org.biomage.DesignElement
Class Feature

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.DesignElement.DesignElement
                  extended by org.biomage.DesignElement.Feature
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasControlFeatures, HasControlledFeatures, HasControlType, HasDescriptions, HasFeatureGroup, HasFeatureLocation, HasPosition, HasPropertySets, HasSecurity, HasZone

public class Feature
extends DesignElement
implements java.io.Serializable, HasZone, HasFeatureGroup, HasPosition, HasControlledFeatures, HasControlFeatures, HasFeatureLocation

An intended position on an array.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasControlledFeatures
HasControlledFeatures.ControlledFeatures_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasControlFeatures
HasControlFeatures.ControlFeatures_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  FeatureGroup featureGroup
          The features that belong to this group.
protected  FeatureLocation featureLocation
          Location of this feature relative to a grid.
protected  Position position
          The position of the feature on the array, relative to the top, left corner.
protected  Zone zone
          A reference to the zone this feature is in.
 
Fields inherited from class org.biomage.DesignElement.DesignElement
controlType
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
Feature()
          Default constructor.
Feature(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToControlFeatures(Feature feature)
          Method to add Feature to ControlFeatures_list
 void addToControlFeatures(int position, Feature feature)
          Method to add Feature at position to ControlFeatures_list
 void addToControlledFeatures(Feature feature)
          Method to add Feature to ControlledFeatures_list
 void addToControlledFeatures(int position, Feature feature)
          Method to add Feature at position to ControlledFeatures_list
 boolean emptyMAGEobject()
           
 HasControlFeatures.ControlFeatures_list getControlFeatures()
          Get method for controlFeatures
 HasControlledFeatures.ControlledFeatures_list getControlledFeatures()
          Get method for controlledFeatures
 FeatureGroup getFeatureGroup()
          Get method for featureGroup
 FeatureLocation getFeatureLocation()
          Get method for featureLocation
 Feature getFromControlFeatures(int position)
          Method to get Feature from ControlFeatures_list
 Feature getFromControlledFeatures(int position)
          Method to get Feature from ControlledFeatures_list
 java.lang.String getModelClassName()
           
 Position getPosition()
          Get method for position
 Zone getZone()
          Get method for zone
 void removeElementAtFromControlFeatures(int position)
          Method to remove by position from ControlFeatures_list
 void removeElementAtFromControlledFeatures(int position)
          Method to remove by position from ControlledFeatures_list
 void removeFromControlFeatures(Feature feature)
          Method to remove first Feature from ControlFeatures_list
 void removeFromControlledFeatures(Feature feature)
          Method to remove first Feature from ControlledFeatures_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setControlFeatures(HasControlFeatures.ControlFeatures_list controlFeatures)
          Set method for controlFeatures
 void setControlledFeatures(HasControlledFeatures.ControlledFeatures_list controlledFeatures)
          Set method for controlledFeatures
 void setFeatureGroup(FeatureGroup featureGroup)
          Set method for featureGroup
 void setFeatureLocation(FeatureLocation featureLocation)
          Set method for featureLocation
 void setPosition(Position position)
          Set method for position
 void setZone(Zone zone)
          Set method for zone
 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.DesignElement.DesignElement
getControlType, setControlType
 
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

position

protected Position position
The position of the feature on the array, relative to the top, left corner.


zone

protected Zone zone
A reference to the zone this feature is in.


featureLocation

protected FeatureLocation featureLocation
Location of this feature relative to a grid.


featureGroup

protected FeatureGroup featureGroup
The features that belong to this group.

Constructor Detail

Feature

public Feature()
Default constructor.


