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java.lang.Objectpal.treesearch.UnrootedMLSearcher
public class UnrootedMLSearcher
Nested Class Summary | |
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static class |
UnrootedMLSearcher.StateObject
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Constructor Summary | |
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UnrootedMLSearcher(Alignment alignment,
SubstitutionModel model)
Build an unconstrained optimiser based on a randomly generated tree. |
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UnrootedMLSearcher(Alignment alignment,
SubstitutionModel model,
LHCalculator.Factory calcFactory)
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UnrootedMLSearcher(Node root)
Create a searcher based on a given tree, that has no alignment , or model, specified (useful as backbone tree for attaching new nodes) |
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UnrootedMLSearcher(Node root,
Alignment alignment,
SubstitutionModel model)
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UnrootedMLSearcher(Node root,
Alignment alignment,
SubstitutionModel model,
LHCalculator.Factory calcFactory)
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UnrootedMLSearcher(Node root,
SubstitutionModel model)
Create a searcher based on a given tree, that has no alignment specified (useful as backbone tree for attaching new nodes) |
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UnrootedMLSearcher(Tree t,
Alignment alignment,
SubstitutionModel model)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public UnrootedMLSearcher(Alignment alignment, SubstitutionModel model)
alignment
- the alignment used to represent each OTUmodel
- the substitution model that is used for calcuation. If optimisation on the model occurs than
this model will be alteredpublic UnrootedMLSearcher(Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)
public UnrootedMLSearcher(Tree t, Alignment alignment, SubstitutionModel model)
public UnrootedMLSearcher(Node root, Alignment alignment, SubstitutionModel model)
public UnrootedMLSearcher(Node root, SubstitutionModel model)
root
- the root of the tree to base things on (doesn't matter if it's rooted)model
- the substitution model to be usedpublic UnrootedMLSearcher(Node root)
root
- the root of the tree to base things on (doesn't matter if it's rooted)public UnrootedMLSearcher(Node root, Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)
Method Detail |
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public BranchAccess[] getAccessToBranches()
public NodeAccess[] getAccessToNodes()
public java.lang.Object getStateReference()
getStateReference
in interface StateProvider
public void restoreState(java.lang.Object stateReference)
restoreState
in interface StateProvider
public void instruct(UnrootedTreeInterface treeInterface)
instruct
in interface UnrootedTreeInterface.Instructee
public UndoableAction getNNIAction(StoppingCriteria.Factory stopper)
public UndoableAction getBranchLengthOptimiseAction(StoppingCriteria.Factory stopper)
public UndoableAction getNNIBranchLengthOptimiseAction(StoppingCriteria.Factory stopper)
stopper
- The means for determining when a set of round should be stopped
public UndoableAction getBranchLengthWithModelOptimiseAction(StoppingCriteria.Factory stopper, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
public UndoableAction getModelOptimiseAction(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
public UndoableAction getModelOptimiseAction(MultivariateMinimum minimiser, MinimiserMonitor monitor, int fxFracDigits, int xFracDigits)
public UndoableAction getSPRAction(StoppingCriteria.Factory stopper)
public UndoableAction getSweepSPRAction(StoppingCriteria.Factory stopper)
public UndoableAction getFullSweepSPRAction(StoppingCriteria.Factory stopper)
public final void mark()
mark
in interface Markable
public final void undoToMark()
undoToMark
in interface Markable
public void testLiklihood()
public double calculateLogLikelihood()
public double calculateLogLikelihood2()
public SiteDetails calculateSiteDetails()
public double simpleOptimiseLikelihood(double epsilon, AlgorithmCallback callback)
epsilon
- the tolerance places for convergence (on the likelihood score)callback
- a callback to monitor progress
public double simpleOptimiseLikelihood(StoppingCriteria stopper, AlgorithmCallback callback)
stopper
- the stopping criteria (on the likelihood score)callback
- a callback to monitor progress
public Tree buildPALTree()
public Node buildPALNode()
public final Assessor getSimpleAssessor(StoppingCriteria.Factory stopper)
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