org.biomage.BioAssayData
Class FeatureDimension

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.BioAssayData.DesignElementDimension
                  extended by org.biomage.BioAssayData.FeatureDimension
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasContainedFeatures, HasDescriptions, HasPropertySets, HasSecurity

public class FeatureDimension
extends DesignElementDimension
implements java.io.Serializable, HasContainedFeatures

Specialized DesignElementDimension to hold Features.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasContainedFeatures
HasContainedFeatures.ContainedFeatures_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.util.List containedFeatures
          The features for this dimension.
 
Fields inherited from class org.biomage.BioAssayData.DesignElementDimension
ojbConcreteClass
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
FeatureDimension()
          Default constructor.
FeatureDimension(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToContainedFeatures(Feature feature)
          Method to add Feature to ContainedFeatures_list
 void addToContainedFeatures(int position, Feature feature)
          Method to add Feature at position to ContainedFeatures_list
 boolean emptyMAGEobject()
           
 HasContainedFeatures.ContainedFeatures_list getContainedFeatures()
          Get method for containedFeatures
 Feature getFromContainedFeatures(int position)
          Method to get Feature from ContainedFeatures_list
 java.lang.String getModelClassName()
           
 void removeElementAtFromContainedFeatures(int position)
          Method to remove by position from ContainedFeatures_list
 void removeFromContainedFeatures(Feature feature)
          Method to remove first Feature from ContainedFeatures_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setContainedFeatures(HasContainedFeatures.ContainedFeatures_list containedFeatures)
          Set method for containedFeatures
 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.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
Methods inherited from class org.biomage.Common.Describable
addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

containedFeatures

protected java.util.List containedFeatures
The features for this dimension.

Constructor Detail

FeatureDimension

public FeatureDimension()
Default constructor.


FeatureDimension

public FeatureDimension(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

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class DesignElementDimension

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 DesignElementDimension
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 DesignElementDimension
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 DesignElementDimension
Throws:
java.io.IOException

getModelClassName

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

setContainedFeatures

public void setContainedFeatures(HasContainedFeatures.ContainedFeatures_list containedFeatures)
Set method for containedFeatures

Specified by:
setContainedFeatures in interface HasContainedFeatures
Parameters:
value - to set

getContainedFeatures

public HasContainedFeatures.ContainedFeatures_list getContainedFeatures()
Get method for containedFeatures

Specified by:
getContainedFeatures in interface HasContainedFeatures
Returns:
value of the attribute

addToContainedFeatures

public void addToContainedFeatures(Feature feature)
Method to add Feature to ContainedFeatures_list

Specified by:
addToContainedFeatures in interface HasContainedFeatures

addToContainedFeatures

public void addToContainedFeatures(int position,
                                   Feature feature)
Method to add Feature at position to ContainedFeatures_list

Specified by:
addToContainedFeatures in interface HasContainedFeatures

getFromContainedFeatures

public Feature getFromContainedFeatures(int position)
Method to get Feature from ContainedFeatures_list

Specified by:
getFromContainedFeatures in interface HasContainedFeatures

removeElementAtFromContainedFeatures

public void removeElementAtFromContainedFeatures(int position)
Method to remove by position from ContainedFeatures_list

Specified by:
removeElementAtFromContainedFeatures in interface HasContainedFeatures

removeFromContainedFeatures

public void removeFromContainedFeatures(Feature feature)
Method to remove first Feature from ContainedFeatures_list

Specified by:
removeFromContainedFeatures in interface HasContainedFeatures