Class PhylogeneticInferenceOptions


  • public final class PhylogeneticInferenceOptions
    extends java.lang.Object
    • Field Detail

      • RANDOM_NUMBER_SEED_DEFAULT

        public static final long RANDOM_NUMBER_SEED_DEFAULT
        See Also:
        Constant Field Values
    • Constructor Detail

      • PhylogeneticInferenceOptions

        public PhylogeneticInferenceOptions()
    • Method Detail

      • getMsaPrgParameters

        public java.lang.String getMsaPrgParameters()
      • setMsaPrgParameters

        public void setMsaPrgParameters​(java.lang.String msa_prg_parameters)
      • getIntermediateFilesBase

        public java.lang.String getIntermediateFilesBase()
      • getMsaPrg

        public java.lang.String getMsaPrg()
      • setIntermediateFilesBase

        public void setIntermediateFilesBase​(java.lang.String intermediate_files_base)
      • setBootstrapSamples

        public void setBootstrapSamples​(int bootstrap_samples)
      • getBootstrapSamples

        public int getBootstrapSamples()
      • 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()
      • getTempDir

        public java.io.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()