Class Hierarchy
- java.lang.Object
- pal.treesearch.AbstractLeafNode
- pal.treesearch.ConstrainedLeafNode (implements pal.treesearch.ConstrainedNode)
- pal.treesearch.FreeLeafNode (implements pal.treesearch.FreeNode)
- pal.treesearch.AbstractParentableConstrainedNode (implements pal.treesearch.ParentableConstrainedNode)
- pal.treesearch.ConstrainedInternalNode (implements pal.treesearch.ConstrainedNode, pal.treesearch.GeneralOptimisable)
- pal.treesearch.PivotNode (implements pal.treesearch.FreeNode, pal.treesearch.GeneralOptimisable, pal.treesearch.GroupLeader, pal.treesearch.ParentableConstrainedNode, pal.treesearch.RootAccess)
- pal.treesearch.BranchAccess.Utils
- pal.treesearch.FixedBSRDTGlobalClockModel (implements pal.treesearch.ConstraintModel, pal.treesearch.ConstraintModel.GroupManager, pal.eval.MolecularClockLikelihoodModel.HeightConverter, pal.misc.NeoParameterized)
- pal.treesearch.FixedSRDTGlobalClockModel (implements pal.treesearch.ConstraintModel, pal.treesearch.ConstraintModel.GroupManager, pal.eval.MolecularClockLikelihoodModel.HeightConverter)
- pal.treesearch.FreeBranch (implements pal.treesearch.GeneralOptimisable, pal.treesearch.RootAccess)
- pal.treesearch.FreeInternalNode (implements pal.treesearch.FreeNode)
- pal.treesearch.GeneralConstraintGroupManager
- pal.treesearch.GeneralConstraintGroupManager.Store
- pal.treesearch.GeneralConstructionTool
- pal.treesearch.GeneralLikelihoodSearcher
- pal.treesearch.GlobalClockModel (implements pal.treesearch.ConstraintModel, pal.treesearch.ConstraintModel.GroupManager, pal.eval.MolecularClockLikelihoodModel.HeightConverter, pal.misc.NeoParameterized)
- pal.treesearch.HeightInformationUser
- pal.treesearch.MRDTGlobalClockModel (implements pal.treesearch.ConstraintModel, pal.treesearch.ConstraintModel.GroupManager, pal.eval.MolecularClockLikelihoodModel.HeightConverter, pal.misc.NeoParameterized)
- pal.treesearch.SearcherUtils
- pal.treesearch.SearchMonitor.Utils
- pal.treesearch.SRDTGlobalClockModel (implements pal.treesearch.ConstraintModel, pal.treesearch.ConstraintModel.GroupManager, pal.eval.MolecularClockLikelihoodModel.HeightConverter, pal.misc.NeoParameterized)
- pal.treesearch.TreeSearchTool
- pal.treesearch.UnconstrainedModel (implements pal.treesearch.ConstraintModel)
- pal.treesearch.UnrootedMLSearcher (implements pal.algorithmics.Markable, pal.algorithmics.StateProvider, pal.tree.UnrootedTreeInterface.Instructee)
- pal.treesearch.UnrootedMLSearcher.StateObject
- pal.treesearch.AbstractLeafNode
Interface Hierarchy
- pal.treesearch.BranchAccess
- pal.treesearch.Constants
- pal.treesearch.ConstrainedNode.HeightAdjustment
- pal.treesearch.ConstraintModel
- pal.treesearch.ConstraintModel.GroupManager
- pal.treesearch.GeneralConstraintGroupManager.LikelihoodScoreAccess
- pal.treesearch.GeneralOptimisable
- pal.treesearch.GeneralTreeComponent
- pal.treesearch.ConstrainedNode
- pal.treesearch.FreeNode
- pal.treesearch.GroupLeader
- pal.treesearch.NodeAccess
- pal.treesearch.ParentableConstrainedNode
- pal.treesearch.RootAccess
- pal.treesearch.SearchMonitor