pal.alignment
Class DataTranslator

java.lang.Object
  extended by pal.alignment.DataTranslator

public class DataTranslator
extends java.lang.Object


Constructor Summary
DataTranslator(Alignment base)
           
DataTranslator(int[][] stateData)
          Base DataType is assumed to be IUPAC
DataTranslator(int[][] stateData, MolecularDataType dt)
           
DataTranslator(int[][] stateData, MolecularDataType dt, IdGroup ids)
           
DataTranslator(MolecularDataType dt, char[][] charData)
           
 
Method Summary
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)
           
 Alignment toAlignment(MolecularDataType dt, int startingIndex)
           
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)
           
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)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

DataTranslator

public DataTranslator(Alignment base)
Parameters:
base - the base alignment that will be translated. The data type of this alignment must be of type MolecularDataType
Throws:
java.lang.IllegalArgumentException - if base DataType not of type MolecularDataType

DataTranslator

public DataTranslator(int[][] stateData)
Base DataType is assumed to be IUPAC


DataTranslator

public DataTranslator(int[][] stateData,
                      MolecularDataType dt)

DataTranslator

public DataTranslator(int[][] stateData,
                      MolecularDataType dt,
                      IdGroup ids)

DataTranslator

public DataTranslator(MolecularDataType dt,
                      char[][] charData)
Method Detail

toStates

public int[][] toStates(MolecularDataType dt,
                        int startingIndex)
Returns:
an array of states, where the states are of the form dictated by dt, and based on the base alignment

getFrequencies

public double[] getFrequencies(MolecularDataType dt,
                               int startingIndex)

ensureUnknownState

public void ensureUnknownState(int[] states,
                               int unknownState)
Ensures that all states that are "unknown" get set to the value of 'unknownState'


toChars

public char[][] toChars(MolecularDataType dt,
                        int startingIndex)
Returns:
an array of characters, where the characters are of the form dictated by dt, and based on the base alignment

toAlignment

public Alignment toAlignment(MolecularDataType dt,
                             int startingIndex)

toReverseComplementNucleotides

public Alignment toReverseComplementNucleotides(int startingIndex)

toLeftAlignedReverseComplementNucleotides

public Alignment toLeftAlignedReverseComplementNucleotides(int startingIndex)

toStates

public static final int[][] toStates(Alignment a)
Converts an alignment to a state matrix Stored as [sequnce][site]


toStates

public static final int[][] toStates(Alignment a,
                                     int gapUnknownState)
Converts an alignment to a state matrix Stored as [sequnce][site]


toNucleotides

public static final int[][] toNucleotides(int[][] dtStates,
                                          MolecularDataType dt)
Converts an alignment to a state matrix Stored as [sequnce][site]


toStates

public static final int[][] toStates(char[][] dtChars,
                                     DataType dt)
Converts an alignment to a state matrix Stored as [sequnce][site]


toChars

public static final char[][] toChars(int[][] dtStates,
                                     DataType dt)
Converts an state matrix to a char matrix Stored as [sequnce][site]


ensureUnknownState

public static final 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'