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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.BioSequence.impl.SeqFeatureImpl
public class SeqFeatureImpl
Represents, in general, what would be a GenBank Feature Table annotation for a sequence.
| Field Summary | |
|---|---|
protected static java.util.ArrayList |
allAssociationMethods
|
protected static java.util.Hashtable |
associationMethods
|
protected java.lang.String |
basis
How the evidence for a SeqFeature was determined. |
protected SeqFeatureLocation[] |
regions
DOCUMENT ME |
protected int |
regionsCount
The count of SeqFeatureLocation objects. |
| 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 | |
|---|---|
SeqFeatureImpl()
Default constructor |
|
| Method Summary | |
|---|---|
java.lang.String |
getBasis()
Returns the value of this SeqFeature object's basis attribute. |
SeqFeatureLocation[] |
getRegions()
Returns the value of this SeqFeature object's regions attribute. |
int |
getRegionsCount()
Returns the count of all SeqFeatureLocation
associated with this SeqFeature object. |
java.util.Hashtable |
getXMLMethodDescriptors()
Returns a Hashtable containing XMLMethodDescriptors descriptors of
the association methods of this object. |
protected void |
init()
|
SeqFeature[] |
searchSeqFeatures(SeqFeatureSearchCriteria criteria)
Returns an array of SeqFeature objects that
satisfy the given SeqFeatureSearchCriteria. |
void |
setBasis(java.lang.String p_basis)
Sets the basis attribute. |
void |
setRegions(SeqFeatureLocation[] p_regions)
Sets the regions 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.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.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 java.lang.String basis
protected int regionsCount
protected SeqFeatureLocation[] regions
| Constructor Detail |
|---|
public SeqFeatureImpl()
| Method Detail |
|---|
protected void init()
init in class DescribableImpl
public SeqFeature[] searchSeqFeatures(SeqFeatureSearchCriteria criteria)
throws gov.nih.nci.common.search.SearchException
SeqFeature objects that
satisfy the given SeqFeatureSearchCriteria.
criteria - The SeqFeatureSearchCriteria
which represents a query for SeqFeature objects.
SeqFeature objects.
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchExceptionpublic void setBasis(java.lang.String p_basis)
SeqFeature object.
setBasis in interface SeqFeaturep_basis - The new value for basis.SeqFeature.getBasis()public java.lang.String getBasis()
SeqFeatureSeqFeature object's basis attribute.
Description of basis:
How the evidence for a SeqFeature was determined.
getBasis in interface SeqFeatureenum {experimental, computational,both,unknown,NA} The value of basis.SeqFeature.getBasis()public void setRegions(SeqFeatureLocation[] p_regions)
SeqFeature object.
setRegions in interface SeqFeaturep_regions - The new value for regions.SeqFeature.getRegions()public SeqFeatureLocation[] getRegions()
SeqFeatureSeqFeature object's regions attribute.
getRegions in interface SeqFeaturegov.nih.nci.mageom.bean.BioSequence.SeqFeatureLocation[] The value of regions.SeqFeature.getRegions()public int getRegionsCount()
SeqFeatureLocation
associated with this SeqFeature object.
SeqFeature.getRegions()public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
toXML in class DescribableImplpublic org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
toXMLDoc in class DescribableImpl
public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
java.util.ArrayList fillOutValues)
toXMLProcessor in class DescribableImpldoc - 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 DescribableImplpublic java.lang.String toString()
toString in class DescribableImpl
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