Package pal.tree

Class ParameterizedTree.ParameterizedTreeBase

java.lang.Object
pal.tree.ParameterizedTree.ParameterizedTreeBase
All Implemented Interfaces:
Serializable, IdGroup, Parameterized, Units, UnitsProvider, Tree
Direct Known Subclasses:
ClockTree, LogParameterizedTree, MutationRateModelTree, UnconstrainedTree
Enclosing interface:
ParameterizedTree
public abstract static class ParameterizedTree.ParameterizedTreeBase extends Object implements Parameterized, Tree
For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)
See Also:

  • Constructor Details

    • ParameterizedTreeBase

      protected ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase toCopy)
      Cloning constructor

    • ParameterizedTreeBase

      public ParameterizedTreeBase()

    • ParameterizedTreeBase

      public ParameterizedTreeBase(Tree baseTree)

  • Method Details

    • setBaseTree

      protected void setBaseTree(Tree baseTree)

    • getBaseTree

      protected Tree getBaseTree()

    • getRoot

      public final Node getRoot()
      Returns the root node of this tree.
      Specified by:
      getRoot in interface Tree
      Returns:
      the root node of this tree.

    • setRoot

      public final void setRoot(Node root)
      Description copied from interface: Tree
      This method constructs a tree from the given root node.
      Specified by:
      setRoot in interface Tree
      Parameters:
      root - the root node of the tree to construct.

    • getIdentifier

      public final Identifier getIdentifier(int i)
      Description copied from interface: IdGroup
      Returns the ith identifier.
      Specified by:
      getIdentifier in interface IdGroup

    • setIdentifier

      public final void setIdentifier(int i, Identifier id)
      Description copied from interface: IdGroup
      Sets the ith identifier.
      Specified by:
      setIdentifier in interface IdGroup

    • getIdCount

      public final int getIdCount()
      Description copied from interface: IdGroup
      Returns the number of identifiers in this group
      Specified by:
      getIdCount in interface IdGroup

    • whichIdNumber

      public final int whichIdNumber(String s)
      Description copied from interface: IdGroup
      returns the index of the identifier with the given name.
      Specified by:
      whichIdNumber in interface IdGroup

    • getExternalNodeCount

      public final int getExternalNodeCount()
      returns a count of the number of external nodes (tips) in this tree.
      Specified by:
      getExternalNodeCount in interface Tree
      Returns:
      a count of the number of external nodes (tips) in this tree.

    • getInternalNodeCount

      public final int getInternalNodeCount()
      returns a count of the number of internal nodes (and hence clades) in this tree.
      Specified by:
      getInternalNodeCount in interface Tree
      Returns:
      a count of the number of internal nodes (and hence clades) in this tree.

    • getNodeCount

      public final int getNodeCount()

    • getExternalNode

      public final Node getExternalNode(int i)
      returns the ith external node in the tree.
      Specified by:
      getExternalNode in interface Tree
      Returns:
      the ith external node in the tree.

    • getInternalNode

      public final Node getInternalNode(int i)
      returns the ith internal node in the tree.
      Specified by:
      getInternalNode in interface Tree
      Returns:
      the ith internal node in the tree.

    • createNodeList

      public final void createNodeList()
      This method is called to ensure that the calls to other methods in this interface are valid.
      Specified by:
      createNodeList in interface Tree

    • getUnits

      public final int getUnits()
      Description copied from interface: Tree
      Gets the units that this tree's branch lengths and node heights are expressed in.
      Specified by:
      getUnits in interface Tree
      Specified by:
      getUnits in interface UnitsProvider
      Returns:
      the units relating to this object.

    • setAttribute

      public final void setAttribute(Node node, String name, Object value)
      Description copied from interface: Tree
      Sets an named attribute for a given node.
      Specified by:
      setAttribute in interface Tree
      Parameters:
      node - the node whose attribute is being set.
      name - the name of the attribute.
      value - the new value of the attribute.

    • getAttribute

      public final Object getAttribute(Node node, String name)
      Specified by:
      getAttribute in interface Tree
      Parameters:
      node - the node being interrogated.
      name - the name of the attribute of interest.
      Returns:
      an object representing the named attributed for the numbered node.

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getCopy

      public Tree getCopy()
      The cheapy copy that just creates a SimpleTree
      Specified by:
      getCopy in interface Tree
      Returns:
      a clone of this tree

    • getOrthogonalHints

      public OrthogonalHints getOrthogonalHints()
      Returns:
      null by default (implying not hint information)