Package pal.datatype

Interface AmbiguousDataType

  • All Superinterfaces:
    DataType, java.io.Serializable
    All Known Implementing Classes:
    IUPACNucleotides

    public interface AmbiguousDataType
    extends DataType
    Additional interface information for data types which represent ambiguity in sub types.
    Version:
    $Id: AmbiguousDataType.java,v 1.1 2002/11/25 05:38:40 matt Exp $
    Author:
    Matthew Goode
    • Method Detail

      • getSpecificStates

        int[] getSpecificStates​(int ambiguousState)
        returns an array containing the non-ambiguous states that this state represents.
      • getSpecificDataType

        DataType getSpecificDataType()
        Returns:
        the DataType that this datatype is the Ambiguous Version of.
      • getAmbiguity

        void getAmbiguity​(int ambiguousState,
                          boolean[] specificInclusion)
        Attempts to "resolve" the ambiguity in a state with regard to the specific data type.
        Parameters:
        ambiguousState - the state of this data type (the ambiguous one!)
        specificInclusion - An array of length equal to or greater than the number of states of the specific DataType. Each state of the specific data type is represented by the corresponding element in this array. The result of this method will be to set the states that the ambiguous state cannot represent to false, and those states that the ambiguous state might represent to true.
      • getAmbiguity

        void getAmbiguity​(int ambiguousState,
                          double[] specificInclusion)
        A more accurate attempt to "resolve" the ambiguity in a state with regard to the specific data type.
        Parameters:
        ambiguousState - the state of this data type (the ambiguous one!)
        specificInclusion - An array of length equal to or greater than the number of states of the specific DataType. Each state of the specific data type is represented by the corresponding element in this array. The result of this method will be to set the states that the ambiguous state cannot represent to zero, and those states that the ambiguous state might represent to a value representing the frequency that the ambiguous state is actually that specific state. In general this should be one for each specific state covered by the ambiguous state (result should be suitable for use in likelihood calculations).