jprotein.data.datatype
Class Alignment

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

public class Alignment
extends Sequence

See Also:
Serialized Form

Constructor Summary
Alignment()
           
Alignment(java.lang.String sequenceName, java.lang.String residueSequence)
           
 
Method Summary
 int getSequencePosition(int index)
           
 int nonGappedSequenceLength()
           
 
Methods inherited from class jprotein.data.datatype.Sequence
equals, getNonGappedPosition, getNonGappedSequenceLength, getResidue, getSequence, getSequenceLength, getSequenceName, isIdentical, setSequence, setSequenceName, toFasta, toString
 
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

Alignment

public Alignment()

Alignment

public Alignment(java.lang.String sequenceName,
                 java.lang.String residueSequence)
Method Detail

getSequencePosition

public int getSequencePosition(int index)

nonGappedSequenceLength

public int nonGappedSequenceLength()