Package pal.treesearch
Class UnconstrainedModel
java.lang.Object
pal.treesearch.UnconstrainedModel
- All Implemented Interfaces:
ConstraintModel
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.treesearch.ConstraintModel
ConstraintModel.GroupManager
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncreateAppropriateConditionalProbabilityStore
(boolean isForLeaf) createNewFreeLeaf
(int[] patternStateMatchup, int numberOfPatterns) String[][]
getCladeConstraints
(String[] allLabelSet) Obtain the permanent clade sets.getGlobalClockConstraintGrouping
(String[] leafLabelSet) Enquire about the clock constraint grouping of the leaf
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Constructor Details
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UnconstrainedModel
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Method Details
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getCladeConstraints
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
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
- Specified by:
createNewFreeExternal
in interfaceConstraintModel
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createNewFreeInternal
- Specified by:
createNewFreeInternal
in interfaceConstraintModel
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createAppropriateConditionalProbabilityStore
- Specified by:
createAppropriateConditionalProbabilityStore
in interfaceConstraintModel
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getGlobalParameterAccess
- Specified by:
getGlobalParameterAccess
in interfaceConstraintModel
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getRateModelSummary
- Specified by:
getRateModelSummary
in interfaceConstraintModel
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