Tree (GeLL)

java.lang.Object
- Trees.Tree

All Implemented Interfaces:

java.lang.Iterable<Branch>
```
public class Tree
extends java.lang.Object
implements java.lang.Iterable<Branch>
```
Represents a phylogenetic tree. Trees are defined as a list of Branch. Nodes are defined by a String. This entire class deals with rooted and unrooted trees the same. Traditionally a rooted tree is detected by a node of degree two but if we allow multifurcations at the root then a rooted tree need not have any degree two nodes. Users should be aware of the type of tree they're using and any consequences.

Version:

2.0

Constructor Summary

Constructors
Constructor and Description
`Tree(java.util.List<Branch> branches)` Creates a tree from a list of branches
`Tree(Tree old, Parameters p)` Duplicates a tree topology while replacing branch lengths using the appropriate parameter

Method Summary

Methods
Modifier and Type	Method and Description
`double`	`branchScore(Tree t)` Calculates the branch score distance between this tree and another tree
`boolean`	`equals(java.lang.Object o)`
`static Tree`	`fromFile(java.io.File f)` Creates a tree from a file containing a Newick string
`static Tree`	`fromNewickString(java.lang.String newick)` Creates a tree from a newick string
`Branch`	`getBranchByChild(java.lang.String child)` Gets the branch which has the given node as the child node
`java.util.List<Branch>`	`getBranches()` Gets a list of branches.
`java.util.Set<Branch>`	`getBranchesByParent(java.lang.String parent)` Gets the set of branches which have the passed node as a parent
`java.util.List<Branch>`	`getBranchesReversed()` Gets the branches in the reverse order to that returned by `getBranches()`.
`java.util.List<java.lang.String>`	`getInternal()` Gets a list of internal nodes.
`java.util.List<java.lang.String>`	`getLeaves()` Gets a list of leaves
`double`	`getLength()` Gets the length of the tree
`int`	`getNumberBranches()` Gets the number of branches
`Parameters`	`getParameters()` Returns a Parameters object containing a parameter for each branch length.
`Parameters`	`getParametersForEstimation()` Returns a Parameters object containing a parameter for each branch length.
`java.lang.String`	`getParent(java.lang.String child)` Gets the parent node of the given node
`java.lang.String`	`getRoot()` Get the root node
`int`	`getSize()` Gets the size of the tree, that is the number of taxa
`java.util.Set<Split>`	`getSplits()` Gets the splits that represent the tree
`int`	`hashCode()`
`boolean`	`isExternal(Branch b)` Tests whether the given branch is an external branch (i.e.
`java.util.Iterator<Branch>`	`iterator()`
`Tree`	`midPointRoot(java.lang.String newRootName)` Mid point roots the tree and returns a new tree
`java.lang.String`	`MRCA(java.util.List<java.lang.String> leaves)` Returns the most recent common ancestor of a set of leaves.
`static Tree`	`randomTree(java.util.List<java.lang.String> taxa, boolean rooted)` Creates a random rooted or unrooted tree from a list of taxa
`int`	`RF(Tree t)` Calculates the RF distance between this tree and another tree
`Tree`	`scaledTo(double length)` Returns a new tree where the lengths are scales so the total length is different
`void`	`toFile(java.io.File f)` Writes the tree to a file in Newick format.
`void`	`toFile(java.io.File f, boolean nameInternal)` Write the tree to a file in Newick format.
`void`	`toFilePAML(java.io.File f)` Writes the tree to a file with taxa names limited to 25 characters for use in PAML.
`java.lang.String`	`toString()`
`java.lang.String`	`toString(boolean nameInternal)` Returns a textual representation of the tree in Newick format
`double`	`weightedRF(Tree t)` Calculates the weighted (by branch length) RF distance between this tree and another tree

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - Tree
```
public Tree(java.util.List<Branch> branches)
     throws TreeException
```
    Creates a tree from a list of branches
    
    Parameters:
    branches - A list of branches
    
    Throws:
    
    TreeException - Thrown if the list of branches passed do not represent a tree
  - Tree
```
public Tree(Tree old,
    Parameters p)
     throws Parameters.ParameterException
```
    Duplicates a tree topology while replacing branch lengths using the appropriate parameter
    
    Parameters:
    old - The old tree
    p - The parameters used for the new branch lengths
    
    Throws:
    
    Parameters.ParameterException - Thrown if there is a problem with the parameters, e.g. a required parameter not existing.
- Method Detail
  - getBranches
```
public java.util.List<Branch> getBranches()
```
    Gets a list of branches. Returned in a order that ensures external branches are visited first and then work towars the root.
    
