Package pal.treesearch
Interface ConstraintModel
- All Known Implementing Classes:
FixedBSRDTGlobalClockModel
,FixedSRDTGlobalClockModel
,GlobalClockModel
,MRDTGlobalClockModel
,SRDTGlobalClockModel
,UnconstrainedModel
public interface ConstraintModel
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Nested Class Summary
Nested Classes -
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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Method Details
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getGlobalClockConstraintGrouping
Enquire about the clock constraint grouping of the leaf- Parameters:
leafLabel
- the label of the leaf- Returns:
- the grouping of the leaf, or null if outside the leaf is unconstrained (free)
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getCladeConstraints
Obtain the permanent clade sets. That is, when randomly building the tree, and when tree searching, what labels must always form a clade.- 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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createNewFreeLeaf
UnconstrainedLikelihoodModel.Leaf createNewFreeLeaf(int[] patternStateMatchup, int numberOfPatterns) -
createNewFreeExternal
UnconstrainedLikelihoodModel.External createNewFreeExternal() -
createNewFreeInternal
UnconstrainedLikelihoodModel.Internal createNewFreeInternal() -
createAppropriateConditionalProbabilityStore
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getGlobalParameterAccess
NeoParameterized getGlobalParameterAccess() -
getRateModelSummary
String getRateModelSummary()
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