jprotein.tree.tools
Class DistanceMatrix

java.lang.Object
  extended by java.util.AbstractCollection
      extended by java.util.AbstractList
          extended by java.util.Vector
              extended by jprotein.tree.tools.DistanceMatrix
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

public class DistanceMatrix
extends java.util.Vector

See Also:
Serialized Form

Constructor Summary
DistanceMatrix(MultiAlignment multiAlignment, SubstitutionMatrix sm)
           
 
Method Summary
 java.util.Vector getDistantCouple()
           
 Leaf getLeaf(int index)
           
 java.lang.Double getLowerLimitScore(int i, int j)
           
 int getNonGappedAlignedLength(int i, int j)
           
 double getUpperLimitScore(int i, int j)
           
 boolean isExtension(int i, int j, int k)
           
 boolean isGapped(int i, int j, int k)
           
 void setDistantCouple(Sequence seq1, Sequence seq2)
           
 void setMultipleAlignment(MultiAlignment multiAlignment)
           
 void setSubstitutionMatrix(SubstitutionMatrix sm)
           
 java.lang.String toString()
           
 
Methods inherited from class java.util.Vector
add, add, addAll, addAll, addElement, capacity, clear, clone, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, equals, 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

DistanceMatrix

public DistanceMatrix(MultiAlignment multiAlignment,
                      SubstitutionMatrix sm)
               throws java.lang.Exception
Throws:
java.lang.Exception
Method Detail

getLeaf

public Leaf getLeaf(int index)

setSubstitutionMatrix

public void setSubstitutionMatrix(SubstitutionMatrix sm)

setMultipleAlignment

public void setMultipleAlignment(MultiAlignment multiAlignment)

toString

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

isGapped

public boolean isGapped(int i,
                        int j,
                        int k)

isExtension

public boolean isExtension(int i,
                           int j,
                           int k)

getUpperLimitScore

public double getUpperLimitScore(int i,
                                 int j)

getLowerLimitScore

public java.lang.Double getLowerLimitScore(int i,
                                           int j)

getNonGappedAlignedLength

public int getNonGappedAlignedLength(int i,
                                     int j)

setDistantCouple

public void setDistantCouple(Sequence seq1,
                             Sequence seq2)

getDistantCouple

public java.util.Vector getDistantCouple()