gov.nih.nci.mageom.domain.QuantitationType.impl
Class QuantitationTypeImpl

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.QuantitationType.impl.QuantitationTypeImpl
All Implemented Interfaces:
Describable, Extendable, Identifiable, QuantitationType, java.io.Serializable
Direct Known Subclasses:
SpecializedQuantitationTypeImpl, StandardQuantitationTypeImpl

public class QuantitationTypeImpl
extends IdentifiableImpl
implements QuantitationType

A method for calculating a single datum of the matrix (e.g. raw intensity, background, error).

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  Channel channel
          DOCUMENT ME
protected  java.lang.Long channelId
          The internal ID of the associated channel object.
protected  ConfidenceIndicator[] confidenceIndicators
          DOCUMENT ME
protected  int confidenceIndicatorsCount
          The count of ConfidenceIndicator objects.
protected  OntologyEntry dataType
          DOCUMENT ME
protected  java.lang.Long dataTypeId
          The internal ID of the associated dataType object.
protected  java.lang.Boolean isBackground
          Indicates whether the quantitation has been measured from the background or from the feature
protected  QuantitationTypeMap[] quantitationTypeMaps
          DOCUMENT ME
protected  int quantitationTypeMapsCount
          The count of QuantitationTypeMap objects.
protected  OntologyEntry scale
          DOCUMENT ME
protected  java.lang.Long scaleId
          The internal ID of the associated scale object.
 
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
QuantitationTypeImpl()
          Default constructor
 
Method Summary
 Channel getChannel()
          Returns the value of this QuantitationType object's channel attribute.
 java.lang.Long getChannelId()
           
 ConfidenceIndicator[] getConfidenceIndicators()
          Returns the value of this QuantitationType object's confidenceIndicators attribute.
 int getConfidenceIndicatorsCount()
          Returns the count of all ConfidenceIndicator associated with this QuantitationType object.
 OntologyEntry getDataType()
          Returns the value of this QuantitationType object's dataType attribute.
 java.lang.Long getDataTypeId()
           
 java.lang.Boolean getIsBackground()
          Returns the value of this QuantitationType object's isBackground attribute.
 QuantitationTypeMap[] getQuantitationTypeMaps()
          Returns the value of this QuantitationType object's quantitationTypeMaps attribute.
 int getQuantitationTypeMapsCount()
          Returns the count of all QuantitationTypeMap associated with this QuantitationType object.
 OntologyEntry getScale()
          Returns the value of this QuantitationType object's scale attribute.
 java.lang.Long getScaleId()
           
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 QuantitationType[] searchQuantitationTypes(QuantitationTypeSearchCriteria criteria)
          Returns an array of QuantitationType objects that satisfy the given QuantitationTypeSearchCriteria.
 void setChannel(Channel p_channel)
          Sets the channel attribute.
 void setChannelId(java.lang.Long channelId)
           
 void setConfidenceIndicators(ConfidenceIndicator[] p_confidenceIndicators)
          Sets the confidenceIndicators attribute.
 void setDataType(OntologyEntry p_dataType)
          Sets the dataType attribute.
 void setDataTypeId(java.lang.Long dataTypeId)
           
 void setIsBackground(java.lang.Boolean p_isBackground)
          Sets the isBackground attribute.
 void setQuantitationTypeMaps(QuantitationTypeMap[] p_quantitationTypeMaps)
          Sets the quantitationTypeMaps attribute.
 void setScale(OntologyEntry p_scale)
          Sets the scale attribute.
 void setScaleId(java.lang.Long scaleId)
           
 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

isBackground

protected java.lang.Boolean isBackground
Indicates whether the quantitation has been measured from the background or from the feature


channel

protected Channel channel
DOCUMENT ME


channelId

protected java.lang.Long channelId
The internal ID of the associated channel object.


quantitationTypeMapsCount

protected int quantitationTypeMapsCount
The count of QuantitationTypeMap objects.


quantitationTypeMaps

protected QuantitationTypeMap[] quantitationTypeMaps
DOCUMENT ME


confidenceIndicatorsCount

protected int confidenceIndicatorsCount
The count of ConfidenceIndicator objects.


confidenceIndicators

protected ConfidenceIndicator[] confidenceIndicators
DOCUMENT ME


dataType

protected OntologyEntry dataType
DOCUMENT ME


dataTypeId

protected java.lang.Long dataTypeId
The internal ID of the associated dataType object.


scale

protected OntologyEntry scale
DOCUMENT ME


scaleId

protected java.lang.Long scaleId
The internal ID of the associated scale object.

Constructor Detail

QuantitationTypeImpl

public QuantitationTypeImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class IdentifiableImpl

searchQuantitationTypes

public QuantitationType[] searchQuantitationTypes(QuantitationTypeSearchCriteria criteria)
                                           throws gov.nih.nci.common.search.SearchException
Returns an array of QuantitationType objects that satisfy the given QuantitationTypeSearchCriteria.

