Class SimpleWeightMatrix

  • All Implemented Interfaces:
    java.io.Serializable, WeightMatrix

    public class SimpleWeightMatrix
    extends java.lang.Object
    implements WeightMatrix, java.io.Serializable
    Author:
    Matthew Pocock
    See Also:
    Serialized Form
    • Method Detail

      • getAlphabet

        public Alphabet getAlphabet()
        Description copied from interface: WeightMatrix
        The alphabet for the sequences that this weight matrix models.
        Specified by:
        getAlphabet in interface WeightMatrix
        Returns:
        the Alphabet
      • columns

        public int columns()
        Description copied from interface: WeightMatrix
        The number of columns modeled by the weight matrix.
        Specified by:
        columns in interface WeightMatrix
        Returns:
        the number of columns
      • getColumn

        public Distribution getColumn​(int column)
        Description copied from interface: WeightMatrix
        Retrieve a column as an EmissionState.

        To find the emission probability for Symbol sym at column col use: wm.getColumn(col).getWeight(sym).

        Specified by:
        getColumn in interface WeightMatrix
        Parameters:
        column - the weight matrix column to retrieve
        Returns:
        the EmissionState that represents the individual column
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object
      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object