jprotein.data.datatype
Class Sequence

java.lang.Object
  extended by java.util.AbstractCollection
      extended by java.util.AbstractList
          extended by java.util.Vector
              extended by jprotein.data.datatype.Sequence
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess
Direct Known Subclasses:
Alignment, BlastSequenceInfo, Sequence3D, SequenceInformation

public class Sequence
extends java.util.Vector

See Also:
Serialized Form

Constructor Summary
Sequence()
           
Sequence(java.lang.String sequenceName)
           
Sequence(java.lang.String sequenceName, java.lang.String residueSequence)
           
 
Method Summary
 boolean equals(java.lang.Object o)
           
 int getNonGappedPosition(int index)
           
 int getNonGappedSequenceLength()
           
 Residue getResidue(int pos)
           
 java.util.Vector getSequence()
           
 int getSequenceLength()
           
 java.lang.String getSequenceName()
           
 boolean isIdentical(Sequence seq)
           
 void setSequence(java.lang.String residueSequence)
           
 void setSequenceName(java.lang.String sequenceName)
           
 java.lang.String toFasta()
           
 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, 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

Sequence

public Sequence()

Sequence

public Sequence(java.lang.String sequenceName)

Sequence

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

toString

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

setSequence

public void setSequence(java.lang.String residueSequence)

getSequence

public java.util.Vector getSequence()

getSequenceName

public java.lang.String getSequenceName()

getSequenceLength

public int getSequenceLength()

getResidue

public Residue getResidue(int pos)

setSequenceName

public void setSequenceName(java.lang.String sequenceName)

equals

public boolean equals(java.lang.Object o)
Specified by:
equals in interface java.util.Collection
Specified by:
equals in interface java.util.List
Overrides:
equals in class java.util.Vector

toFasta

public java.lang.String toFasta()

getNonGappedSequenceLength

public int getNonGappedSequenceLength()

getNonGappedPosition

public int getNonGappedPosition(int index)

isIdentical

public boolean isIdentical(Sequence seq)