	Description
pal.alignment	Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating.
pal.datatype	Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)

Uses of MolecularDataType in pal.alignment

Methods in pal.alignment with parameters of type MolecularDataType
Modifier and Type	Method	Description
`double[]`	DataTranslator.`getFrequencies(MolecularDataType dt, int startingIndex)`
`Alignment`	DataTranslator.`toAlignment(MolecularDataType dt, int startingIndex)`
`char[][]`	DataTranslator.`toChars(MolecularDataType dt, int startingIndex)`
`static int[][]`	DataTranslator.`toNucleotides(int[][] dtStates, MolecularDataType dt)`	Converts an alignment to a state matrix Stored as [sequnce][site]
`int[][]`	DataTranslator.`toStates(MolecularDataType dt, int startingIndex)`

Constructors in pal.alignment with parameters of type MolecularDataType
Constructor	Description
`DataTranslator(int[][] stateData, MolecularDataType dt)`
`DataTranslator(int[][] stateData, MolecularDataType dt, IdGroup ids)`
`DataTranslator(MolecularDataType dt, char[][] charData)`

Uses of MolecularDataType in pal.datatype

Classes in pal.datatype that implement MolecularDataType
Modifier and Type	Class	Description
`class`	`Codons`	implements DataType for all Codons (including terminators).
`class`	`GapBalanced`	implements a ResidueDataType for GapBalanced notation.
`class`	`IUPACNucleotides`	implements DataType for nucleotides with ambiguous characters
`class`	`Nucleotides`	implements DataType for nucleotides
`class`	`SpecificAminoAcids`	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.

Methods in pal.datatype that return MolecularDataType
Modifier and Type	Method	Description
`static MolecularDataType`	MolecularDataType.Utils.`getMolecularDataType(DataType dt)`	Converts (if possible) a DataType into a MolecularDataType.
`static MolecularDataType`	DataTypeTool.`getNucleotides()`	A set access point for a data type object describing nucleotides (DNA)
`static MolecularDataType`	DataTypeTool.`getRNANucleotides()`	A set access point for a data type object describing nucleotides (RNA)
`static MolecularDataType`	DataTypeTool.`getUniverisalAminoAcids()`	A set access point for a data type object describing amino acids (used with relation to the Universal codon table)