Uses of Interface
pal.datatype.MolecularDataType

Packages that use MolecularDataType
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
 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
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
 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
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)