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.)
|
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) |
Constructor | Description |
---|---|
DataTranslator(int[][] stateData,
MolecularDataType dt) |
|
DataTranslator(int[][] stateData,
MolecularDataType dt,
IdGroup ids) |
|
DataTranslator(MolecularDataType dt,
char[][] charData) |
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.
|
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)
|