jprotein.data.datatype
Class MultiAlignment

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

public class MultiAlignment
extends java.util.Vector

See Also:
Serialized Form

Constructor Summary
MultiAlignment()
           
MultiAlignment(java.util.Vector sequenceList)
           
 
Method Summary
 void addAlignment(Sequence ali)
           
 Sequence getAlignment(int index)
           
 java.util.Vector getAlignmentComposition(Sequence ref)
           
static java.util.Vector getCompositionFrequencies(java.util.Vector ac)
           
static java.util.Vector getInformationContent(java.util.Vector acf)
           
static java.util.Vector sumAlignmentComposition(java.util.Vector ac1, java.util.Vector ac2)
           
 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

MultiAlignment

public MultiAlignment()

MultiAlignment

public MultiAlignment(java.util.Vector sequenceList)
Method Detail

getAlignment

public Sequence getAlignment(int index)

toString

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

addAlignment

public void addAlignment(Sequence ali)

getAlignmentComposition

public java.util.Vector getAlignmentComposition(Sequence ref)

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)