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java.lang.Objectpal.alignment.DataTranslator
public class DataTranslator
Constructor Summary | |
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DataTranslator(Alignment base)
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DataTranslator(int[][] stateData)
Base DataType is assumed to be IUPAC |
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DataTranslator(int[][] stateData,
MolecularDataType dt)
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DataTranslator(int[][] stateData,
MolecularDataType dt,
IdGroup ids)
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DataTranslator(MolecularDataType dt,
char[][] charData)
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Method Summary | |
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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' |
void |
ensureUnknownState(int[] states,
int unknownState)
Ensures that all states that are "unknown" get set to the value of 'unknownState' |
double[] |
getFrequencies(MolecularDataType dt,
int startingIndex)
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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)
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Alignment |
toLeftAlignedReverseComplementNucleotides(int startingIndex)
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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(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] |
static int[][] |
toStates(char[][] dtChars,
DataType dt)
Converts an alignment to a state matrix Stored as [sequnce][site] |
int[][] |
toStates(MolecularDataType dt,
int startingIndex)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public DataTranslator(Alignment base)
base
- the base alignment that will be translated. The data type of this
alignment must be of type MolecularDataType
java.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)
Method Detail |
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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)
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