public class DataTranslator
extends java.lang.Object
Constructor | Description |
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DataTranslator(int[][] stateData) |
Base DataType is assumed to be IUPAC
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DataTranslator(int[][] stateData,
MolecularDataType dt) |
|
DataTranslator(int[][] stateData,
MolecularDataType dt,
IdGroup ids) |
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DataTranslator(Alignment base) |
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DataTranslator(MolecularDataType dt,
char[][] charData) |
Modifier and Type | Method | Description |
---|---|---|
void |
ensureUnknownState(int[] states,
int unknownState) |
Ensures that all states that are "unknown" get set to the value of 'unknownState'
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static void |
ensureUnknownState(DataType dt,
int[] states,
int unknownState) |
Ensures that all states that are "unknown" (according to a certain DataType) get set to the value of 'unknownState'
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double[] |
getFrequencies(MolecularDataType dt,
int startingIndex) |
|
Alignment |
toAlignment(MolecularDataType dt,
int startingIndex) |
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static char[][] |
toChars(int[][] dtStates,
DataType dt) |
Converts an state matrix to a char matrix
Stored as [sequnce][site]
|
char[][] |
toChars(MolecularDataType dt,
int startingIndex) |
|
Alignment |
toLeftAlignedReverseComplementNucleotides(int startingIndex) |
|
static int[][] |
toNucleotides(int[][] dtStates,
MolecularDataType dt) |
Converts an alignment to a state matrix
Stored as [sequnce][site]
|
Alignment |
toReverseComplementNucleotides(int startingIndex) |
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static int[][] |
toStates(char[][] dtChars,
DataType dt) |
Converts an alignment to a state matrix
Stored as [sequnce][site]
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static int[][] |
toStates(Alignment a) |
Converts an alignment to a state matrix
Stored as [sequnce][site]
|
static int[][] |
toStates(Alignment a,
int gapUnknownState) |
Converts an alignment to a state matrix
Stored as [sequnce][site]
|
int[][] |
toStates(MolecularDataType dt,
int startingIndex) |
public DataTranslator(Alignment base)
base
- the base alignment that will be translated. The data type of this
alignment must be of type MolecularDataTypejava.lang.IllegalArgumentException
- if base DataType not of type MolecularDataTypepublic DataTranslator(int[][] stateData)
public DataTranslator(int[][] stateData, MolecularDataType dt)
public DataTranslator(int[][] stateData, MolecularDataType dt, IdGroup ids)
public DataTranslator(MolecularDataType dt, char[][] charData)
public int[][] toStates(MolecularDataType dt, int startingIndex)
public double[] getFrequencies(MolecularDataType dt, int startingIndex)
public void ensureUnknownState(int[] states, int unknownState)
public char[][] toChars(MolecularDataType dt, int startingIndex)
public Alignment toAlignment(MolecularDataType dt, int startingIndex)
public Alignment toReverseComplementNucleotides(int startingIndex)
public Alignment toLeftAlignedReverseComplementNucleotides(int startingIndex)
public static final int[][] toStates(Alignment a)
public static final int[][] toStates(Alignment a, int gapUnknownState)
public static final int[][] toNucleotides(int[][] dtStates, MolecularDataType dt)
public static final int[][] toStates(char[][] dtChars, DataType dt)
public static final char[][] toChars(int[][] dtStates, DataType dt)
public static final void ensureUnknownState(DataType dt, int[] states, int unknownState)