Feature

public Feature(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 DesignElement

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 DesignElement
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 DesignElement
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 DesignElement
Throws:
java.io.IOException

getModelClassName

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

setControlFeatures

public void setControlFeatures(HasControlFeatures.ControlFeatures_list controlFeatures)
Set method for controlFeatures

Specified by:
setControlFeatures in interface HasControlFeatures
Parameters:
value - to set

getControlFeatures

public HasControlFeatures.ControlFeatures_list getControlFeatures()
Get method for controlFeatures

Specified by:
getControlFeatures in interface HasControlFeatures
Returns:
value of the attribute

addToControlFeatures

public void addToControlFeatures(Feature feature)
Method to add Feature to ControlFeatures_list

Specified by:
addToControlFeatures in interface HasControlFeatures

addToControlFeatures

public void addToControlFeatures(int position,
                                 Feature feature)
Method to add Feature at position to ControlFeatures_list

Specified by:
addToControlFeatures in interface HasControlFeatures

getFromControlFeatures

public Feature getFromControlFeatures(int position)
Method to get Feature from ControlFeatures_list

Specified by:
getFromControlFeatures in interface HasControlFeatures

removeElementAtFromControlFeatures

public void removeElementAtFromControlFeatures(int position)
Method to remove by position from ControlFeatures_list

Specified by:
removeElementAtFromControlFeatures in interface HasControlFeatures

removeFromControlFeatures

public void removeFromControlFeatures(Feature feature)
Method to remove first Feature from ControlFeatures_list

Specified by:
removeFromControlFeatures in interface HasControlFeatures

setControlledFeatures

public void setControlledFeatures(HasControlledFeatures.ControlledFeatures_list controlledFeatures)
Set method for controlledFeatures

Specified by:
setControlledFeatures in interface HasControlledFeatures
Parameters:
value - to set

getControlledFeatures

public HasControlledFeatures.ControlledFeatures_list getControlledFeatures()
Get method for controlledFeatures

Specified by:
getControlledFeatures in interface HasControlledFeatures
Returns:
value of the attribute

addToControlledFeatures

public void addToControlledFeatures(Feature feature)
Method to add Feature to ControlledFeatures_list

Specified by:
addToControlledFeatures in interface HasControlledFeatures

addToControlledFeatures

public void addToControlledFeatures(int position,
                                    Feature feature)
Method to add Feature at position to ControlledFeatures_list

Specified by:
addToControlledFeatures in interface HasControlledFeatures

getFromControlledFeatures

public Feature getFromControlledFeatures(int position)
Method to get Feature from ControlledFeatures_list

Specified by:
getFromControlledFeatures in interface HasControlledFeatures

removeElementAtFromControlledFeatures

public void removeElementAtFromControlledFeatures(int position)
Method to remove by position from ControlledFeatures_list

Specified by:
removeElementAtFromControlledFeatures in interface HasControlledFeatures

removeFromControlledFeatures

public void removeFromControlledFeatures(Feature feature)
Method to remove first Feature from ControlledFeatures_list

Specified by:
removeFromControlledFeatures in interface HasControlledFeatures

setPosition

public void setPosition(Position position)
Set method for position

Specified by:
setPosition in interface HasPosition
Parameters:
value - to set

getPosition

public Position getPosition()
Get method for position

Specified by:
getPosition in interface HasPosition
Returns:
value of the attribute

setZone

public void setZone(Zone zone)
Set method for zone

Specified by:
setZone in interface HasZone
Parameters:
value - to set

getZone

public Zone getZone()
Get method for zone

Specified by:
getZone in interface HasZone
Returns:
value of the attribute

setFeatureLocation

public void setFeatureLocation(FeatureLocation featureLocation)
Set method for featureLocation

Specified by:
setFeatureLocation in interface HasFeatureLocation
Parameters:
value - to set

getFeatureLocation

public FeatureLocation getFeatureLocation()
Get method for featureLocation

Specified by:
getFeatureLocation in interface HasFeatureLocation
Returns:
value of the attribute

setFeatureGroup

public void setFeatureGroup(FeatureGroup featureGroup)
Set method for featureGroup

Specified by:
setFeatureGroup in interface HasFeatureGroup
Parameters:
value - to set

getFeatureGroup

public FeatureGroup getFeatureGroup()
Get method for featureGroup

Specified by:
getFeatureGroup in interface HasFeatureGroup
Returns:
value of the attribute