Uses of Interface
pal.eval.UnconstrainedLikelihoodModel.External

Packages that use UnconstrainedLikelihoodModel.External
pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters. 
pal.treesearch   
 

Uses of UnconstrainedLikelihoodModel.External in pal.eval
 

Methods in pal.eval that return UnconstrainedLikelihoodModel.External
 UnconstrainedLikelihoodModel.External UnconstrainedLikelihoodModel.Instance.createNewExternal()
           
 

Uses of UnconstrainedLikelihoodModel.External in pal.treesearch
 

Methods in pal.treesearch that return UnconstrainedLikelihoodModel.External
 UnconstrainedLikelihoodModel.External MRDTGlobalClockModel.createNewFreeExternal()
           
 UnconstrainedLikelihoodModel.External ConstraintModel.createNewFreeExternal()
           
 UnconstrainedLikelihoodModel.External SRDTGlobalClockModel.createNewFreeExternal()
           
 UnconstrainedLikelihoodModel.External FixedBSRDTGlobalClockModel.createNewFreeExternal()
           
 UnconstrainedLikelihoodModel.External FixedSRDTGlobalClockModel.createNewFreeExternal()
           
 UnconstrainedLikelihoodModel.External GlobalClockModel.createNewFreeExternal()
           
 UnconstrainedLikelihoodModel.External UnconstrainedModel.createNewFreeExternal()
           
 UnconstrainedLikelihoodModel.External GeneralConstructionTool.obtainFreeExternalCalculator()
           
 

Methods in pal.treesearch with parameters of type UnconstrainedLikelihoodModel.External
 SiteDetails FreeBranch.calculateSiteDetails(UnconstrainedLikelihoodModel.External calculator, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore PivotNode.getExtendedConditionalProbabilities(double distance, FreeBranch caller, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeInternalNode.getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getFlatConditionalProbabilities(FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getLeftExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore)
           
 ConditionalProbabilityStore FreeInternalNode.getLeftExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getRightExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore)
           
 ConditionalProbabilityStore FreeInternalNode.getRightExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)