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

setIsBackground

public void setIsBackground(java.lang.Boolean p_isBackground)
Sets the isBackground attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a QuantitationType object.

Specified by:
setIsBackground in interface QuantitationType
Parameters:
p_isBackground - The new value for isBackground.
See Also:
QuantitationType.getIsBackground()

getIsBackground

public java.lang.Boolean getIsBackground()
Description copied from interface: QuantitationType
Returns the value of this QuantitationType object's isBackground attribute. Description of isBackground: Indicates whether the quantitation has been measured from the background or from the feature itself.

Specified by:
getIsBackground in interface QuantitationType
Returns:
boolean The value of isBackground.
See Also:
QuantitationType.getIsBackground()

setChannel

public void setChannel(Channel p_channel)
Sets the channel attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a QuantitationType object.

Specified by:
setChannel in interface QuantitationType
Parameters:
p_channel - The new value for channel.
See Also:
QuantitationType.getChannel()

getChannel

public Channel getChannel()
Description copied from interface: QuantitationType
Returns the value of this QuantitationType object's channel attribute.

Specified by:
getChannel in interface QuantitationType
Returns:
gov.nih.nci.mageom.bean.BioAssay.Channel The value of channel.
See Also:
QuantitationType.getChannel()

setQuantitationTypeMaps

public void setQuantitationTypeMaps(QuantitationTypeMap[] p_quantitationTypeMaps)
Sets the quantitationTypeMaps attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a QuantitationType object.

Specified by:
setQuantitationTypeMaps in interface QuantitationType
Parameters:
p_quantitationTypeMaps - The new value for quantitationTypeMaps.
See Also:
QuantitationType.getQuantitationTypeMaps()

getQuantitationTypeMaps

public QuantitationTypeMap[] getQuantitationTypeMaps()
Description copied from interface: QuantitationType
Returns the value of this QuantitationType object's quantitationTypeMaps attribute.

Specified by:
getQuantitationTypeMaps in interface QuantitationType
Returns:
gov.nih.nci.mageom.bean.BioAssayData.QuantitationTypeMap[] The value of quantitationTypeMaps.
See Also:
QuantitationType.getQuantitationTypeMaps()

setConfidenceIndicators

public void setConfidenceIndicators(ConfidenceIndicator[] p_confidenceIndicators)
Sets the confidenceIndicators attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a QuantitationType object.

Specified by:
setConfidenceIndicators in interface QuantitationType
Parameters:
p_confidenceIndicators - The new value for confidenceIndicators.
See Also:
QuantitationType.getConfidenceIndicators()

getConfidenceIndicators

public ConfidenceIndicator[] getConfidenceIndicators()
Description copied from interface: QuantitationType
Returns the value of this QuantitationType object's confidenceIndicators attribute.

Specified by:
getConfidenceIndicators in interface QuantitationType
Returns:
gov.nih.nci.mageom.bean.QuantitationType.ConfidenceIndicator[] The value of confidenceIndicators.
See Also:
QuantitationType.getConfidenceIndicators()

setDataType

public void setDataType(OntologyEntry p_dataType)
Sets the dataType attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a QuantitationType object.

Specified by:
setDataType in interface QuantitationType
Parameters:
p_dataType - The new value for dataType.
See Also:
QuantitationType.getDataType()

getDataType

public OntologyEntry getDataType()
Description copied from interface: QuantitationType
Returns the value of this QuantitationType object's dataType attribute.

Specified by:
getDataType in interface QuantitationType
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of dataType.
See Also:
QuantitationType.getDataType()

setScale

public void setScale(OntologyEntry p_scale)
Sets the scale attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a QuantitationType object.

Specified by:
setScale in interface QuantitationType
Parameters:
p_scale - The new value for scale.
See Also:
QuantitationType.getScale()

getScale

public OntologyEntry getScale()
Description copied from interface: QuantitationType
Returns the value of this QuantitationType object's scale attribute.

Specified by:
getScale in interface QuantitationType
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of scale.
See Also:
QuantitationType.getScale()

getQuantitationTypeMapsCount

public int getQuantitationTypeMapsCount()
Returns the count of all QuantitationTypeMap associated with this QuantitationType object.

Returns:
the count
See Also:
QuantitationType.getQuantitationTypeMaps()

getConfidenceIndicatorsCount

public int getConfidenceIndicatorsCount()
Returns the count of all ConfidenceIndicator associated with this QuantitationType object.

Returns:
the count
See Also:
QuantitationType.getConfidenceIndicators()

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.

getChannelId

public java.lang.Long getChannelId()

setChannelId

public void setChannelId(java.lang.Long channelId)

getDataTypeId

public java.lang.Long getDataTypeId()

setDataTypeId

public void setDataTypeId(java.lang.Long dataTypeId)

getScaleId

public java.lang.Long getScaleId()

setScaleId

public void setScaleId(java.lang.Long scaleId)