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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.CompositeCompositeMapImpl
public class CompositeCompositeMapImpl
A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. For instance, several CompositeSequences could represent different sequence regions for a Gene and could be mapped to different CompositeSequences, each representing a different splice variant for that Gene.
| Field Summary | |
|---|---|
protected static java.util.ArrayList |
allAssociationMethods
|
protected static java.util.Hashtable |
associationMethods
|
protected CompositePosition[] |
compositePositionSources
DOCUMENT ME |
protected int |
compositePositionSourcesCount
The count of CompositePosition objects. |
protected CompositeSequence |
compositeSequence
DOCUMENT ME |
protected java.lang.Long |
compositeSequenceId
The internal ID of the associated compositeSequence object. |
| 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 | |
|---|---|
CompositeCompositeMapImpl()
Default constructor |
|
| Method Summary | |
|---|---|
CompositePosition[] |
getCompositePositionSources()
Returns the value of this CompositeCompositeMap object's compositePositionSources attribute. |
int |
getCompositePositionSourcesCount()
Returns the count of all CompositePosition
associated with this CompositeCompositeMap object. |
CompositeSequence |
getCompositeSequence()
Returns the value of this CompositeCompositeMap object's compositeSequence attribute. |
java.util.Hashtable |
getXMLMethodDescriptors()
Returns a Hashtable containing XMLMethodDescriptors descriptors of
the association methods of this object. |
protected void |
init()
|
CompositeCompositeMap[] |
searchCompositeCompositeMaps(CompositeCompositeMapSearchCriteria criteria)
Returns an array of CompositeCompositeMap objects that
satisfy the given CompositeCompositeMapSearchCriteria. |
void |
setCompositePositionSources(CompositePosition[] p_compositePositionSources)
Sets the compositePositionSources attribute. |
void |
setCompositeSequence(CompositeSequence p_compositeSequence)
Sets the compositeSequence 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 CompositeSequence compositeSequence
protected java.lang.Long compositeSequenceId
protected int compositePositionSourcesCount
protected CompositePosition[] compositePositionSources
| Constructor Detail |
|---|
public CompositeCompositeMapImpl()
| Method Detail |
|---|
protected void init()
init in class DesignElementMapImpl
public CompositeCompositeMap[] searchCompositeCompositeMaps(CompositeCompositeMapSearchCriteria criteria)
throws gov.nih.nci.common.search.SearchException
CompositeCompositeMap objects that
satisfy the given CompositeCompositeMapSearchCriteria.
criteria - The CompositeCompositeMapSearchCriteria
which represents a query for CompositeCompositeMap objects.
CompositeCompositeMap objects.
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchExceptionpublic void setCompositeSequence(CompositeSequence p_compositeSequence)
CompositeCompositeMap object.
setCompositeSequence in interface CompositeCompositeMapp_compositeSequence - The new value for compositeSequence.CompositeCompositeMap.getCompositeSequence()public CompositeSequence getCompositeSequence()
CompositeCompositeMapCompositeCompositeMap object's compositeSequence attribute.
getCompositeSequence in interface CompositeCompositeMapgov.nih.nci.mageom.bean.DesignElement.CompositeSequence The value of compositeSequence.CompositeCompositeMap.getCompositeSequence()public void setCompositePositionSources(CompositePosition[] p_compositePositionSources)
CompositeCompositeMap object.
setCompositePositionSources in interface CompositeCompositeMapp_compositePositionSources - The new value for compositePositionSources.CompositeCompositeMap.getCompositePositionSources()public CompositePosition[] getCompositePositionSources()
CompositeCompositeMapCompositeCompositeMap object's compositePositionSources attribute.
getCompositePositionSources in interface CompositeCompositeMapgov.nih.nci.mageom.bean.DesignElement.CompositePosition[] The value of compositePositionSources.CompositeCompositeMap.getCompositePositionSources()public int getCompositePositionSourcesCount()
CompositePosition
associated with this CompositeCompositeMap object.
CompositeCompositeMap.getCompositePositionSources()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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