edu.mssm.crover.domain2d.rbdg.xml
Class SecondaryStructure

java.lang.Object
  |
  +--edu.mssm.crover.domain2d.rbdg.xml.SecondaryStructure
All Implemented Interfaces:
java.io.Serializable

public class SecondaryStructure
extends java.lang.Object
implements java.io.Serializable

Defines the secondary structure for this protein.

Version:
$Revision$ $Date$
See Also:
Serialized Form

Constructor Summary
SecondaryStructure()
           
 
Method Summary
 void addDisulfideBridge(DisulfideBridge vDisulfideBridge)
           
 void addDisulfideBridge(int index, DisulfideBridge vDisulfideBridge)
           
 void addSegment(int index, Segment vSegment)
           
 void addSegment(Segment vSegment)
           
 void clearDisulfideBridge()
           
 void clearSegment()
           
 java.util.Enumeration enumerateDisulfideBridge()
           
 java.util.Enumeration enumerateSegment()
           
 DisulfideBridge[] getDisulfideBridge()
           
 DisulfideBridge getDisulfideBridge(int index)
           
 int getDisulfideBridgeCount()
           
 Segment[] getSegment()
           
 Segment getSegment(int index)
           
 int getSegmentCount()
           
 boolean isValid()
           
 void marshal(org.xml.sax.DocumentHandler handler)
           
 void marshal(java.io.Writer out)
           
 boolean removeDisulfideBridge(DisulfideBridge vDisulfideBridge)
           
 boolean removeSegment(Segment vSegment)
           
 void setDisulfideBridge(DisulfideBridge[] disulfideBridgeArray)
           
 void setDisulfideBridge(int index, DisulfideBridge vDisulfideBridge)
           
 void setSegment(int index, Segment vSegment)
           
 void setSegment(Segment[] segmentArray)
           
static SecondaryStructure unmarshal(java.io.Reader reader)
           
 void validate()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SecondaryStructure

public SecondaryStructure()
Method Detail

addDisulfideBridge

public void addDisulfideBridge(DisulfideBridge vDisulfideBridge)
                        throws java.lang.IndexOutOfBoundsException
Parameters:
vDisulfideBridge -
java.lang.IndexOutOfBoundsException

addDisulfideBridge

public void addDisulfideBridge(int index,
                               DisulfideBridge vDisulfideBridge)
                        throws java.lang.IndexOutOfBoundsException
Parameters:
index -
vDisulfideBridge -
java.lang.IndexOutOfBoundsException

addSegment

public void addSegment(Segment vSegment)
                throws java.lang.IndexOutOfBoundsException
Parameters:
vSegment -
java.lang.IndexOutOfBoundsException

addSegment

public void addSegment(int index,
                       Segment vSegment)
                throws java.lang.IndexOutOfBoundsException
Parameters:
index -
vSegment -
java.lang.IndexOutOfBoundsException

clearDisulfideBridge

public void clearDisulfideBridge()

clearSegment

public void clearSegment()

enumerateDisulfideBridge

public java.util.Enumeration enumerateDisulfideBridge()

enumerateSegment

public java.util.Enumeration enumerateSegment()

getDisulfideBridge

public DisulfideBridge getDisulfideBridge(int index)
                                   throws java.lang.IndexOutOfBoundsException
Parameters:
index -
java.lang.IndexOutOfBoundsException

getDisulfideBridge

public DisulfideBridge[] getDisulfideBridge()

getDisulfideBridgeCount

public int getDisulfideBridgeCount()

getSegment

public Segment getSegment(int index)
                   throws java.lang.IndexOutOfBoundsException
Parameters:
index -
java.lang.IndexOutOfBoundsException

getSegment

public Segment[] getSegment()

getSegmentCount

public int getSegmentCount()

isValid

public boolean isValid()

marshal

public void marshal(java.io.Writer out)
             throws org.exolab.castor.xml.MarshalException,
                    org.exolab.castor.xml.ValidationException
Parameters:
out -
org.exolab.castor.xml.MarshalException
org.exolab.castor.xml.ValidationException

marshal

public void marshal(org.xml.sax.DocumentHandler handler)
             throws org.exolab.castor.xml.MarshalException,
                    org.exolab.castor.xml.ValidationException
Parameters:
handler -
org.exolab.castor.xml.MarshalException
org.exolab.castor.xml.ValidationException

removeDisulfideBridge

public boolean removeDisulfideBridge(DisulfideBridge vDisulfideBridge)
Parameters:
vDisulfideBridge -

removeSegment

public boolean removeSegment(Segment vSegment)
Parameters:
vSegment -

setDisulfideBridge

public void setDisulfideBridge(int index,
                               DisulfideBridge vDisulfideBridge)
                        throws java.lang.IndexOutOfBoundsException
Parameters:
index -
vDisulfideBridge -
java.lang.IndexOutOfBoundsException

setDisulfideBridge

public void setDisulfideBridge(DisulfideBridge[] disulfideBridgeArray)
Parameters:
disulfideBridgeArray -

setSegment

public void setSegment(int index,
                       Segment vSegment)
                throws java.lang.IndexOutOfBoundsException
Parameters:
index -
vSegment -
java.lang.IndexOutOfBoundsException

setSegment

public void setSegment(Segment[] segmentArray)
Parameters:
segmentArray -

unmarshal

public static SecondaryStructure unmarshal(java.io.Reader reader)
                                    throws org.exolab.castor.xml.MarshalException,
                                           org.exolab.castor.xml.ValidationException
Parameters:
reader -
org.exolab.castor.xml.MarshalException
org.exolab.castor.xml.ValidationException

validate

public void validate()
              throws org.exolab.castor.xml.ValidationException
org.exolab.castor.xml.ValidationException


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.