    Returns:
    A list of branches
  - iterator
```
public java.util.Iterator<Branch> iterator()
```
    Specified by:
    
    iterator in interface java.lang.Iterable<Branch>
  - getInternal
```
public java.util.List<java.lang.String> getInternal()
```
    Gets a list of internal nodes. Nodes are returned in such a way that all child nodes are returned before their parent is.
    
    Returns:
    A list of internal nodes
  - getLeaves
```
public java.util.List<java.lang.String> getLeaves()
```
    Gets a list of leaves
    
    Returns:
    A list of leaves
  - getRoot
```
public java.lang.String getRoot()
```
    Get the root node
    
    Returns:
    The root node
  - getLength
```
public double getLength()
                 throws TreeException
```
    Gets the length of the tree
    
    Returns:
    The length of the tree
    
    Throws:
    
    TreeException - Thrown if the tree does not have branch lengths associated with it
  - getParameters
```
public Parameters getParameters()
                         throws TreeException
```
    Returns a Parameters object containing a parameter for each branch length. Parameters are fixed at the relevance branch length
    
    Returns:
    Parameters object containing branch lengths
    
    Throws:
    
    TreeException - Thrown if the tree does not have branch lengths
  - getParametersForEstimation
```
public Parameters getParametersForEstimation()
```
    Returns a Parameters object containing a parameter for each branch length. Parameters are estimation parameters.
    
    Returns:
    Parameters object containing branch lengths
  - getSize
```
public int getSize()
```
    Gets the size of the tree, that is the number of taxa
    
    Returns:
    The size of the tree
  - getNumberBranches
```
public int getNumberBranches()
```
    Gets the number of branches
    
    Returns:
    The number of branches
  - getBranchByChild
```
public Branch getBranchByChild(java.lang.String child)
                        throws TreeException
```
    Gets the branch which has the given node as the child node
    
    Parameters:
    child - The child node
    
    Returns:
    The branch with the given child
    
    Throws:
    
    TreeException - Thrown if the node does not exist or the root node is passed
  - getBranchesByParent
```
public java.util.Set<Branch> getBranchesByParent(java.lang.String parent)
                                          throws TreeException
```
    Gets the set of branches which have the passed node as a parent
    
    Parameters:
    parent - The parent node
    
    Returns:
    The set of branches with the given parent
    
    Throws:
    
    TreeException - If the node does not exist in the tree or is a leaf
  - getParent
```
public java.lang.String getParent(java.lang.String child)
                           throws TreeException
```
    Gets the parent node of the given node
    
    Parameters:
    child - The child node
    
    Returns:
    The parent of the child
    
    Throws:
    
    TreeException - If the node does not exist or is the root
  - scaledTo
```
public Tree scaledTo(double length)
              throws TreeException
```
    Returns a new tree where the lengths are scales so the total length is different
    
    Parameters:
    length - The new total length
    
    Returns:
    The scaled tree
    
    Throws:
    
    TreeException - Thrown if the tree does not have branch lengths
  - midPointRoot
```
public Tree midPointRoot(java.lang.String newRootName)
                  throws TreeException
```
    Mid point roots the tree and returns a new tree
    
    Parameters:
    newRootName - The name of the new root node
    
    Returns:
    A new tree which is midpoint rooted
    
    Throws:
    
    TreeException - If there is a problem with the tree, e.g. no branch lengths
  - MRCA
```
public java.lang.String MRCA(java.util.List<java.lang.String> leaves)
                      throws TreeException
```
    Returns the most recent common ancestor of a set of leaves. Although this only makes sense for rooted trees it will produce a result for all trees per the explanation in the class description.
    
    Parameters:
    leaves - Set of leaves to calculate the MRCA for
    
    Returns:
    The MRCA
    
    Throws:
    
    TreeException - Thrown if a leave does not exist
  - isExternal
```
public boolean isExternal(Branch b)
```
    Tests whether the given branch is an external branch (i.e. the child is a leaf)
    
    Parameters:
    b - The branch to test
    
    Returns:
    Whether it is an external branch
  - getBranchesReversed
```
public java.util.List<Branch> getBranchesReversed()
```
    Gets the branches in the reverse order to that returned by getBranches().
    
