Uses of Interface
pal.datatype.MolecularDataType
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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.) -
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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)
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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 charactersclass
Nucleotides
implements DataType for nucleotidesclass
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)
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