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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.BioSequence.impl.SequencePositionImpl
gov.nih.nci.mageom.domain.DesignElement.impl.CompositePositionImpl
public class CompositePositionImpl
The location in the compositeSequence target's sequence to which a source compositeSequence maps. The association to MismatchInformation allows the specification, usually for control purposes, of deviations from the CompositeSequence's BioMaterial.
| Field Summary | |
|---|---|
protected static java.util.ArrayList |
allAssociationMethods
|
protected static java.util.Hashtable |
associationMethods
|
protected CompositeSequence |
composite
DOCUMENT ME |
protected java.lang.Long |
compositeId
The internal ID of the associated composite object. |
protected MismatchInformation[] |
mismatchInformation
DOCUMENT ME |
protected int |
mismatchInformationCount
The count of MismatchInformation objects. |
| Fields inherited from class gov.nih.nci.mageom.domain.BioSequence.impl.SequencePositionImpl |
|---|
end, start |
| Fields inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl |
|---|
propertySets, propertySetsCount, securedElementId |
| Constructor Summary | |
|---|---|
CompositePositionImpl()
Default constructor |
|
| Method Summary | |
|---|---|
CompositeSequence |
getComposite()
Returns the value of this CompositePosition object's composite attribute. |
MismatchInformation[] |
getMismatchInformation()
Returns the value of this CompositePosition object's mismatchInformation attribute. |
int |
getMismatchInformationCount()
Returns the count of all MismatchInformation
associated with this CompositePosition object. |
java.util.Hashtable |
getXMLMethodDescriptors()
Returns a Hashtable containing XMLMethodDescriptors descriptors of
the association methods of this object. |
protected void |
init()
|
CompositePosition[] |
searchCompositePositions(CompositePositionSearchCriteria criteria)
Returns an array of CompositePosition objects that
satisfy the given CompositePositionSearchCriteria. |
void |
setComposite(CompositeSequence p_composite)
Sets the composite attribute. |
void |
setMismatchInformation(MismatchInformation[] p_mismatchInformation)
Sets the mismatchInformation 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.BioSequence.impl.SequencePositionImpl |
|---|
getEnd, getStart, searchSequencePositions, setEnd, setStart |
| 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.BioSequence.SequencePosition |
|---|
getEnd, getStart, setEnd, setStart |
| 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 mismatchInformationCount
protected MismatchInformation[] mismatchInformation
protected CompositeSequence composite
protected java.lang.Long compositeId
| Constructor Detail |
|---|
public CompositePositionImpl()
| Method Detail |
|---|
protected void init()
init in class SequencePositionImpl
public CompositePosition[] searchCompositePositions(CompositePositionSearchCriteria criteria)
throws gov.nih.nci.common.search.SearchException
CompositePosition objects that
satisfy the given CompositePositionSearchCriteria.
criteria - The CompositePositionSearchCriteria
which represents a query for CompositePosition objects.
CompositePosition objects.
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchExceptionpublic void setMismatchInformation(MismatchInformation[] p_mismatchInformation)
CompositePosition object.
setMismatchInformation in interface CompositePositionp_mismatchInformation - The new value for mismatchInformation.CompositePosition.getMismatchInformation()public MismatchInformation[] getMismatchInformation()
CompositePositionCompositePosition object's mismatchInformation attribute.
getMismatchInformation in interface CompositePositiongov.nih.nci.mageom.bean.DesignElement.MismatchInformation[] The value of mismatchInformation.CompositePosition.getMismatchInformation()public void setComposite(CompositeSequence p_composite)
CompositePosition object.
setComposite in interface CompositePositionp_composite - The new value for composite.CompositePosition.getComposite()public CompositeSequence getComposite()
CompositePositionCompositePosition object's composite attribute.
getComposite in interface CompositePositiongov.nih.nci.mageom.bean.DesignElement.CompositeSequence The value of composite.CompositePosition.getComposite()public int getMismatchInformationCount()
MismatchInformation
associated with this CompositePosition object.
CompositePosition.getMismatchInformation()public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
toXML in class SequencePositionImplpublic org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
toXMLDoc in class SequencePositionImpl
public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
java.util.ArrayList fillOutValues)
toXMLProcessor in class SequencePositionImpldoc - 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 SequencePositionImplpublic java.lang.String toString()
toString in class SequencePositionImpl
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