java.lang.Object

pal.treesearch.GeneralLikelihoodSearcher

public class GeneralLikelihoodSearcher extends Object

Field Summary

Fields

Modifier and Type

Field

Description

static final int

NO_OPTIMISE

static final int

OPTIMISE_ALL

static final int

OPTIMISE_PRIMARY

static final int

OPTIMISE_SECONDARY
Constructor Summary

Constructors

Constructor

Description

GeneralLikelihoodSearcher(Node baseTopology, Alignment baseAlignment, ConstraintModel constraintModel)
Method Summary

Modifier and Type

Method

Description

Node

buildPALNodeBase()

Node

buildPALNodeES()

Tree

buildPALTreeBase()

Tree

buildPALTreeES()

double

calculatedLogLikelihood()

double

optimiseAllFullHeirarchy(StoppingCriteria mainStopper, StoppingCriteria subStopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)

double

optimiseAllPlusSubstitutionModel(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, MultivariateMinimum substitutionModelMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, int substitutionModelOptimiseFrequency, MinimiserMonitor substitutionModelMonitor, MinimiserMonitor rateMonitor)

double

optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback)

double

optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)

double

optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor, int groupOptimistionType)

double

optimiseAllSimpleHeirarchy(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)

double

optimiseConstraintRateModels(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor rateMonitor)

double

optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback)

double

optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback, SearchMonitor monitor)

double

optimiseSubstitutionModels(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)

void

testLikelihood()

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- OPTIMISE_ALL
  
  public static final int OPTIMISE_ALL
  See Also:
  
  Constant Field Values
- OPTIMISE_PRIMARY
  
  public static final int OPTIMISE_PRIMARY
  See Also:
  
  Constant Field Values
- OPTIMISE_SECONDARY
  
  public static final int OPTIMISE_SECONDARY
  See Also:
  
  Constant Field Values
- NO_OPTIMISE
  
  public static final int NO_OPTIMISE
  See Also:
  
  Constant Field Values
Constructor Details
- GeneralLikelihoodSearcher
  
  public GeneralLikelihoodSearcher(Node baseTopology, Alignment baseAlignment, ConstraintModel constraintModel)
Method Details
- optimiseGeneral
  
  public double optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback)
- optimiseGeneral
  
  public double optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback, SearchMonitor monitor)
- optimiseConstraintRateModels
  
  public double optimiseConstraintRateModels(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor rateMonitor)
- optimiseSubstitutionModels
  
  public double optimiseSubstitutionModels(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
- optimiseAllSimple
  
  public double optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback)
- optimiseAllSimple
  
  public double optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
- optimiseAllSimple
  
  public double optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor, int groupOptimistionType)
- optimiseAllSimpleHeirarchy
  
  public double optimiseAllSimpleHeirarchy(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
- optimiseAllFullHeirarchy
  
  public double optimiseAllFullHeirarchy(StoppingCriteria mainStopper, StoppingCriteria subStopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
- optimiseAllPlusSubstitutionModel
  
  public double optimiseAllPlusSubstitutionModel(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, MultivariateMinimum substitutionModelMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, int substitutionModelOptimiseFrequency, MinimiserMonitor substitutionModelMonitor, MinimiserMonitor rateMonitor)
- buildPALNodeBase
  
  public Node buildPALNodeBase()
- buildPALTreeBase
  
  public Tree buildPALTreeBase()
- buildPALNodeES
  
  public Node buildPALNodeES()
- buildPALTreeES
  
  public Tree buildPALTreeES()
- calculatedLogLikelihood
  
  public double calculatedLogLikelihood()
- testLikelihood
  
  public void testLikelihood()

Class GeneralLikelihoodSearcher

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

OPTIMISE_ALL

OPTIMISE_PRIMARY

OPTIMISE_SECONDARY

NO_OPTIMISE

Constructor Details

GeneralLikelihoodSearcher

Method Details

optimiseGeneral

optimiseGeneral

optimiseConstraintRateModels

optimiseSubstitutionModels

optimiseAllSimple

optimiseAllSimple

optimiseAllSimple

optimiseAllSimpleHeirarchy

optimiseAllFullHeirarchy

optimiseAllPlusSubstitutionModel

buildPALNodeBase

buildPALTreeBase

buildPALNodeES

buildPALTreeES

calculatedLogLikelihood

testLikelihood