java.lang.Object
- pal.treesearch.GeneralLikelihoodSearcher

public class GeneralLikelihoodSearcher
extends java.lang.Object

Field Summary

Fields
Modifier and Type Field Description

static int NO_OPTIMISE

static int OPTIMISE_ALL

static int OPTIMISE_PRIMARY

static int OPTIMISE_SECONDARY

Constructor Summary

Constructors
Constructor	Description
`GeneralLikelihoodSearcher(Node baseTopology, Alignment baseAlignment, ConstraintModel constraintModel)`

Method Summary

All Methods Instance Methods Concrete Methods
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 Detail
- 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 Detail

GeneralLikelihoodSearcher

public GeneralLikelihoodSearcher(Node baseTopology,
                                 Alignment baseAlignment,
                                 ConstraintModel constraintModel)

Method Detail

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()
```

Modifier and Type	Field	Description
`static int`	`NO_OPTIMISE`
`static int`	`OPTIMISE_ALL`
`static int`	`OPTIMISE_PRIMARY`
`static int`	`OPTIMISE_SECONDARY`

Class GeneralLikelihoodSearcher

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

OPTIMISE_ALL

OPTIMISE_PRIMARY

OPTIMISE_SECONDARY

NO_OPTIMISE

Constructor Detail

GeneralLikelihoodSearcher

Method Detail

optimiseGeneral

optimiseGeneral

optimiseConstraintRateModels

optimiseSubstitutionModels

optimiseAllSimple

optimiseAllSimple

optimiseAllSimple

optimiseAllSimpleHeirarchy

optimiseAllFullHeirarchy

optimiseAllPlusSubstitutionModel

buildPALNodeBase

buildPALTreeBase

buildPALNodeES

buildPALTreeES

calculatedLogLikelihood

testLikelihood