public final class PhylogeneticInferenceOptions
extends java.lang.Object
Modifier and Type | Field and Description |
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static long |
RANDOM_NUMBER_SEED_DEFAULT |
Constructor and Description |
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PhylogeneticInferenceOptions() |
public static final long RANDOM_NUMBER_SEED_DEFAULT
public java.lang.String getMsaPrgParameters()
public void setMsaPrgParameters(java.lang.String msa_prg_parameters)
public java.lang.String getIntermediateFilesBase()
public java.lang.String getMsaPrg()
public void setIntermediateFilesBase(java.lang.String intermediate_files_base)
public PhylogeneticInferenceOptions copy()
public void setBootstrapSamples(int bootstrap_samples)
public int getBootstrapSamples()
public void setPwdDistanceMethod(PairwiseDistanceCalculator.PWD_DISTANCE_METHOD pwd_distance_method)
public PairwiseDistanceCalculator.PWD_DISTANCE_METHOD getPwdDistanceMethod()
public void setRandomNumberGeneratorSeed(long random_number_generator_seed)
public long getRandomNumberGeneratorSeed()
public void setPerformBootstrapResampling(boolean perform_bootstrap_resampling)
public boolean isPerformBootstrapResampling()
public static PhylogeneticInferenceOptions createInstance(Configuration configuration)
public java.io.File getTempDir()
public void setMsaProcessingMaxAllowedGapRatio(double msa_processing_max_allowed_gap_ratio)
public double getMsaProcessingMaxAllowedGapRatio()
public void setMsaProcessingMinAllowedLength(int msa_processing_min_allowed_length)
public int getMsaProcessingMinAllowedLength()