Package org.forester.archaeopteryx.tools
Class PhylogeneticInferenceOptions
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- org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
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public final class PhylogeneticInferenceOptions extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static long
RANDOM_NUMBER_SEED_DEFAULT
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Constructor Summary
Constructors Constructor Description PhylogeneticInferenceOptions()
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Method Summary
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Field Detail
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RANDOM_NUMBER_SEED_DEFAULT
public static final long RANDOM_NUMBER_SEED_DEFAULT
- See Also:
- Constant Field Values
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Method Detail
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getMsaPrgParameters
public java.lang.String getMsaPrgParameters()
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setMsaPrgParameters
public void setMsaPrgParameters(java.lang.String msa_prg_parameters)
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getIntermediateFilesBase
public java.lang.String getIntermediateFilesBase()
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getMsaPrg
public java.lang.String getMsaPrg()
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setIntermediateFilesBase
public void setIntermediateFilesBase(java.lang.String intermediate_files_base)
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copy
public PhylogeneticInferenceOptions copy()
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setBootstrapSamples
public void setBootstrapSamples(int bootstrap_samples)
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getBootstrapSamples
public int getBootstrapSamples()
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setPwdDistanceMethod
public void setPwdDistanceMethod(PairwiseDistanceCalculator.PWD_DISTANCE_METHOD pwd_distance_method)
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getPwdDistanceMethod
public PairwiseDistanceCalculator.PWD_DISTANCE_METHOD getPwdDistanceMethod()
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setRandomNumberGeneratorSeed
public void setRandomNumberGeneratorSeed(long random_number_generator_seed)
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getRandomNumberGeneratorSeed
public long getRandomNumberGeneratorSeed()
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setPerformBootstrapResampling
public void setPerformBootstrapResampling(boolean perform_bootstrap_resampling)
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isPerformBootstrapResampling
public boolean isPerformBootstrapResampling()
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createInstance
public static PhylogeneticInferenceOptions createInstance(Configuration configuration)
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getTempDir
public java.io.File getTempDir()
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setMsaProcessingMaxAllowedGapRatio
public void setMsaProcessingMaxAllowedGapRatio(double msa_processing_max_allowed_gap_ratio)
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getMsaProcessingMaxAllowedGapRatio
public double getMsaProcessingMaxAllowedGapRatio()
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setMsaProcessingMinAllowedLength
public void setMsaProcessingMinAllowedLength(int msa_processing_min_allowed_length)
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getMsaProcessingMinAllowedLength
public int getMsaProcessingMinAllowedLength()
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