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## de.jstacs.sequenceScores.statisticalModels.trainable.phylo
Class PhyloNode

    java.lang.Object
      de.jstacs.sequenceScores.statisticalModels.trainable.phylo.PhyloNode

All Implemented Interfaces:
  Storable, Cloneable

    public class PhyloNode

extends Object
implements Cloneable, Storable

This class implements a node in a `PhyloTree` A PhyloNode contains some basic informations of itself and the incoming edge Furthermore it contains a list of `PhyloNode`s that represent the children nodes

Author:
  Michael Scharfe

Constructor Summary
`PhyloNode()` Basic constructor
`PhyloNode(StringBuffer xml)` The standard constructor for the interface `Storable`.

Method Summary
`void` | `addChild(PhyloNode node)` This method adds a children node to the current instance
`PhyloNode` | `clone()`
`ArrayList<PhyloNode>` | `getAllLeafs()` This method returns a list of `PhyloNode`s that are leafs in the subtree starting from this instance
`ArrayList<PhyloNode>` | `getChildrenNodes()` This method returns a list of `PhyloNode`s that are children of this instance
`int` | `getId()` This method returns the ID of the current PhyloNode
`String` | `getName()` This method returns the name of the current instance
`int` | `getNumberOfAllNodesBelow()` This method returns the total number of `PhyloNode`s in the subtree starting from this instance
`double` | `getWeight()` This method return the weight (length, rate ...) for the incoming edge
`void` | `setId(int id)` This method set the ID of the current PhyloNode The ID should be unique in the PhyloTree
`void` | `setName(String name)` This method set a name for the current instance
`void` | `setWeight(double w)` This method set the weight (length, rate ...) for the incoming edge
`StringBuffer` | `toXML()` This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

Methods inherited from class java.lang.Object
`equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

### PhyloNode

    public PhyloNode()

  Basic constructor

### PhyloNode

    public PhyloNode(StringBuffer xml)
              throws NonParsableException

  The standard constructor for the interface `Storable`. Constructs a `PhyloNode` out of an XML representation.

  Parameters:
    `xml` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the `PhyloNode` could not be reconstructed out of the `StringBuffer` `xml`

Method Detail

### clone

    public PhyloNode clone()
                    throws CloneNotSupportedException

  Overrides:
    `clone` in class `Object`
  Throws:
    `CloneNotSupportedException`

### addChild

    public void addChild(PhyloNode node)

  This method adds a children node to the current instance

  Parameters:
    `node` - the children node

### setName

    public void setName(String name)

  This method set a name for the current instance

  Parameters:
    `name` - the name of the PhyloNode

### getName

    public String getName()

  This method returns the name of the current instance

  Returns:
    the name of the PhyloNode

### setId

    public void setId(int id)

  This method set the ID of the current PhyloNode The ID should be unique in the PhyloTree

  Parameters:
    `id` - the ID of the node

### getId

    public int getId()

  This method returns the ID of the current PhyloNode

  Returns:
    the ID of the node

### setWeight

    public void setWeight(double w)

  This method set the weight (length, rate ...) for the incoming edge

  Parameters:
    `w` - the weight

### getWeight

    public double getWeight()

  This method return the weight (length, rate ...) for the incoming edge

  Returns:
    the weight

### getNumberOfAllNodesBelow

    public int getNumberOfAllNodesBelow()

  This method returns the total number of `PhyloNode`s in the subtree starting from this instance

  Returns:
    the total number of nodes

### getChildrenNodes

    public ArrayList<PhyloNode> getChildrenNodes()

  This method returns a list of `PhyloNode`s that are children of this instance

  Returns:
    the children nodes

### getAllLeafs

    public ArrayList<PhyloNode> getAllLeafs()

  This method returns a list of `PhyloNode`s that are leafs in the subtree starting from this instance

  Returns:
    the list of leafs

### toXML

    public StringBuffer toXML()

  Description copied from interface: `Storable`
  This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

  Specified by:
    `toXML` in interface `Storable`
  Returns:
    the XML representation

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