Package pal.treesearch
Interface ConstraintModel
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- All Known Implementing Classes:
FixedBSRDTGlobalClockModel
,FixedSRDTGlobalClockModel
,GlobalClockModel
,MRDTGlobalClockModel
,SRDTGlobalClockModel
,UnconstrainedModel
public interface ConstraintModel
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Nested Class Summary
Nested Classes Modifier and Type Interface Description static interface
ConstraintModel.GroupManager
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Method Summary
All Methods Instance Methods Abstract 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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Method Detail
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getGlobalClockConstraintGrouping
ConstraintModel.GroupManager getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet)
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
java.lang.String[][] getCladeConstraints(java.lang.String[] allLabelSet)
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)
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createNewFreeExternal
UnconstrainedLikelihoodModel.External createNewFreeExternal()
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createNewFreeInternal
UnconstrainedLikelihoodModel.Internal createNewFreeInternal()
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createAppropriateConditionalProbabilityStore
ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
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getGlobalParameterAccess
NeoParameterized getGlobalParameterAccess()
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getRateModelSummary
java.lang.String getRateModelSummary()
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