Interface WeightMatrix

All Known Implementing Classes:
SimpleWeightMatrix

public interface WeightMatrix
A log odds weight matrix.

The weight matrix uses computer-coordinates. Thus, a 10 column weight matrix has columns (0 - 9). I guess that if you try to access columns outside the logical range, the implementation may throw an IndexOutOfBoundsException.

Author:
Matthew Pocock
  • Method Summary

    Modifier and Type
    Method
    Description
    int
    The number of columns modeled by the weight matrix.
    The alphabet for the sequences that this weight matrix models.
    getColumn(int column)
    Retrieve a column as an EmissionState.
  • Method Details

    • getAlphabet

      The alphabet for the sequences that this weight matrix models.
      Returns:
      the Alphabet
    • columns

      int columns()
      The number of columns modeled by the weight matrix.
      Returns:
      the number of columns
    • getColumn

      Retrieve a column as an EmissionState.

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

      Parameters:
      column - the weight matrix column to retrieve
      Returns:
      the EmissionState that represents the individual column
      Throws:
      IndexOutOfBoundsException - if column is not between 0 and columns()-1