Package pal.treesearch
Class GeneralLikelihoodSearcher
- java.lang.Object
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- pal.treesearch.GeneralLikelihoodSearcher
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public class GeneralLikelihoodSearcher extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static int
NO_OPTIMISE
static int
OPTIMISE_ALL
static int
OPTIMISE_PRIMARY
static int
OPTIMISE_SECONDARY
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Constructor Summary
Constructors Constructor Description GeneralLikelihoodSearcher(Node baseTopology, Alignment baseAlignment, ConstraintModel constraintModel)
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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()
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Field Detail
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OPTIMISE_ALL
public static final int OPTIMISE_ALL
- See Also:
- Constant Field Values
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OPTIMISE_PRIMARY
public static final int OPTIMISE_PRIMARY
- See Also:
- Constant Field Values
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OPTIMISE_SECONDARY
public static final int OPTIMISE_SECONDARY
- See Also:
- Constant Field Values
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NO_OPTIMISE
public static final int NO_OPTIMISE
- See Also:
- Constant Field Values
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Constructor Detail
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GeneralLikelihoodSearcher
public GeneralLikelihoodSearcher(Node baseTopology, Alignment baseAlignment, ConstraintModel constraintModel)
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Method Detail
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optimiseGeneral
public double optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback)
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optimiseGeneral
public double optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback, SearchMonitor monitor)
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optimiseConstraintRateModels
public double optimiseConstraintRateModels(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor rateMonitor)
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optimiseSubstitutionModels
public double optimiseSubstitutionModels(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
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optimiseAllSimple
public double optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback)
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optimiseAllSimple
public double optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
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optimiseAllSimple
public double optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor, int groupOptimistionType)
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optimiseAllSimpleHeirarchy
public double optimiseAllSimpleHeirarchy(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
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optimiseAllFullHeirarchy
public double optimiseAllFullHeirarchy(StoppingCriteria mainStopper, StoppingCriteria subStopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
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optimiseAllPlusSubstitutionModel
public double optimiseAllPlusSubstitutionModel(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, MultivariateMinimum substitutionModelMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, int substitutionModelOptimiseFrequency, MinimiserMonitor substitutionModelMonitor, MinimiserMonitor rateMonitor)
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buildPALNodeBase
public Node buildPALNodeBase()
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buildPALTreeBase
public Tree buildPALTreeBase()
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buildPALNodeES
public Node buildPALNodeES()
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buildPALTreeES
public Tree buildPALTreeES()
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calculatedLogLikelihood
public double calculatedLogLikelihood()
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testLikelihood
public void testLikelihood()
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