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

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.SequencePositionImpl
All Implemented Interfaces:
SequencePosition, Extendable, java.io.Serializable
Direct Known Subclasses:
CompositePositionImpl, ReporterPositionImpl

public class SequencePositionImpl
extends ExtendableImpl
implements SequencePosition

Designates the position of the Feature in its BioSequence.

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  java.lang.Integer end
          The location of the base, for nucleotides, that the SeqFeature ends.
protected  java.lang.Integer start
          The location of the base, for nucleotides, that the SeqFeature starts.
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
propertySets, propertySetsCount, securedElementId
 
Constructor Summary
SequencePositionImpl()
          Default constructor
 
Method Summary
 java.lang.Integer getEnd()
          Returns the value of this SequencePosition object's end attribute.
 java.lang.Integer getStart()
          Returns the value of this SequencePosition object's start attribute.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 SequencePosition[] searchSequencePositions(SequencePositionSearchCriteria criteria)
          Returns an array of SequencePosition objects that satisfy the given SequencePositionSearchCriteria.
 void setEnd(java.lang.Integer p_end)
          Sets the end attribute.
 void setStart(java.lang.Integer p_start)
          Sets the start 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

start

protected java.lang.Integer start
The location of the base, for nucleotides, that the SeqFeature starts.


end

protected java.lang.Integer end
The location of the base, for nucleotides, that the SeqFeature ends.

Constructor Detail

SequencePositionImpl

public SequencePositionImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class ExtendableImpl

searchSequencePositions

public SequencePosition[] searchSequencePositions(SequencePositionSearchCriteria criteria)
                                           throws gov.nih.nci.common.search.SearchException
Returns an array of SequencePosition objects that satisfy the given SequencePositionSearchCriteria.

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

setStart

public void setStart(java.lang.Integer p_start)
Sets the start attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a SequencePosition object.

Specified by:
setStart in interface SequencePosition
Parameters:
p_start - The new value for start.
See Also:
SequencePosition.getStart()

getStart

public java.lang.Integer getStart()
Description copied from interface: SequencePosition
Returns the value of this SequencePosition object's start attribute. Description of start: The location of the base, for nucleotides, that the SeqFeature starts.

Specified by:
getStart in interface SequencePosition
Returns:
int The value of start.
See Also:
SequencePosition.getStart()

setEnd

public void setEnd(java.lang.Integer p_end)
Sets the end attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a SequencePosition object.

Specified by:
setEnd in interface SequencePosition
Parameters:
p_end - The new value for end.
See Also:
SequencePosition.getEnd()

getEnd

public java.lang.Integer getEnd()
Description copied from interface: SequencePosition
Returns the value of this SequencePosition object's end attribute. Description of end: The location of the base, for nucleotides, that the SeqFeature ends.

Specified by:
getEnd in interface SequencePosition
Returns:
int The value of end.
See Also:
SequencePosition.getEnd()

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.