    Returns:
    The branches in reverse order
  - getSplits
```
public java.util.Set<Split> getSplits()
                               throws TreeException
```
    Gets the splits that represent the tree
    
    Returns:
    A set of splits
    
    Throws:
    
    TreeException - If the tree is invalid
  - RF
```
public int RF(Tree t)
       throws TreeException
```
    Calculates the RF distance between this tree and another tree
    
    Parameters:
    t - The other tree
    
    Returns:
    The RF distance
    
    Throws:
    
    TreeException - If one tree or the other is not valid
  - weightedRF
```
public double weightedRF(Tree t)
                  throws TreeException
```
    Calculates the weighted (by branch length) RF distance between this tree and another tree
    
    Parameters:
    t - The other tree
    
    Returns:
    The weighted RF distance
    
    Throws:
    
    TreeException - If one tree or the other is not valid
  - branchScore
```
public double branchScore(Tree t)
                   throws TreeException
```
    Calculates the branch score distance between this tree and another tree
    
    Parameters:
    t - The other tree
    
    Returns:
    The branch score distance
    
    Throws:
    
    TreeException - If one tree or the other is not valid
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - toString
```
public java.lang.String toString(boolean nameInternal)
```
    Returns a textual representation of the tree in Newick format
    
    Parameters:
    nameInternal - Whether internal branches should be named
    
    Returns:
    A Newick string representing the tree
  - toFile
```
public void toFile(java.io.File f)
            throws OutputException
```
    Writes the tree to a file in Newick format. This will not work correctly if any internal node names have a $ sign as both first and large character. Does not name internal nodes.
    
    Parameters:
    f - The file to write the tree to
    
    Throws:
    
    OutputException - Thrown if there is a problem writing the file
  - toFile
```
public void toFile(java.io.File f,
          boolean nameInternal)
            throws OutputException
```
    Write the tree to a file in Newick format. This will not work correctly if any internal node names have a $ sign as both first and large character.
    
    Parameters:
    f - The file to write the tree to
    nameInternal - Whether internal branches should be named
    
    Throws:
    
    OutputException - Thrown if there is a problem writing the file
  - toFilePAML
```
public void toFilePAML(java.io.File f)
                throws OutputException
```
    Writes the tree to a file with taxa names limited to 25 characters for use in PAML. At the moment no checking is done for any duplicated taxa names that may be created.
    
    Parameters:
    f - The file to write the tree to
    
    Throws:
    
    OutputException - Thrown if there is a problem writing the file
  - equals
```
public boolean equals(java.lang.Object o)
```
    Overrides:
    
    equals in class java.lang.Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object
  - fromNewickString
```
public static Tree fromNewickString(java.lang.String newick)
                             throws TreeException
```
    Creates a tree from a newick string
    
    Parameters:
    newick - The newick string
    
    Returns:
    The tree
    
    Throws:
    
    TreeException - Thrown if the tree cannot be created (e.g. incorrectly formatted string)
  - fromFile
```
public static Tree fromFile(java.io.File f)
                     throws InputException
```
    Creates a tree from a file containing a Newick string
    
    Parameters:
    f - The input file
    
    Returns:
    The tree
    
    Throws:
    
    InputException - If there is a problem reading from the input file
  - randomTree
```
public static Tree randomTree(java.util.List<java.lang.String> taxa,
              boolean rooted)
                       throws TreeException
```
    Creates a random rooted or unrooted tree from a list of taxa
    
    Parameters:
    taxa - A list of taxa to include in the tree
    rooted - Whether the tree should be rooted
    
    Returns:
    A random tree
    
    Throws:
    
    TreeException - Thrown if there are too through taxa passed and so there are no trees to select a random tree from.

Class Tree

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Tree

Tree

Method Detail

getBranches

iterator

getInternal

getLeaves

getRoot

getLength

getParameters

getParametersForEstimation

getSize

getNumberBranches

getBranchByChild

getBranchesByParent

getParent

scaledTo

midPointRoot

MRCA

isExternal

getBranchesReversed

getSplits

RF

weightedRF

branchScore

toString

toString

toFile

toFile

toFilePAML

equals

hashCode

fromNewickString

fromFile

randomTree