gov.nih.nci.mageom.domain.DesignElement.impl
Class CompositePositionImpl

java.lang.Object
  extended by gov.nih.nci.mageom.domain.impl.MAGEOMObject
      extended by gov.nih.nci.mageom.domain.impl.ExtendableImpl
          extended by gov.nih.nci.mageom.domain.BioSequence.impl.SequencePositionImpl
              extended by gov.nih.nci.mageom.domain.DesignElement.impl.CompositePositionImpl
All Implemented Interfaces:
SequencePosition, CompositePosition, Extendable, java.io.Serializable

public class CompositePositionImpl
extends SequencePositionImpl
implements CompositePosition

The location in the compositeSequence target's sequence to which a source compositeSequence maps. The association to MismatchInformation allows the specification, usually for control purposes, of deviations from the CompositeSequence's BioMaterial.

Version:
%I%, %G%
See Also:
Serialized Form

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  CompositeSequence composite
          DOCUMENT ME
protected  java.lang.Long compositeId
          The internal ID of the associated composite object.
protected  MismatchInformation[] mismatchInformation
          DOCUMENT ME
protected  int mismatchInformationCount
          The count of MismatchInformation objects.
 
Fields inherited from class gov.nih.nci.mageom.domain.BioSequence.impl.SequencePositionImpl
end, start
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
propertySets, propertySetsCount, securedElementId
 
Constructor Summary
CompositePositionImpl()
          Default constructor
 
Method Summary
 CompositeSequence getComposite()
          Returns the value of this CompositePosition object's composite attribute.
 MismatchInformation[] getMismatchInformation()
          Returns the value of this CompositePosition object's mismatchInformation attribute.
 int getMismatchInformationCount()
          Returns the count of all MismatchInformation associated with this CompositePosition object.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 CompositePosition[] searchCompositePositions(CompositePositionSearchCriteria criteria)
          Returns an array of CompositePosition objects that satisfy the given CompositePositionSearchCriteria.
 void setComposite(CompositeSequence p_composite)
          Sets the composite attribute.
 void setMismatchInformation(MismatchInformation[] p_mismatchInformation)
          Sets the mismatchInformation attribute.
 java.lang.String toString()
          Returns a String representation of this object suitable for console display.
 org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
           
 org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
           
 org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc, java.util.ArrayList fillOutValues)
          Returns an XML representation of the object.
 
Methods inherited from class gov.nih.nci.mageom.domain.BioSequence.impl.SequencePositionImpl
getEnd, getStart, searchSequencePositions, setEnd, setStart
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
getPropertySets, getPropertySetsCount, getSecuredElementId, searchExtendables, setPropertySets, setSecuredElementId
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.MAGEOMObject
getId, getIsEditable, setId
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface gov.nih.nci.mageom.domain.BioSequence.SequencePosition
getEnd, getStart, setEnd, setStart
 
Methods inherited from interface gov.nih.nci.mageom.domain.Extendable
getPropertySets, setPropertySets
 

Field Detail

allAssociationMethods

protected static java.util.ArrayList allAssociationMethods

associationMethods

protected static java.util.Hashtable associationMethods

mismatchInformationCount

protected int mismatchInformationCount
The count of MismatchInformation objects.


mismatchInformation

protected MismatchInformation[] mismatchInformation
DOCUMENT ME


composite

protected CompositeSequence composite
DOCUMENT ME


compositeId

protected java.lang.Long compositeId
The internal ID of the associated composite object.

Constructor Detail

CompositePositionImpl

public CompositePositionImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class SequencePositionImpl

searchCompositePositions

public CompositePosition[] searchCompositePositions(CompositePositionSearchCriteria criteria)
                                             throws gov.nih.nci.common.search.SearchException
Returns an array of CompositePosition objects that satisfy the given CompositePositionSearchCriteria.

Parameters:
criteria - The CompositePositionSearchCriteria which represents a query for CompositePosition objects.
Returns:
An array of CompositePosition objects.
Throws:
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchException

setMismatchInformation

public void setMismatchInformation(MismatchInformation[] p_mismatchInformation)
Sets the mismatchInformation attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a CompositePosition object.

Specified by:
setMismatchInformation in interface CompositePosition
Parameters:
p_mismatchInformation - The new value for mismatchInformation.
See Also:
CompositePosition.getMismatchInformation()

getMismatchInformation

public MismatchInformation[] getMismatchInformation()
Description copied from interface: CompositePosition
Returns the value of this CompositePosition object's mismatchInformation attribute.

Specified by:
getMismatchInformation in interface CompositePosition
Returns:
gov.nih.nci.mageom.bean.DesignElement.MismatchInformation[] The value of mismatchInformation.
See Also:
CompositePosition.getMismatchInformation()

setComposite

public void setComposite(CompositeSequence p_composite)
Sets the composite attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a CompositePosition object.

Specified by:
setComposite in interface CompositePosition
Parameters:
p_composite - The new value for composite.
See Also:
CompositePosition.getComposite()

getComposite

public CompositeSequence getComposite()
Description copied from interface: CompositePosition
Returns the value of this CompositePosition object's composite attribute.

Specified by:
getComposite in interface CompositePosition
Returns:
gov.nih.nci.mageom.bean.DesignElement.CompositeSequence The value of composite.
See Also:
CompositePosition.getComposite()

getMismatchInformationCount

public int getMismatchInformationCount()
Returns the count of all MismatchInformation associated with this CompositePosition object.

Returns:
the count
See Also:
CompositePosition.getMismatchInformation()

toXML

public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
Overrides:
toXML in class SequencePositionImpl

toXMLDoc

public org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
Overrides:
toXMLDoc in class SequencePositionImpl

toXMLProcessor

public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
                                          java.util.ArrayList fillOutValues)
Returns an XML representation of the object. The document is not modified.

Overrides:
toXMLProcessor in class SequencePositionImpl
Parameters:
doc - the working document
fillOutValues - a list of attribute names that should have full XML for their values.
Returns:
org.w3c.dom.Element an XML representation

getXMLMethodDescriptors

public java.util.Hashtable getXMLMethodDescriptors()
Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.

Overrides:
getXMLMethodDescriptors in class SequencePositionImpl
Returns:
Hashtable The Hashtable of descriptors.

toString

public java.lang.String toString()
Returns a String representation of this object suitable for console display.

Overrides:
toString in class SequencePositionImpl
Returns:
the String representation.