gov.nih.nci.mageom.domain.BioAssayData.impl
Class BioAssayDataImpl

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.BioAssayData.impl.BioAssayDataImpl
All Implemented Interfaces:
BioAssayData, Describable, Extendable, Identifiable, java.io.Serializable
Direct Known Subclasses:
DerivedBioAssayDataImpl, MeasuredBioAssayDataImpl

public class BioAssayDataImpl
extends IdentifiableImpl
implements BioAssayData

Represents the dataset created when the BioAssays are created. BioAssayData is the entry point to the values. Because the actual values are represented by a different object, BioDataValues, which can be memory intensive, the annotation of the transformation can be gotten separate from the data.

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  BioAssayDimension bioAssayDimension
          DOCUMENT ME
protected  java.lang.Long bioAssayDimensionId
          The internal ID of the associated bioAssayDimension object.
protected  BioDataValues bioDataValues
          DOCUMENT ME
protected  java.lang.Long bioDataValuesId
          The internal ID of the associated bioDataValues object.
protected  DesignElementDimension designElementDimension
          DOCUMENT ME
protected  java.lang.Long designElementDimensionId
          The internal ID of the associated designElementDimension object.
protected  QuantitationTypeDimension quantitationTypeDimension
          DOCUMENT ME
protected  java.lang.Long quantitationTypeDimensionId
          The internal ID of the associated quantitationTypeDimension object.
protected  NameValueType[] summaryStatistics
          DOCUMENT ME
protected  int summaryStatisticsCount
          The count of NameValueType objects.
 
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
BioAssayDataImpl()
          Default constructor
 
Method Summary
 BioAssayDimension getBioAssayDimension()
          Returns the value of this BioAssayData object's bioAssayDimension attribute.
 long getBioAssayDimensionId()
           
 BioDataValues getBioDataValues()
          Returns the value of this BioAssayData object's bioDataValues attribute.
 DesignElementDimension getDesignElementDimension()
          Returns the value of this BioAssayData object's designElementDimension attribute.
 long getDesignElementDimensionId()
           
 QuantitationTypeDimension getQuantitationTypeDimension()
          Returns the value of this BioAssayData object's quantitationTypeDimension attribute.
 NameValueType[] getSummaryStatistics()
          Returns the value of this BioAssayData object's summaryStatistics attribute.
 int getSummaryStatisticsCount()
          Returns the count of all NameValueType associated with this BioAssayData object.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 BioAssayData[] searchBioAssayDatas(BioAssayDataSearchCriteria criteria)
          Returns an array of BioAssayData objects that satisfy the given BioAssayDataSearchCriteria.
 void setBioAssayDimension(BioAssayDimension p_bioAssayDimension)
          Sets the bioAssayDimension attribute.
 void setBioDataValues(BioDataValues p_bioDataValues)
          Sets the bioDataValues attribute.
 void setDesignElementDimension(DesignElementDimension p_designElementDimension)
          Sets the designElementDimension attribute.
 void setQuantitationTypeDimension(QuantitationTypeDimension p_quantitationTypeDimension)
          Sets the quantitationTypeDimension attribute.
 void setSummaryStatistics(NameValueType[] p_summaryStatistics)
          Sets the summaryStatistics 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.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.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

bioAssayDimension

protected BioAssayDimension bioAssayDimension
DOCUMENT ME


bioAssayDimensionId

protected java.lang.Long bioAssayDimensionId
The internal ID of the associated bioAssayDimension object.


designElementDimension

protected DesignElementDimension designElementDimension
DOCUMENT ME


designElementDimensionId

protected java.lang.Long designElementDimensionId
The internal ID of the associated designElementDimension object.


quantitationTypeDimension

protected QuantitationTypeDimension quantitationTypeDimension
DOCUMENT ME


quantitationTypeDimensionId

protected java.lang.Long quantitationTypeDimensionId
The internal ID of the associated quantitationTypeDimension object.


summaryStatisticsCount

protected int summaryStatisticsCount
The count of NameValueType objects.


summaryStatistics

protected NameValueType[] summaryStatistics
DOCUMENT ME


bioDataValues

protected BioDataValues bioDataValues
DOCUMENT ME


bioDataValuesId

protected java.lang.Long bioDataValuesId
The internal ID of the associated bioDataValues object.

Constructor Detail

BioAssayDataImpl

public BioAssayDataImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class IdentifiableImpl

searchBioAssayDatas

public BioAssayData[] searchBioAssayDatas(BioAssayDataSearchCriteria criteria)
                                   throws gov.nih.nci.common.search.SearchException
Returns an array of BioAssayData objects that satisfy the given BioAssayDataSearchCriteria.

