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

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.impl.DescribableImpl
              extended by gov.nih.nci.mageom.domain.impl.IdentifiableImpl
                  extended by gov.nih.nci.mageom.domain.DesignElement.impl.DesignElementImpl
                      extended by gov.nih.nci.mageom.domain.DesignElement.impl.ReporterImpl
All Implemented Interfaces:
Describable, DesignElement, Reporter, Extendable, Identifiable, java.io.Serializable

public class ReporterImpl
extends DesignElementImpl
implements Reporter

A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences. The derived data from the measured data of its Features represents the presence or absence of the biosequence or biosequences it is reporting on in the BioAssay. Reporters are Identifiable and several Features on the same array can be mapped to the same reporter as can Features from a different ArrayDesign. The granularity of the Reporters independence is dependent on the technology and the intent of the ArrayDesign. Oligos using mature technologies can in general be assumed to be safely replicated on many features where as with PCR Products there might be the desire for quality assurence to make reporters one to one with features and use the mappings to CompositeSequences for replication purposes.

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  OntologyEntry[] failTypes
          DOCUMENT ME
protected  int failTypesCount
          The count of OntologyEntry objects.
protected  FeatureReporterMap[] featureReporterMaps
          DOCUMENT ME
protected  int featureReporterMapsCount
          The count of FeatureReporterMap objects.
protected  BioSequence[] immobilizedCharacteristics
          DOCUMENT ME
protected  int immobilizedCharacteristicsCount
          The count of BioSequence objects.
protected  OntologyEntry warningType
          DOCUMENT ME
protected  java.lang.Long warningTypeId
          The internal ID of the associated warningType object.
 
Fields inherited from class gov.nih.nci.mageom.domain.DesignElement.impl.DesignElementImpl
controlType, controlTypeId
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.IdentifiableImpl
identifier, name
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.DescribableImpl
auditTrail, auditTrailCount, descriptions, descriptionsCount, security, securityId
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
propertySets, propertySetsCount, securedElementId
 
Constructor Summary
ReporterImpl()
          Default constructor
 
Method Summary
 OntologyEntry[] getFailTypes()
          Returns the value of this Reporter object's failTypes attribute.
 int getFailTypesCount()
          Returns the count of all OntologyEntry associated with this Reporter object.
 FeatureReporterMap[] getFeatureReporterMaps()
          Returns the value of this Reporter object's featureReporterMaps attribute.
 int getFeatureReporterMapsCount()
          Returns the count of all FeatureReporterMap associated with this Reporter object.
 BioSequence[] getImmobilizedCharacteristics()
          Returns the value of this Reporter object's immobilizedCharacteristics attribute.
 int getImmobilizedCharacteristicsCount()
          Returns the count of all BioSequence associated with this Reporter object.
 OntologyEntry getWarningType()
          Returns the value of this Reporter object's warningType attribute.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 Reporter[] searchReporters(ReporterSearchCriteria criteria)
          Returns an array of Reporter objects that satisfy the given ReporterSearchCriteria.
 void setFailTypes(OntologyEntry[] p_failTypes)
          Sets the failTypes attribute.
 void setFeatureReporterMaps(FeatureReporterMap[] p_featureReporterMaps)
          Sets the featureReporterMaps attribute.
 void setImmobilizedCharacteristics(BioSequence[] p_immobilizedCharacteristics)
          Sets the immobilizedCharacteristics attribute.
 void setWarningType(OntologyEntry p_warningType)
          Sets the warningType 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.DesignElement.impl.DesignElementImpl
getControlType, searchDesignElements, setControlType
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.IdentifiableImpl
getIdentifier, getName, searchIdentifiables, setIdentifier, setName
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.DescribableImpl
getAuditTrail, getAuditTrailCount, getDescriptions, getDescriptionsCount, getSecurity, searchDescribables, setAuditTrail, setDescriptions, setSecurity
 
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.DesignElement.DesignElement
getControlType, setControlType
 
Methods inherited from interface gov.nih.nci.mageom.domain.Identifiable
getIdentifier, getName, setIdentifier, setName
 
Methods inherited from interface gov.nih.nci.mageom.domain.Describable
getAuditTrail, getDescriptions, getSecurity, setAuditTrail, setDescriptions, setSecurity
 
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

failTypesCount

protected int failTypesCount
The count of OntologyEntry objects.


