Package net.maizegenetics.taxa.tree

Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).

See: Description

Interface Summary

Interface	Description
AttributeNode	interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree.
BranchLimits	limits for branch lengths
MultiParameterized.ParameterAccessWatcher	An interface for classes that wish to find out about particular parameter access
Node	interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree
Parameterized	interface for class with (optimizable) parameters
Tree	Interface for a phylogenetic or genealogical tree.
Units	interface holding unit constants
UnitsProvider	interface for classes that can provide the related Units used, (as

Class Summary

Class	Description
CladeSystem	data structure for a set of splits
LabelMapping
MultiParameterized	Title: MultiParameterized
NeighborJoiningTree	constructs a neighbor-joining tree from pairwise distances Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees.
NodeFactory
NodeUtils	Helper routines for dealing with nodes.
Parameterized.Null	NullParameterized Object Can be used by subclasses to implement parameterized without actually having paramters
Parameterized.ParameterizedBase	A Utility class for using as the superclass to subclasses which are based on double arrays
Parameterized.ParameterizedUser	A Utility class for using as the superclass to subclasses which work by adding functionality to a general Parameterized object (the base Parameterized object)
Parameterized.Utils
RootedTreeUtils	This class contains utility methods.
SimpleNode	data structure for a node (includes branch) in a binary/non-binary rooted/unrooted tree
SimpleTree	data structure for a binary/non-binary rooted/unrooted trees
SplitSystem	data structure for a set of splits
SplitUtils	utilities for split systems
TreeClusters
TreeUtils	various utility functions on trees.
UPGMATree	constructs a UPGMA tree from pairwise distances

Exception Summary

Exception	Description
TreeParseException	exception thrown by ReadTree

Package net.maizegenetics.taxa.tree Description

Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).