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

setBioAssayDimension

public void setBioAssayDimension(BioAssayDimension p_bioAssayDimension)
Sets the bioAssayDimension attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioAssayData object.

Specified by:
setBioAssayDimension in interface BioAssayData
Parameters:
p_bioAssayDimension - The new value for bioAssayDimension.
See Also:
BioAssayData.getBioAssayDimension()

getBioAssayDimension

public BioAssayDimension getBioAssayDimension()
Description copied from interface: BioAssayData
Returns the value of this BioAssayData object's bioAssayDimension attribute.

Specified by:
getBioAssayDimension in interface BioAssayData
Returns:
gov.nih.nci.mageom.bean.BioAssayData.BioAssayDimension The value of bioAssayDimension.
See Also:
BioAssayData.getBioAssayDimension()

setDesignElementDimension

public void setDesignElementDimension(DesignElementDimension p_designElementDimension)
Sets the designElementDimension attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioAssayData object.

Specified by:
setDesignElementDimension in interface BioAssayData
Parameters:
p_designElementDimension - The new value for designElementDimension.
See Also:
BioAssayData.getDesignElementDimension()

getDesignElementDimension

public DesignElementDimension getDesignElementDimension()
Description copied from interface: BioAssayData
Returns the value of this BioAssayData object's designElementDimension attribute.

Specified by:
getDesignElementDimension in interface BioAssayData
Returns:
gov.nih.nci.mageom.bean.BioAssayData.DesignElementDimension The value of designElementDimension.
See Also:
BioAssayData.getDesignElementDimension()

setQuantitationTypeDimension

public void setQuantitationTypeDimension(QuantitationTypeDimension p_quantitationTypeDimension)
Sets the quantitationTypeDimension attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioAssayData object.

Specified by:
setQuantitationTypeDimension in interface BioAssayData
Parameters:
p_quantitationTypeDimension - The new value for quantitationTypeDimension.
See Also:
BioAssayData.getQuantitationTypeDimension()

getQuantitationTypeDimension

public QuantitationTypeDimension getQuantitationTypeDimension()
Description copied from interface: BioAssayData
Returns the value of this BioAssayData object's quantitationTypeDimension attribute.

Specified by:
getQuantitationTypeDimension in interface BioAssayData
Returns:
gov.nih.nci.mageom.bean.BioAssayData.QuantitationTypeDimension The value of quantitationTypeDimension.
See Also:
BioAssayData.getQuantitationTypeDimension()

setSummaryStatistics

public void setSummaryStatistics(NameValueType[] p_summaryStatistics)
Sets the summaryStatistics attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioAssayData object.

Specified by:
setSummaryStatistics in interface BioAssayData
Parameters:
p_summaryStatistics - The new value for summaryStatistics.
See Also:
BioAssayData.getSummaryStatistics()

getSummaryStatistics

public NameValueType[] getSummaryStatistics()
Description copied from interface: BioAssayData
Returns the value of this BioAssayData object's summaryStatistics attribute.

Specified by:
getSummaryStatistics in interface BioAssayData
Returns:
gov.nih.nci.mageom.bean.NameValueType[] The value of summaryStatistics.
See Also:
BioAssayData.getSummaryStatistics()

setBioDataValues

public void setBioDataValues(BioDataValues p_bioDataValues)
Sets the bioDataValues attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioAssayData object.

Specified by:
setBioDataValues in interface BioAssayData
Parameters:
p_bioDataValues - The new value for bioDataValues.
See Also:
BioAssayData.getBioDataValues()

getBioDataValues

public BioDataValues getBioDataValues()
Description copied from interface: BioAssayData
Returns the value of this BioAssayData object's bioDataValues attribute.

Specified by:
getBioDataValues in interface BioAssayData
Returns:
gov.nih.nci.mageom.bean.BioAssayData.BioDataValues The value of bioDataValues.
See Also:
BioAssayData.getBioDataValues()

getSummaryStatisticsCount

public int getSummaryStatisticsCount()
Returns the count of all NameValueType associated with this BioAssayData object.

Returns:
the count
See Also:
BioAssayData.getSummaryStatistics()

toXML

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

toXMLDoc

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

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 IdentifiableImpl
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 IdentifiableImpl
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 IdentifiableImpl
Returns:
the String representation.

getDesignElementDimensionId

public long getDesignElementDimensionId()

getBioAssayDimensionId

public long getBioAssayDimensionId()