org.forester.archaeopteryx.tools

Class PhylogeneticInferenceOptions

java.lang.Object

org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

public final class PhylogeneticInferenceOptions
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static long	RANDOM_NUMBER_SEED_DEFAULT

Constructor Summary

Constructors

Constructor and Description
PhylogeneticInferenceOptions()

Method Summary

Modifier and Type	Method and Description
PhylogeneticInferenceOptions	copy()
static PhylogeneticInferenceOptions	createInstance(Configuration configuration)
int	getBootstrapSamples()
String	getIntermediateFilesBase()
String	getMsaPrg()
String	getMsaPrgParameters()
double	getMsaProcessingMaxAllowedGapRatio()
int	getMsaProcessingMinAllowedLength()
PairwiseDistanceCalculator.PWD_DISTANCE_METHOD	getPwdDistanceMethod()
long	getRandomNumberGeneratorSeed()
File	getTempDir()
boolean	isPerformBootstrapResampling()
void	setBootstrapSamples(int bootstrap_samples)
void	setIntermediateFilesBase(String intermediate_files_base)
void	setMsaPrgParameters(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 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()