jprotein.data.datatype
Class MultiPairwiseAlignment

java.lang.Object
  extended by java.util.AbstractCollection
      extended by java.util.AbstractList
          extended by java.util.Vector
              extended by jprotein.data.datatype.MultiPairwiseAlignment
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

public class MultiPairwiseAlignment
extends java.util.Vector

See Also:
Serialized Form

Constructor Summary
MultiPairwiseAlignment(Sequence ref)
           
 
Method Summary
 void addPairwiseAlignment(PairwiseAlignment ali)
           
 java.util.Vector getAlignmentComposition()
           
static java.util.Vector getCompositionFrequencies(java.util.Vector ac)
           
static java.util.Vector getInformationContent(java.util.Vector acf)
           
 PairwiseAlignment getPairwiseAlignment(int index)
           
static java.util.Vector sumAlignmentComposition(java.util.Vector ac1, java.util.Vector ac2)
           
 
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, toString, 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

MultiPairwiseAlignment

public MultiPairwiseAlignment(Sequence ref)
Method Detail

getPairwiseAlignment

public PairwiseAlignment getPairwiseAlignment(int index)

addPairwiseAlignment

public void addPairwiseAlignment(PairwiseAlignment ali)

getAlignmentComposition

public java.util.Vector getAlignmentComposition()

sumAlignmentComposition

public static java.util.Vector sumAlignmentComposition(java.util.Vector ac1,
                                                       java.util.Vector ac2)

getCompositionFrequencies

public static java.util.Vector getCompositionFrequencies(java.util.Vector ac)

getInformationContent

public static java.util.Vector getInformationContent(java.util.Vector acf)