failTypes

protected OntologyEntry[] failTypes
DOCUMENT ME


warningType

protected OntologyEntry warningType
DOCUMENT ME


warningTypeId

protected java.lang.Long warningTypeId
The internal ID of the associated warningType object.


immobilizedCharacteristicsCount

protected int immobilizedCharacteristicsCount
The count of BioSequence objects.


immobilizedCharacteristics

protected BioSequence[] immobilizedCharacteristics
DOCUMENT ME


featureReporterMapsCount

protected int featureReporterMapsCount
The count of FeatureReporterMap objects.


featureReporterMaps

protected FeatureReporterMap[] featureReporterMaps
DOCUMENT ME

Constructor Detail

ReporterImpl

public ReporterImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class DesignElementImpl

searchReporters

public Reporter[] searchReporters(ReporterSearchCriteria criteria)
                           throws gov.nih.nci.common.search.SearchException
Returns an array of Reporter objects that satisfy the given ReporterSearchCriteria.

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

setFailTypes

public void setFailTypes(OntologyEntry[] p_failTypes)
Sets the failTypes attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Reporter object.

Specified by:
setFailTypes in interface Reporter
Parameters:
p_failTypes - The new value for failTypes.
See Also:
Reporter.getFailTypes()

getFailTypes

public OntologyEntry[] getFailTypes()
Description copied from interface: Reporter
Returns the value of this Reporter object's failTypes attribute.

Specified by:
getFailTypes in interface Reporter
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry[] The value of failTypes.
See Also:
Reporter.getFailTypes()

setWarningType

public void setWarningType(OntologyEntry p_warningType)
Sets the warningType attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Reporter object.

Specified by:
setWarningType in interface Reporter
Parameters:
p_warningType - The new value for warningType.
See Also:
Reporter.getWarningType()

getWarningType

public OntologyEntry getWarningType()
Description copied from interface: Reporter
Returns the value of this Reporter object's warningType attribute.

Specified by:
getWarningType in interface Reporter
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of warningType.
See Also:
Reporter.getWarningType()

setImmobilizedCharacteristics

public void setImmobilizedCharacteristics(BioSequence[] p_immobilizedCharacteristics)
Sets the immobilizedCharacteristics attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Reporter object.

Specified by:
setImmobilizedCharacteristics in interface Reporter
Parameters:
p_immobilizedCharacteristics - The new value for immobilizedCharacteristics.
See Also:
Reporter.getImmobilizedCharacteristics()

getImmobilizedCharacteristics

public BioSequence[] getImmobilizedCharacteristics()
Description copied from interface: Reporter
Returns the value of this Reporter object's immobilizedCharacteristics attribute.

Specified by:
getImmobilizedCharacteristics in interface Reporter
Returns:
gov.nih.nci.mageom.bean.BioSequence.BioSequence[] The value of immobilizedCharacteristics.
See Also:
Reporter.getImmobilizedCharacteristics()

setFeatureReporterMaps

public void setFeatureReporterMaps(FeatureReporterMap[] p_featureReporterMaps)
Sets the featureReporterMaps attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Reporter object.

Specified by:
setFeatureReporterMaps in interface Reporter
Parameters:
p_featureReporterMaps - The new value for featureReporterMaps.
See Also:
Reporter.getFeatureReporterMaps()

getFeatureReporterMaps

public FeatureReporterMap[] getFeatureReporterMaps()
Description copied from interface: Reporter
Returns the value of this Reporter object's featureReporterMaps attribute.

Specified by:
getFeatureReporterMaps in interface Reporter
Returns:
gov.nih.nci.mageom.bean.DesignElement.FeatureReporterMap[] The value of featureReporterMaps.
See Also:
Reporter.getFeatureReporterMaps()

getFailTypesCount

public int getFailTypesCount()
Returns the count of all OntologyEntry associated with this Reporter object.

Returns:
the count
See Also:
Reporter.getFailTypes()

getImmobilizedCharacteristicsCount

public int getImmobilizedCharacteristicsCount()
Returns the count of all BioSequence associated with this Reporter object.

Returns:
the count
See Also:
Reporter.getImmobilizedCharacteristics()

getFeatureReporterMapsCount

public int getFeatureReporterMapsCount()
Returns the count of all FeatureReporterMap associated with this Reporter object.

Returns:
the count
See Also:
Reporter.getFeatureReporterMaps()

toXML

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

toXMLDoc

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

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 DesignElementImpl
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 DesignElementImpl
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 DesignElementImpl
Returns:
the String representation.