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java.lang.Objectgov.nih.nci.mageom.domain.impl.MAGEOMObject
gov.nih.nci.mageom.domain.impl.ExtendableImpl
gov.nih.nci.mageom.domain.impl.DescribableImpl
gov.nih.nci.mageom.domain.impl.IdentifiableImpl
gov.nih.nci.mageom.domain.DesignElement.impl.DesignElementImpl
gov.nih.nci.mageom.domain.DesignElement.impl.ReporterImpl
public class ReporterImpl
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.
| 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 |
|---|
protected static java.util.ArrayList allAssociationMethods
protected static java.util.Hashtable associationMethods
protected int failTypesCount
protected OntologyEntry[] failTypes
protected OntologyEntry warningType
protected java.lang.Long warningTypeId
protected int immobilizedCharacteristicsCount
protected BioSequence[] immobilizedCharacteristics
protected int featureReporterMapsCount
protected FeatureReporterMap[] featureReporterMaps
| Constructor Detail |
|---|
public ReporterImpl()
| Method Detail |
|---|
protected void init()
init in class DesignElementImpl
public Reporter[] searchReporters(ReporterSearchCriteria criteria)
throws gov.nih.nci.common.search.SearchException
Reporter objects that
satisfy the given ReporterSearchCriteria.
criteria - The ReporterSearchCriteria
which represents a query for Reporter objects.
Reporter objects.
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchExceptionpublic void setFailTypes(OntologyEntry[] p_failTypes)
Reporter object.
setFailTypes in interface Reporterp_failTypes - The new value for failTypes.Reporter.getFailTypes()public OntologyEntry[] getFailTypes()
ReporterReporter object's failTypes attribute.
getFailTypes in interface Reportergov.nih.nci.mageom.bean.Description.OntologyEntry[] The value of failTypes.Reporter.getFailTypes()public void setWarningType(OntologyEntry p_warningType)
Reporter object.
setWarningType in interface Reporterp_warningType - The new value for warningType.Reporter.getWarningType()public OntologyEntry getWarningType()
ReporterReporter object's warningType attribute.
getWarningType in interface Reportergov.nih.nci.mageom.bean.Description.OntologyEntry The value of warningType.Reporter.getWarningType()public void setImmobilizedCharacteristics(BioSequence[] p_immobilizedCharacteristics)
Reporter object.
setImmobilizedCharacteristics in interface Reporterp_immobilizedCharacteristics - The new value for immobilizedCharacteristics.Reporter.getImmobilizedCharacteristics()public BioSequence[] getImmobilizedCharacteristics()
ReporterReporter object's immobilizedCharacteristics attribute.
getImmobilizedCharacteristics in interface Reportergov.nih.nci.mageom.bean.BioSequence.BioSequence[] The value of immobilizedCharacteristics.Reporter.getImmobilizedCharacteristics()public void setFeatureReporterMaps(FeatureReporterMap[] p_featureReporterMaps)
Reporter object.
setFeatureReporterMaps in interface Reporterp_featureReporterMaps - The new value for featureReporterMaps.Reporter.getFeatureReporterMaps()public FeatureReporterMap[] getFeatureReporterMaps()
ReporterReporter object's featureReporterMaps attribute.
getFeatureReporterMaps in interface Reportergov.nih.nci.mageom.bean.DesignElement.FeatureReporterMap[] The value of featureReporterMaps.Reporter.getFeatureReporterMaps()public int getFailTypesCount()
OntologyEntry
associated with this Reporter object.
Reporter.getFailTypes()public int getImmobilizedCharacteristicsCount()
BioSequence
associated with this Reporter object.
Reporter.getImmobilizedCharacteristics()public int getFeatureReporterMapsCount()
FeatureReporterMap
associated with this Reporter object.
Reporter.getFeatureReporterMaps()public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
toXML in class DesignElementImplpublic org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
toXMLDoc in class DesignElementImpl
public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
java.util.ArrayList fillOutValues)
toXMLProcessor in class DesignElementImpldoc - the working documentfillOutValues - a list of attribute names that should have
full XML for their values.
public java.util.Hashtable getXMLMethodDescriptors()
XMLMethodDescriptors descriptors of
the association methods of this object.
getXMLMethodDescriptors in class DesignElementImplpublic java.lang.String toString()
toString in class DesignElementImpl
|
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