jprotein.tree.data
Class Leaf

java.lang.Object
  extended by java.util.AbstractCollection
      extended by java.util.AbstractList
          extended by java.util.Vector
              extended by jprotein.tree.data.Leaf
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess
Direct Known Subclasses:
SimpleNode

public class Leaf
extends java.util.Vector

See Also:
Serialized Form

Constructor Summary
Leaf()
           
Leaf(Sequence ali, java.util.Vector distances)
           
 
Method Summary
 void addDistance(double d)
           
 boolean equals(java.lang.Object o)
           
 java.util.Vector getBackTrace()
           
 java.util.Vector getConservedResidue()
           
 double getDistance(int index)
           
 java.lang.Double getDoubleDistance(int index)
           
 Sequence getSequence()
           
 double getSum()
           
 void initConservedResidue()
           
 void removeDistance(int index)
           
 void resetConservedResidue()
           
 void setBackTrace(java.util.Vector backtrace)
           
 void setConservedResidue(java.util.Vector conservedIndex)
           
 java.lang.String toString()
           
 void unload()
           
 
Methods inherited from class java.util.Vector
add, add, addAll, addAll, addElement, capacity, clear, clone, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, firstElement, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, lastElement, lastIndexOf, lastIndexOf, remove, remove, removeAll, removeAllElements, removeElement, removeElementAt, retainAll, set, setElementAt, setSize, size, subList, toArray, toArray, trimToSize
 
Methods inherited from class java.util.AbstractList
iterator, listIterator, listIterator
 
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface java.util.List
iterator, listIterator, listIterator
 

Constructor Detail

Leaf

public Leaf()

Leaf

public Leaf(Sequence ali,
            java.util.Vector distances)
Method Detail

getSequence

public Sequence getSequence()

toString

public java.lang.String toString()
Overrides:
toString in class java.util.Vector

getSum

public double getSum()

addDistance

public void addDistance(double d)

removeDistance

public void removeDistance(int index)

getDistance

public double getDistance(int index)

getDoubleDistance

public java.lang.Double getDoubleDistance(int index)

unload

public void unload()

getConservedResidue

public java.util.Vector getConservedResidue()

setConservedResidue

public void setConservedResidue(java.util.Vector conservedIndex)

resetConservedResidue

public void resetConservedResidue()

getBackTrace

public java.util.Vector getBackTrace()

setBackTrace

public void setBackTrace(java.util.Vector backtrace)

initConservedResidue

public void initConservedResidue()

equals

public boolean equals(java.lang.Object o)
Specified by:
equals in interface java.util.Collection
Specified by:
equals in interface java.util.List
Overrides:
equals in class java.util.Vector