gov.nih.nci.mageom.domain.BioSequence.impl
Class SeqFeatureImpl

java.lang.Object
  extended by gov.nih.nci.mageom.domain.impl.MAGEOMObject
      extended by gov.nih.nci.mageom.domain.impl.ExtendableImpl
          extended by gov.nih.nci.mageom.domain.impl.DescribableImpl
              extended by gov.nih.nci.mageom.domain.BioSequence.impl.SeqFeatureImpl
All Implemented Interfaces:
SeqFeature, Describable, Extendable, java.io.Serializable

public class SeqFeatureImpl
extends DescribableImpl
implements SeqFeature

Represents, in general, what would be a GenBank Feature Table annotation for a sequence.

Version:
%I%, %G%
See Also:
Serialized Form

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

allAssociationMethods

protected static java.util.ArrayList allAssociationMethods

associationMethods

protected static java.util.Hashtable associationMethods

basis

protected java.lang.String basis
How the evidence for a SeqFeature was determined.


regionsCount

protected int regionsCount
The count of SeqFeatureLocation objects.


regions

protected SeqFeatureLocation[] regions
DOCUMENT ME

Constructor Detail

SeqFeatureImpl

public SeqFeatureImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class DescribableImpl

searchSeqFeatures

public SeqFeature[] searchSeqFeatures(SeqFeatureSearchCriteria criteria)
                               throws gov.nih.nci.common.search.SearchException
Returns an array of SeqFeature objects that satisfy the given SeqFeatureSearchCriteria.

Parameters:
criteria - The SeqFeatureSearchCriteria which represents a query for SeqFeature objects.
Returns:
An array of SeqFeature objects.
Throws:
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchException

setBasis

public void setBasis(java.lang.String p_basis)
Sets the basis attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a SeqFeature object.

Specified by:
setBasis in interface SeqFeature
Parameters:
p_basis - The new value for basis.
See Also:
SeqFeature.getBasis()

getBasis

public java.lang.String getBasis()
Description copied from interface: SeqFeature
Returns the value of this SeqFeature object's basis attribute. Description of basis: How the evidence for a SeqFeature was determined.

Specified by:
getBasis in interface SeqFeature
Returns:
enum {experimental, computational,both,unknown,NA} The value of basis.
See Also:
SeqFeature.getBasis()

setRegions

public void setRegions(SeqFeatureLocation[] p_regions)
Sets the regions attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a SeqFeature object.

Specified by:
setRegions in interface SeqFeature
Parameters:
p_regions - The new value for regions.
See Also:
SeqFeature.getRegions()

getRegions

public SeqFeatureLocation[] getRegions()
Description copied from interface: SeqFeature
Returns the value of this SeqFeature object's regions attribute.

Specified by:
getRegions in interface SeqFeature
Returns:
gov.nih.nci.mageom.bean.BioSequence.SeqFeatureLocation[] The value of regions.
See Also:
SeqFeature.getRegions()

getRegionsCount

public int getRegionsCount()
Returns the count of all SeqFeatureLocation associated with this SeqFeature object.

Returns:
the count
See Also:
SeqFeature.getRegions()

toXML

public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
Overrides:
toXML in class DescribableImpl

toXMLDoc

public org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
Overrides:
toXMLDoc in class DescribableImpl

toXMLProcessor

public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
                                          java.util.ArrayList fillOutValues)
Returns an XML representation of the object. The document is not modified.

Overrides:
toXMLProcessor in class DescribableImpl
Parameters:
doc - the working document
fillOutValues - a list of attribute names that should have full XML for their values.
Returns:
org.w3c.dom.Element an XML representation

getXMLMethodDescriptors

public java.util.Hashtable getXMLMethodDescriptors()
Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.

Overrides:
getXMLMethodDescriptors in class DescribableImpl
Returns:
Hashtable The Hashtable of descriptors.

toString

public java.lang.String toString()
Returns a String representation of this object suitable for console display.

Overrides:
toString in class DescribableImpl
Returns:
the String representation.