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

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.ReporterPositionImpl
All Implemented Interfaces:
SequencePosition, ReporterPosition, Extendable, java.io.Serializable

public class ReporterPositionImpl
extends SequencePositionImpl
implements ReporterPosition

The location in the composite target's sequence to which a source reporter 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  MismatchInformation[] mismatchInformation
          DOCUMENT ME
protected  int mismatchInformationCount
          The count of MismatchInformation objects.
protected  Reporter reporter
          DOCUMENT ME
protected  java.lang.Long reporterId
          The internal ID of the associated reporter object.
 
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
ReporterPositionImpl()
          Default constructor
 
Method Summary
 MismatchInformation[] getMismatchInformation()
          Returns the value of this ReporterPosition object's mismatchInformation attribute.
 int getMismatchInformationCount()
          Returns the count of all MismatchInformation associated with this ReporterPosition object.
 Reporter getReporter()
          Returns the value of this ReporterPosition object's reporter attribute.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 ReporterPosition[] searchReporterPositions(ReporterPositionSearchCriteria criteria)
          Returns an array of ReporterPosition objects that satisfy the given ReporterPositionSearchCriteria.
 void setMismatchInformation(MismatchInformation[] p_mismatchInformation)
          Sets the mismatchInformation attribute.
 void setReporter(Reporter p_reporter)
          Sets the reporter 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


reporter

protected Reporter reporter
DOCUMENT ME


reporterId

protected java.lang.Long reporterId
The internal ID of the associated reporter object.

Constructor Detail

ReporterPositionImpl

public ReporterPositionImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class SequencePositionImpl

searchReporterPositions

public ReporterPosition[] searchReporterPositions(ReporterPositionSearchCriteria criteria)
                                           throws gov.nih.nci.common.search.SearchException
Returns an array of ReporterPosition objects that satisfy the given ReporterPositionSearchCriteria.

Parameters:
criteria - The ReporterPositionSearchCriteria which represents a query for ReporterPosition objects.
Returns:
An array of ReporterPosition 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 ReporterPosition object.

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

getMismatchInformation

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

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

setReporter

public void setReporter(Reporter p_reporter)
Sets the reporter attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ReporterPosition object.

Specified by:
setReporter in interface ReporterPosition
Parameters:
p_reporter - The new value for reporter.
See Also:
ReporterPosition.getReporter()

getReporter

public Reporter getReporter()
Description copied from interface: ReporterPosition
Returns the value of this ReporterPosition object's reporter attribute.

Specified by:
getReporter in interface ReporterPosition
Returns:
gov.nih.nci.mageom.bean.DesignElement.Reporter The value of reporter.
See Also:
ReporterPosition.getReporter()

getMismatchInformationCount

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

Returns:
the count
See Also:
ReporterPosition.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.