org.forester.archaeopteryx.tools
Class PhylogeneticInferenceOptions

java.lang.Object
  org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

public final class PhylogeneticInferenceOptions
extends java.lang.Object

Field Summary

static long

RANDOM_NUMBER_SEED_DEFAULT

Constructor Summary

PhylogeneticInferenceOptions()

Method Summary

PhylogeneticInferenceOptions	copy()
static PhylogeneticInferenceOptions	createInstance(Configuration configuration)
int	getBootstrapSamples()
java.lang.String	getIntermediateFilesBase()
java.lang.String	getMsaPrg()
java.lang.String	getMsaPrgParameters()
double	getMsaProcessingMaxAllowedGapRatio()
int	getMsaProcessingMinAllowedLength()
PairwiseDistanceCalculator.PWD_DISTANCE_METHOD	getPwdDistanceMethod()
long	getRandomNumberGeneratorSeed()
java.io.File	getTempDir()
boolean	isPerformBootstrapResampling()
void	setBootstrapSamples(int bootstrap_samples)
void	setIntermediateFilesBase(java.lang.String intermediate_files_base)
void	setMsaPrgParameters(java.lang.String msa_prg_parameters)
void	setMsaProcessingMaxAllowedGapRatio(double msa_processing_max_allowed_gap_ratio)
void	setMsaProcessingMinAllowedLength(int msa_processing_min_allowed_length)
void	setPerformBootstrapResampling(boolean perform_bootstrap_resampling)
void	setPwdDistanceMethod(PairwiseDistanceCalculator.PWD_DISTANCE_METHOD pwd_distance_method)
void	setRandomNumberGeneratorSeed(long random_number_generator_seed)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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)

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 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()