Package org.forester.archaeopteryx.tools

Class PhylogeneticInferenceOptions

java.lang.Object
org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
public final class PhylogeneticInferenceOptions extends Object

  • Field Details

    • RANDOM_NUMBER_SEED_DEFAULT

      public static final long RANDOM_NUMBER_SEED_DEFAULT
      See Also:

  • Constructor Details

    • PhylogeneticInferenceOptions

      public PhylogeneticInferenceOptions()

  • Method Details

    • getMsaPrgParameters

      public String getMsaPrgParameters()

    • setMsaPrgParameters

      public void setMsaPrgParameters(String msa_prg_parameters)

    • getIntermediateFilesBase

      public String getIntermediateFilesBase()

    • getMsaPrg

      public String getMsaPrg()

    • setIntermediateFilesBase

      public void setIntermediateFilesBase(String intermediate_files_base)

    • copy

      public PhylogeneticInferenceOptions copy()

    • setBootstrapSamples

      public void setBootstrapSamples(int bootstrap_samples)

    • getBootstrapSamples

      public int getBootstrapSamples()

    • setPwdDistanceMethod

      public void setPwdDistanceMethod(PairwiseDistanceCalculator.PWD_DISTANCE_METHOD pwd_distance_method)

    • getPwdDistanceMethod

      public PairwiseDistanceCalculator.PWD_DISTANCE_METHOD getPwdDistanceMethod()

    • setRandomNumberGeneratorSeed

      public void setRandomNumberGeneratorSeed(long random_number_generator_seed)

    • getRandomNumberGeneratorSeed

      public long getRandomNumberGeneratorSeed()

    • setPerformBootstrapResampling

      public void setPerformBootstrapResampling(boolean perform_bootstrap_resampling)

    • isPerformBootstrapResampling

      public boolean isPerformBootstrapResampling()

    • createInstance

      public static PhylogeneticInferenceOptions createInstance(Configuration configuration)

    • getTempDir

      public File getTempDir()

    • setMsaProcessingMaxAllowedGapRatio

      public void setMsaProcessingMaxAllowedGapRatio(double msa_processing_max_allowed_gap_ratio)

    • getMsaProcessingMaxAllowedGapRatio

      public double getMsaProcessingMaxAllowedGapRatio()

    • setMsaProcessingMinAllowedLength

      public void setMsaProcessingMinAllowedLength(int msa_processing_min_allowed_length)

    • getMsaProcessingMinAllowedLength

      public int getMsaProcessingMinAllowedLength()