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

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.BioSequence.impl.SeqFeatureLocationImpl
All Implemented Interfaces:
SeqFeatureLocation, Extendable, java.io.Serializable

public class SeqFeatureLocationImpl
extends ExtendableImpl
implements SeqFeatureLocation

The location of the SeqFeature annotation.

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

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

allAssociationMethods

protected static java.util.ArrayList allAssociationMethods

associationMethods

protected static java.util.Hashtable associationMethods

strandType

protected java.lang.String strandType
Indicates the direction and/or type of the SeqFeature, i.e. whether it is in the 5' or 3' is double stranded, etc.


subregionsCount

protected int subregionsCount
The count of SeqFeatureLocation objects.


subregions

protected SeqFeatureLocation[] subregions
DOCUMENT ME


coordinate

protected SequencePosition coordinate
DOCUMENT ME


coordinateId

protected java.lang.Long coordinateId
The internal ID of the associated coordinate object.

Constructor Detail

SeqFeatureLocationImpl

public SeqFeatureLocationImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class ExtendableImpl

searchSeqFeatureLocations

public SeqFeatureLocation[] searchSeqFeatureLocations(SeqFeatureLocationSearchCriteria criteria)
                                               throws gov.nih.nci.common.search.SearchException
Returns an array of SeqFeatureLocation objects that satisfy the given SeqFeatureLocationSearchCriteria.

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

setStrandType

public void setStrandType(java.lang.String p_strandType)
Sets the strandType attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a SeqFeatureLocation object.

Specified by:
setStrandType in interface SeqFeatureLocation
Parameters:
p_strandType - The new value for strandType.
See Also:
SeqFeatureLocation.getStrandType()

getStrandType

public java.lang.String getStrandType()
Description copied from interface: SeqFeatureLocation
Returns the value of this SeqFeatureLocation 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.

Specified by:
getStrandType in interface SeqFeatureLocation
Returns:
String The value of strandType.
See Also:
SeqFeatureLocation.getStrandType()

setSubregions

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

Specified by:
setSubregions in interface SeqFeatureLocation
Parameters:
p_subregions - The new value for subregions.
See Also:
SeqFeatureLocation.getSubregions()

getSubregions

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

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

setCoordinate

public void setCoordinate(SequencePosition p_coordinate)
Sets the coordinate attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a SeqFeatureLocation object.

Specified by:
setCoordinate in interface SeqFeatureLocation
Parameters:
p_coordinate - The new value for coordinate.
See Also:
SeqFeatureLocation.getCoordinate()

getCoordinate

public SequencePosition getCoordinate()
Description copied from interface: SeqFeatureLocation
Returns the value of this SeqFeatureLocation object's coordinate attribute.

Specified by:
getCoordinate in interface SeqFeatureLocation
Returns:
gov.nih.nci.mageom.bean.BioSequence.SequencePosition The value of coordinate.
See Also:
SeqFeatureLocation.getCoordinate()

getSubregionsCount

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

Returns:
the count
See Also:
SeqFeatureLocation.getSubregions()

toXML

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

toXMLDoc

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

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 ExtendableImpl
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 ExtendableImpl
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 ExtendableImpl
Returns:
the String representation.