uk.ac.vamsas.objects.utils.trees
Class SequenceNode

java.lang.Object
  extended byuk.ac.vamsas.objects.utils.trees.BinaryNode
      extended byuk.ac.vamsas.objects.utils.trees.SequenceNode

public class SequenceNode
extends BinaryNode


Field Summary
 float dist
          DOCUMENT ME!!
 boolean dummy
          DOCUMENT ME!!
 
Fields inherited from class uk.ac.vamsas.objects.utils.trees.BinaryNode
bootstrap
 
Constructor Summary
SequenceNode()
          Creates a new SequenceNode object.
SequenceNode(Vobject val, SequenceNode parent, float dist, java.lang.String name)
          Creates a new SequenceNode object.
SequenceNode(Vobject val, SequenceNode parent, java.lang.String name, float dist, int bootstrap, boolean dummy)
          Creates a new SequenceNode object.
 
Method Summary
 SequenceNode AscendTree()
          ascends the tree but doesn't stop until a non-dummy node is discovered.
 boolean isDummy()
           
 boolean isPlaceholder()
           
 boolean setDummy(boolean newstate)
          DOCUMENT ME!
 void setPlaceholder(boolean Placeholder)
          DOCUMENT ME!
 
Methods inherited from class uk.ac.vamsas.objects.utils.trees.BinaryNode
ascendLeft, ascendRight, detach, element, getBootstrap, getName, isLeaf, left, parent, right, setBootstrap, SetChildren, setElement, setLeft, setName, setParent, setRight
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

dist

public float dist
DOCUMENT ME!!


dummy

public boolean dummy
DOCUMENT ME!!

Constructor Detail

SequenceNode

public SequenceNode()
Creates a new SequenceNode object.


SequenceNode

public SequenceNode(Vobject val,
                    SequenceNode parent,
                    float dist,
                    java.lang.String name)
Creates a new SequenceNode object.

Parameters:
val - DOCUMENT ME!
parent - DOCUMENT ME!
dist - DOCUMENT ME!
name - DOCUMENT ME!

SequenceNode

public SequenceNode(Vobject val,
                    SequenceNode parent,
                    java.lang.String name,
                    float dist,
                    int bootstrap,
                    boolean dummy)
Creates a new SequenceNode object.

Parameters:
val - DOCUMENT ME!
parent - DOCUMENT ME!
name - DOCUMENT ME!
dist - DOCUMENT ME!
bootstrap - DOCUMENT ME!
dummy - DOCUMENT ME!
Method Detail

isDummy

public boolean isDummy()

isPlaceholder

public boolean isPlaceholder()

setDummy

public boolean setDummy(boolean newstate)
DOCUMENT ME!

Parameters:
newstate - DOCUMENT ME!
Returns:
DOCUMENT ME!

setPlaceholder

public void setPlaceholder(boolean Placeholder)
DOCUMENT ME!

Parameters:
Placeholder - DOCUMENT ME!

AscendTree

public SequenceNode AscendTree()
ascends the tree but doesn't stop until a non-dummy node is discovered. This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.