jprotein.data.datatype
Class Alignment

java.lang.Object
  java.util.AbstractCollection
      java.util.AbstractList
          java.util.Vector
              jprotein.data.datatype.Sequence
                  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()