Package Executable

Class ImputationOption


  • public class ImputationOption
    extends java.lang.Object
    Represents the imputer options to LinkImpute
    • Constructor Summary

      Constructors 
      Constructor Description
      ImputationOption​(Imputer imputer)
      Constructor for when the imputer isn't optimizable.
      ImputationOption​(OptimizeImputer imputer)
      Constructor for when the imputer is optimizable
      ImputationOption​(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
      Constructor from a config (read in from a XML file)
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      org.apache.commons.configuration2.tree.ImmutableNode getConfig()
      Get the imputer options config
      Imputer getImputer()
      Returns the imputer if the imputer option was for a non-optimizable imputer, else throws an exception
      Imputer getImputer​(double[][][] original, int[][][] readCounts, java.util.List<SingleGenotypeProbability> maskedprobs, java.util.List<SingleGenotypeMasked> list)
      Gets an imputer.
      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • ImputationOption

        public ImputationOption​(Imputer imputer)
        Constructor for when the imputer isn't optimizable. May be used when we've already created an optimized imputer.
        Parameters:
        imputer - The imputer
      • ImputationOption

        public ImputationOption​(OptimizeImputer imputer)
        Constructor for when the imputer is optimizable
        Parameters:
        imputer - The imputer
      • ImputationOption

        public ImputationOption​(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
        Constructor from a config (read in from a XML file)
        Parameters:
        params - The config
    • Method Detail

      • getImputer

        public Imputer getImputer​(double[][][] original,
                                  int[][][] readCounts,
                                  java.util.List<SingleGenotypeProbability> maskedprobs,
                                  java.util.List<SingleGenotypeMasked> list)
        Gets an imputer. If the imputer option was for one that was not optimized simply returns that. Else optimizes a imputer and returns the optimized version of it.
        Parameters:
        original - The original called genotype probabilities
        readCounts - The readcounts
        maskedprobs - The masked called genotype probabilities
        list - A list of masked positions
        Returns:
        An imputer
      • getImputer

        public Imputer getImputer()
        Returns the imputer if the imputer option was for a non-optimizable imputer, else throws an exception
        Returns:
        The imputer
      • getConfig

        public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
        Get the imputer options config
        Returns:
        The config