Package Executable
Class ImputationOption
- java.lang.Object
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- Executable.ImputationOption
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public class ImputationOption extends java.lang.Object
Represents the imputer options to LinkImpute
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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 optimizableImputationOption(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Constructor from a config (read in from a XML file)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description org.apache.commons.configuration2.tree.ImmutableNode
getConfig()
Get the imputer options configImputer
getImputer()
Returns the imputer if the imputer option was for a non-optimizable imputer, else throws an exceptionImputer
getImputer(double[][][] original, int[][][] readCounts, java.util.List<SingleGenotypeProbability> maskedprobs, java.util.List<SingleGenotypeMasked> list)
Gets an imputer.
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Constructor Detail
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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
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ImputationOption
public ImputationOption(OptimizeImputer imputer)
Constructor for when the imputer is optimizable- Parameters:
imputer
- The imputer
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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
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Method Detail
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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 probabilitiesreadCounts
- The readcountsmaskedprobs
- The masked called genotype probabilitieslist
- A list of masked positions- Returns:
- An imputer
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getImputer
public Imputer getImputer()
Returns the imputer if the imputer option was for a non-optimizable imputer, else throws an exception- Returns:
- The imputer
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getConfig
public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
Get the imputer options config- Returns:
- The config
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