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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.BioEvent.impl.BioEventImpl
gov.nih.nci.mageom.domain.BioEvent.impl.MapImpl
gov.nih.nci.mageom.domain.BioAssayData.impl.DesignElementMapImpl
gov.nih.nci.mageom.domain.DesignElement.impl.ReporterCompositeMapImpl
public class ReporterCompositeMapImpl
A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. For instance, several reporters that tile across a section of a chromosome could be mapped to a CompositeSequence.
| Field Summary | |
|---|---|
protected static java.util.ArrayList |
allAssociationMethods
|
protected static java.util.Hashtable |
associationMethods
|
protected CompositeSequence |
compositeSequence
DOCUMENT ME |
protected java.lang.Long |
compositeSequenceId
The internal ID of the associated compositeSequence object. |
protected ReporterPosition[] |
reporterPositionSources
DOCUMENT ME |
protected int |
reporterPositionSourcesCount
The count of ReporterPosition objects. |
| Fields inherited from class gov.nih.nci.mageom.domain.BioEvent.impl.BioEventImpl |
|---|
protocolApplications, protocolApplicationsCount |
| 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 | |
|---|---|
ReporterCompositeMapImpl()
Default constructor |
|
| Method Summary | |
|---|---|
CompositeSequence |
getCompositeSequence()
Returns the value of this ReporterCompositeMap object's compositeSequence attribute. |
ReporterPosition[] |
getReporterPositionSources()
Returns the value of this ReporterCompositeMap object's reporterPositionSources attribute. |
int |
getReporterPositionSourcesCount()
Returns the count of all ReporterPosition
associated with this ReporterCompositeMap object. |
java.util.Hashtable |
getXMLMethodDescriptors()
Returns a Hashtable containing XMLMethodDescriptors descriptors of
the association methods of this object. |
protected void |
init()
|
ReporterCompositeMap[] |
searchReporterCompositeMaps(ReporterCompositeMapSearchCriteria criteria)
Returns an array of ReporterCompositeMap objects that
satisfy the given ReporterCompositeMapSearchCriteria. |
void |
setCompositeSequence(CompositeSequence p_compositeSequence)
Sets the compositeSequence attribute. |
void |
setReporterPositionSources(ReporterPosition[] p_reporterPositionSources)
Sets the reporterPositionSources 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.BioAssayData.impl.DesignElementMapImpl |
|---|
searchDesignElementMaps |
| Methods inherited from class gov.nih.nci.mageom.domain.BioEvent.impl.MapImpl |
|---|
searchMaps |
| Methods inherited from class gov.nih.nci.mageom.domain.BioEvent.impl.BioEventImpl |
|---|
getProtocolApplications, getProtocolApplicationsCount, searchBioEvents, setProtocolApplications |
| 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.BioEvent.BioEvent |
|---|
getProtocolApplications, setProtocolApplications |
| 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 reporterPositionSourcesCount
protected ReporterPosition[] reporterPositionSources
protected CompositeSequence compositeSequence
protected java.lang.Long compositeSequenceId
| Constructor Detail |
|---|
public ReporterCompositeMapImpl()
| Method Detail |
|---|
protected void init()
init in class DesignElementMapImpl
public ReporterCompositeMap[] searchReporterCompositeMaps(ReporterCompositeMapSearchCriteria criteria)
throws gov.nih.nci.common.search.SearchException
ReporterCompositeMap objects that
satisfy the given ReporterCompositeMapSearchCriteria.
criteria - The ReporterCompositeMapSearchCriteria
which represents a query for ReporterCompositeMap objects.
ReporterCompositeMap objects.
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchExceptionpublic void setReporterPositionSources(ReporterPosition[] p_reporterPositionSources)
ReporterCompositeMap object.
setReporterPositionSources in interface ReporterCompositeMapp_reporterPositionSources - The new value for reporterPositionSources.ReporterCompositeMap.getReporterPositionSources()public ReporterPosition[] getReporterPositionSources()
ReporterCompositeMapReporterCompositeMap object's reporterPositionSources attribute.
getReporterPositionSources in interface ReporterCompositeMapgov.nih.nci.mageom.bean.DesignElement.ReporterPosition[] The value of reporterPositionSources.ReporterCompositeMap.getReporterPositionSources()public void setCompositeSequence(CompositeSequence p_compositeSequence)
ReporterCompositeMap object.
setCompositeSequence in interface ReporterCompositeMapp_compositeSequence - The new value for compositeSequence.ReporterCompositeMap.getCompositeSequence()public CompositeSequence getCompositeSequence()
ReporterCompositeMapReporterCompositeMap object's compositeSequence attribute.
getCompositeSequence in interface ReporterCompositeMapgov.nih.nci.mageom.bean.DesignElement.CompositeSequence The value of compositeSequence.ReporterCompositeMap.getCompositeSequence()public int getReporterPositionSourcesCount()
ReporterPosition
associated with this ReporterCompositeMap object.
ReporterCompositeMap.getReporterPositionSources()public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
toXML in class DesignElementMapImplpublic org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
toXMLDoc in class DesignElementMapImpl
public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
java.util.ArrayList fillOutValues)
toXMLProcessor in class DesignElementMapImpldoc - 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 DesignElementMapImplpublic java.lang.String toString()
toString in class DesignElementMapImpl
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