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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.DesignElement.impl.MismatchInformationImpl
public class MismatchInformationImpl
Describes how a reporter varies from its ReporterCharacteristics sequence(s) or how a Feature varies from its Reporter sequence.
| Field Summary | |
|---|---|
protected static java.util.ArrayList |
allAssociationMethods
|
protected static java.util.Hashtable |
associationMethods
|
protected java.lang.String |
newSequence
The sequence that replaces the specified sequence starting at start_coord. |
protected java.lang.Integer |
replacedLength
Length of the original sequence that is replaced. |
protected java.lang.Integer |
startCoord
Offset into the sequence that the mismatch occurs. |
| Fields inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl |
|---|
propertySets, propertySetsCount, securedElementId |
| Constructor Summary | |
|---|---|
MismatchInformationImpl()
Default constructor |
|
| Method Summary | |
|---|---|
java.lang.String |
getNewSequence()
Returns the value of this MismatchInformation object's newSequence attribute. |
java.lang.Integer |
getReplacedLength()
Returns the value of this MismatchInformation object's replacedLength attribute. |
java.lang.Integer |
getStartCoord()
Returns the value of this MismatchInformation object's startCoord attribute. |
java.util.Hashtable |
getXMLMethodDescriptors()
Returns a Hashtable containing XMLMethodDescriptors descriptors of
the association methods of this object. |
protected void |
init()
|
MismatchInformation[] |
searchMismatchInformations(MismatchInformationSearchCriteria criteria)
Returns an array of MismatchInformation objects that
satisfy the given MismatchInformationSearchCriteria. |
void |
setNewSequence(java.lang.String p_newSequence)
Sets the newSequence attribute. |
void |
setReplacedLength(java.lang.Integer p_replacedLength)
Sets the replacedLength attribute. |
void |
setStartCoord(java.lang.Integer p_startCoord)
Sets the startCoord 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.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.Extendable |
|---|
getPropertySets, setPropertySets |
| Field Detail |
|---|
protected static java.util.ArrayList allAssociationMethods
protected static java.util.Hashtable associationMethods
protected java.lang.Integer startCoord
protected java.lang.String newSequence
protected java.lang.Integer replacedLength
| Constructor Detail |
|---|
public MismatchInformationImpl()
| Method Detail |
|---|
protected void init()
init in class ExtendableImpl
public MismatchInformation[] searchMismatchInformations(MismatchInformationSearchCriteria criteria)
throws gov.nih.nci.common.search.SearchException
MismatchInformation objects that
satisfy the given MismatchInformationSearchCriteria.
criteria - The MismatchInformationSearchCriteria
which represents a query for MismatchInformation objects.
MismatchInformation objects.
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchExceptionpublic void setStartCoord(java.lang.Integer p_startCoord)
MismatchInformation object.
setStartCoord in interface MismatchInformationp_startCoord - The new value for startCoord.MismatchInformation.getStartCoord()public java.lang.Integer getStartCoord()
MismatchInformationMismatchInformation object's startCoord attribute.
Description of startCoord:
Offset into the sequence that the mismatch occurs.
getStartCoord in interface MismatchInformationint The value of startCoord.MismatchInformation.getStartCoord()public void setNewSequence(java.lang.String p_newSequence)
MismatchInformation object.
setNewSequence in interface MismatchInformationp_newSequence - The new value for newSequence.MismatchInformation.getNewSequence()public java.lang.String getNewSequence()
MismatchInformationMismatchInformation object's newSequence attribute.
Description of newSequence:
The sequence that replaces the specified sequence starting at start_coord.
getNewSequence in interface MismatchInformationString The value of newSequence.MismatchInformation.getNewSequence()public void setReplacedLength(java.lang.Integer p_replacedLength)
MismatchInformation object.
setReplacedLength in interface MismatchInformationp_replacedLength - The new value for replacedLength.MismatchInformation.getReplacedLength()public java.lang.Integer getReplacedLength()
MismatchInformationMismatchInformation object's replacedLength attribute.
Description of replacedLength:
Length of the original sequence that is replaced. A deletion is specified when the length of the newSequence
is less than the replacedLength.
getReplacedLength in interface MismatchInformationint The value of replacedLength.MismatchInformation.getReplacedLength()public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
toXML in class ExtendableImplpublic org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
toXMLDoc in class ExtendableImpl
public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
java.util.ArrayList fillOutValues)
toXMLProcessor in class ExtendableImpldoc - 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 ExtendableImplpublic java.lang.String toString()
toString in class ExtendableImpl
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