jprotein.data.datatype
Class Sequence3D

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.Sequence3D
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

public class Sequence3D
extends Sequence

See Also:
Serialized Form

Field Summary
static int DIRECT
           
static int INDEXED
           
 
Constructor Summary
Sequence3D()
           
Sequence3D(java.lang.String sequenceHeader, java.lang.String chainId)
           
 
Method Summary
 void addResidue(Residue3D residue)
           
 void addResidue(java.lang.String residueCode)
           
 java.lang.String getChainId()
           
 java.lang.String getHeader()
           
 Residue3D getResidue(int index, int mode)
           
 int getSequenceBegin()
           
 int getSequenceLength()
           
 void setChainId(java.lang.String chainId)
           
 void setHeader(java.lang.String header)
           
 void setSequenceBegin(int sequenceOffset)
           
 
Methods inherited from class jprotein.data.datatype.Sequence
equals, getNonGappedPosition, getNonGappedSequenceLength, getResidue, getSequence, 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
 

Field Detail

DIRECT

public static final int DIRECT
See Also:
Constant Field Values

INDEXED

public static final int INDEXED
See Also:
Constant Field Values
Constructor Detail

Sequence3D

public Sequence3D()

Sequence3D

public Sequence3D(java.lang.String sequenceHeader,
                  java.lang.String chainId)
Method Detail

getChainId

public java.lang.String getChainId()

setChainId

public void setChainId(java.lang.String chainId)

setSequenceBegin

public void setSequenceBegin(int sequenceOffset)

getSequenceBegin

public int getSequenceBegin()

addResidue

public void addResidue(java.lang.String residueCode)

addResidue

public void addResidue(Residue3D residue)

getResidue

public Residue3D getResidue(int index,
                            int mode)

getSequenceLength

public int getSequenceLength()
Overrides:
getSequenceLength in class Sequence

getHeader

public java.lang.String getHeader()

setHeader

public void setHeader(java.lang.String header)