org.biomage.Array
Class FeatureDefect

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Array.FeatureDefect
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasDefectType, HasFeature, HasPositionDelta, HasPropertySets

public class FeatureDefect
extends Extendable
implements java.io.Serializable, HasPositionDelta, HasFeature, HasDefectType

Stores the defect information for a feature.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  OntologyEntry defectType
          Indicates the type of defect (e.g.
protected  Feature feature
          The feature that was manufactured defectively.
protected  PositionDelta positionDelta
          How the feature deviates in position from the ArrayDesign.
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
FeatureDefect()
          Default constructor.
FeatureDefect(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 boolean emptyMAGEobject()
           
 OntologyEntry getDefectType()
          Get method for defectType
 Feature getFeature()
          Get method for feature
 java.lang.String getModelClassName()
           
 PositionDelta getPositionDelta()
          Get method for positionDelta
 void setDefectType(OntologyEntry defectType)
          Set method for defectType
 void setFeature(Feature feature)
          Set method for feature
 void setPositionDelta(PositionDelta positionDelta)
          Set method for positionDelta
 void writeAssociations(java.io.Writer out)
          writeAssociations This method is responsible for assembling the association data into XML.
 void writeAttributes(java.io.Writer out)
          writeAttributes This method is responsible for assembling the attribute data into XML.
 void writeMAGEML(java.io.Writer out)
          writeMAGEML This method is responsible for assembling the attribute and association data into XML.
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setAttributes, setId, setIsEditable, setPropertySets, setSecuredElementId, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

defectType

protected OntologyEntry defectType
Indicates the type of defect (e.g. a missing feature or a moved feature).


positionDelta

protected PositionDelta positionDelta
How the feature deviates in position from the ArrayDesign.


feature

protected Feature feature
The feature that was manufactured defectively.

Constructor Detail

FeatureDefect

public FeatureDefect()
Default constructor.


FeatureDefect

public FeatureDefect(org.xml.sax.Attributes atts)
Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Parameters:
atts: - the attribute list.
Method Detail

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException
writeMAGEML This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.

Overrides:
writeMAGEML in class Extendable
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException
writeAttributes This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.

Overrides:
writeAttributes in class Extendable
Throws:
java.io.IOException

writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException
writeAssociations This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.

Overrides:
writeAssociations in class Extendable
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Extendable

setDefectType

public void setDefectType(OntologyEntry defectType)
Set method for defectType

Specified by:
setDefectType in interface HasDefectType
Parameters:
value - to set

getDefectType

public OntologyEntry getDefectType()
Get method for defectType

Specified by:
getDefectType in interface HasDefectType
Returns:
value of the attribute

setPositionDelta

public void setPositionDelta(PositionDelta positionDelta)
Set method for positionDelta

Specified by:
setPositionDelta in interface HasPositionDelta
Parameters:
value - to set

getPositionDelta

public PositionDelta getPositionDelta()
Get method for positionDelta

Specified by:
getPositionDelta in interface HasPositionDelta
Returns:
value of the attribute

setFeature

public void setFeature(Feature feature)
Set method for feature

Specified by:
setFeature in interface HasFeature
Parameters:
value - to set

getFeature

public Feature getFeature()
Get method for feature

Specified by:
getFeature in interface HasFeature
Returns:
value of the attribute