Class WeightMatrixAnnotator

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

    public class WeightMatrixAnnotator
    extends java.lang.Object
    implements SequenceAnnotator, java.io.Serializable
    Annotates a sequence with hits to a weight-matrix.

    This SequenceAnnotator implementation returns a new ViewSequence wrapping the underlying Sequence

    Author:
    Matthew Pocock, Thomas Down, Tanya Vavouri
    See Also:
    Serialized Form
    • Constructor Detail

      • WeightMatrixAnnotator

        public WeightMatrixAnnotator​(WeightMatrix wm,
                                     ScoreType scoreType,
                                     double threshold,
                                     java.lang.String wmID)
        Create a new annotator that uses the PROBABILITY score type and an ID for the weight matrix.
        Parameters:
        wm - the weight matrix
        threshold - the threshold
        wmID - the weight matrix ID
      • WeightMatrixAnnotator

        public WeightMatrixAnnotator​(WeightMatrix wm,
                                     double threshold)
        Create a new annotator that uses PROBABILITY score type.
        Parameters:
        wm - a WeightMatrix value
        threshold - a double value
      • WeightMatrixAnnotator

        public WeightMatrixAnnotator​(WeightMatrix wm,
                                     ScoreType scoreType,
                                     double threshold)
        Create a new annotator that uses a specific score type.
        Parameters:
        wm - the weigth matrix
        scoreType - the score type
        threshold - the threshold
        Since:
        1.4
    • Method Detail

      • getWeightMatrixID

        public java.lang.String getWeightMatrixID()
        Get the value of the weight matrix id.
        Returns:
        value of the weight matrix id.
      • setWeightMatrixID

        public void setWeightMatrixID​(java.lang.String id)
        Set the weight matrix id.
        Parameters:
        id - Value to assign to the weight matrix id.