Package pal.treesearch
Class UnconstrainedModel
- java.lang.Object
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- pal.treesearch.UnconstrainedModel
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- All Implemented Interfaces:
ConstraintModel
public class UnconstrainedModel extends java.lang.Object implements ConstraintModel
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.treesearch.ConstraintModel
ConstraintModel.GroupManager
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Constructor Summary
Constructors Constructor Description UnconstrainedModel(UnconstrainedLikelihoodModel.Instance likelihoodModel)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description ConditionalProbabilityStore
createAppropriateConditionalProbabilityStore(boolean isForLeaf)
UnconstrainedLikelihoodModel.External
createNewFreeExternal()
UnconstrainedLikelihoodModel.Internal
createNewFreeInternal()
UnconstrainedLikelihoodModel.Leaf
createNewFreeLeaf(int[] patternStateMatchup, int numberOfPatterns)
java.lang.String[][]
getCladeConstraints(java.lang.String[] allLabelSet)
Obtain the permanent clade sets.ConstraintModel.GroupManager
getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet)
Enquire about the clock constraint grouping of the leafNeoParameterized
getGlobalParameterAccess()
java.lang.String
getRateModelSummary()
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Constructor Detail
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UnconstrainedModel
public UnconstrainedModel(UnconstrainedLikelihoodModel.Instance likelihoodModel)
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Method Detail
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getCladeConstraints
public java.lang.String[][] getCladeConstraints(java.lang.String[] allLabelSet)
Description copied from interface:ConstraintModel
Obtain the permanent clade sets. That is, when randomly building the tree, and when tree searching, what labels must always form a clade.- Specified by:
getCladeConstraints
in interfaceConstraintModel
- Parameters:
allLabelSet
- The set of all leaf labels in the tree- Returns:
- An array of string arrays dividing up the label set
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getGlobalClockConstraintGrouping
public ConstraintModel.GroupManager getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet)
Description copied from interface:ConstraintModel
Enquire about the clock constraint grouping of the leaf- Specified by:
getGlobalClockConstraintGrouping
in interfaceConstraintModel
- Returns:
- the grouping of the leaf, or null if outside the leaf is unconstrained (free)
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createNewFreeLeaf
public UnconstrainedLikelihoodModel.Leaf createNewFreeLeaf(int[] patternStateMatchup, int numberOfPatterns)
- Specified by:
createNewFreeLeaf
in interfaceConstraintModel
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createNewFreeExternal
public UnconstrainedLikelihoodModel.External createNewFreeExternal()
- Specified by:
createNewFreeExternal
in interfaceConstraintModel
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createNewFreeInternal
public UnconstrainedLikelihoodModel.Internal createNewFreeInternal()
- Specified by:
createNewFreeInternal
in interfaceConstraintModel
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createAppropriateConditionalProbabilityStore
public ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
- Specified by:
createAppropriateConditionalProbabilityStore
in interfaceConstraintModel
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getGlobalParameterAccess
public NeoParameterized getGlobalParameterAccess()
- Specified by:
getGlobalParameterAccess
in interfaceConstraintModel
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getRateModelSummary
public java.lang.String getRateModelSummary()
- Specified by:
getRateModelSummary
in interfaceConstraintModel
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