Class WeightMatrixAnnotator

java.lang.Object
org.biojava.bio.dp.WeightMatrixAnnotator
All Implemented Interfaces:
Serializable, SequenceAnnotator

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:
  • Constructor Details

    • WeightMatrixAnnotator

      public WeightMatrixAnnotator(WeightMatrix wm, ScoreType scoreType, double threshold, 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 Details