|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
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) |
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |