Package pal.alignment

Class DataTranslator


  • public class DataTranslator
    extends java.lang.Object
    • 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​(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
      • 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'