Package Executable
Class CombinerOption
- java.lang.Object
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- Executable.CombinerOption
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public class CombinerOption extends java.lang.Object
Represents the combiner options to LinkImpute
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Constructor Summary
Constructors Constructor Description CombinerOption(Combiner combiner)
Constructor for when the combiner isn't optimizable.CombinerOption(OptimizeCombiner combiner)
Constructor for when the combiner is optimizableCombinerOption(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 Combiner
getCombiner()
Returns the combiner if the combiner option was for a non-optimizable combiner, else throws an exceptionCombiner
getCombiner(java.util.List<SingleGenotypeProbability> called, java.util.List<SingleGenotypeProbability> imputed, java.util.List<SingleGenotypeReads> reads, java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeMasked> masked)
Gets a combiner.org.apache.commons.configuration2.tree.ImmutableNode
getConfig()
Get the combiner options config
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Constructor Detail
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CombinerOption
public CombinerOption(Combiner combiner)
Constructor for when the combiner isn't optimizable. May be used when we've already created an optimized combiner.- Parameters:
combiner
- The combiner
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CombinerOption
public CombinerOption(OptimizeCombiner combiner)
Constructor for when the combiner is optimizable- Parameters:
combiner
- The combiner
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CombinerOption
public CombinerOption(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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getCombiner
public Combiner getCombiner(java.util.List<SingleGenotypeProbability> called, java.util.List<SingleGenotypeProbability> imputed, java.util.List<SingleGenotypeReads> reads, java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeMasked> masked)
Gets a combiner. If the combiner option was for one that was not optimized simply returns that. Else optimizes a combiner and returns the optimized version of it.- Parameters:
called
- The called genotype probabilitiesimputed
- The imputed genotype probabilitiesreads
- The readscorrect
- The correct genotypesmasked
- A list of masked genotypes- Returns:
- A combiner
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getCombiner
public Combiner getCombiner()
Returns the combiner if the combiner option was for a non-optimizable combiner, else throws an exception- Returns:
- The combiner
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getConfig
public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
Get the combiner options config- Returns:
- The config
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