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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.SeqFeatureLocationImpl
public class SeqFeatureLocationImpl
The location of the SeqFeature annotation.
| Field Summary | |
|---|---|
protected static java.util.ArrayList |
allAssociationMethods
|
protected static java.util.Hashtable |
associationMethods
|
protected SequencePosition |
coordinate
DOCUMENT ME |
protected java.lang.Long |
coordinateId
The internal ID of the associated coordinate object. |
protected java.lang.String |
strandType
Indicates the direction and/or type of the SeqFeature, i.e. |
protected SeqFeatureLocation[] |
subregions
DOCUMENT ME |
protected int |
subregionsCount
The count of SeqFeatureLocation objects. |
| Fields inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl |
|---|
propertySets, propertySetsCount, securedElementId |
| Constructor Summary | |
|---|---|
SeqFeatureLocationImpl()
Default constructor |
|
| Method Summary | |
|---|---|
SequencePosition |
getCoordinate()
Returns the value of this SeqFeatureLocation object's coordinate attribute. |
java.lang.String |
getStrandType()
Returns the value of this SeqFeatureLocation object's strandType attribute. |
SeqFeatureLocation[] |
getSubregions()
Returns the value of this SeqFeatureLocation object's subregions attribute. |
int |
getSubregionsCount()
Returns the count of all SeqFeatureLocation
associated with this SeqFeatureLocation object. |
java.util.Hashtable |
getXMLMethodDescriptors()
Returns a Hashtable containing XMLMethodDescriptors descriptors of
the association methods of this object. |
protected void |
init()
|
SeqFeatureLocation[] |
searchSeqFeatureLocations(SeqFeatureLocationSearchCriteria criteria)
Returns an array of SeqFeatureLocation objects that
satisfy the given SeqFeatureLocationSearchCriteria. |
void |
setCoordinate(SequencePosition p_coordinate)
Sets the coordinate attribute. |
void |
setStrandType(java.lang.String p_strandType)
Sets the strandType attribute. |
void |
setSubregions(SeqFeatureLocation[] p_subregions)
Sets the subregions 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.String strandType
protected int subregionsCount
protected SeqFeatureLocation[] subregions
protected SequencePosition coordinate
protected java.lang.Long coordinateId
| Constructor Detail |
|---|
public SeqFeatureLocationImpl()
| Method Detail |
|---|
protected void init()
init in class ExtendableImpl
public SeqFeatureLocation[] searchSeqFeatureLocations(SeqFeatureLocationSearchCriteria criteria)
throws gov.nih.nci.common.search.SearchException
SeqFeatureLocation objects that
satisfy the given SeqFeatureLocationSearchCriteria.
criteria - The SeqFeatureLocationSearchCriteria
which represents a query for SeqFeatureLocation objects.
SeqFeatureLocation objects.
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchExceptionpublic void setStrandType(java.lang.String p_strandType)
SeqFeatureLocation object.
setStrandType in interface SeqFeatureLocationp_strandType - The new value for strandType.SeqFeatureLocation.getStrandType()public java.lang.String getStrandType()
SeqFeatureLocationSeqFeatureLocation object's strandType attribute.
Description of strandType:
Indicates the direction and/or type of the SeqFeature, i.e. whether it is in the 5' or 3' direction,
is double stranded, etc.
getStrandType in interface SeqFeatureLocationString The value of strandType.SeqFeatureLocation.getStrandType()public void setSubregions(SeqFeatureLocation[] p_subregions)
SeqFeatureLocation object.
setSubregions in interface SeqFeatureLocationp_subregions - The new value for subregions.SeqFeatureLocation.getSubregions()public SeqFeatureLocation[] getSubregions()
SeqFeatureLocationSeqFeatureLocation object's subregions attribute.
getSubregions in interface SeqFeatureLocationgov.nih.nci.mageom.bean.BioSequence.SeqFeatureLocation[] The value of subregions.SeqFeatureLocation.getSubregions()public void setCoordinate(SequencePosition p_coordinate)
SeqFeatureLocation object.
setCoordinate in interface SeqFeatureLocationp_coordinate - The new value for coordinate.SeqFeatureLocation.getCoordinate()public SequencePosition getCoordinate()
SeqFeatureLocationSeqFeatureLocation object's coordinate attribute.
getCoordinate in interface SeqFeatureLocationgov.nih.nci.mageom.bean.BioSequence.SequencePosition The value of coordinate.SeqFeatureLocation.getCoordinate()public int getSubregionsCount()
SeqFeatureLocation
associated with this SeqFeatureLocation object.
SeqFeatureLocation.getSubregions()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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