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org.biomage.BioAssayData
Class FeatureDimension  view FeatureDimension download FeatureDimension.java

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

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

Specialized DesignElementDimension to hold Features.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasContainedFeatures
org.biomage.Interface.HasContainedFeatures.ContainedFeatures_list
 
Nested classes inherited from class org.biomage.Interface.HasAuditTrail
org.biomage.Interface.HasAuditTrail.AuditTrail_list
 
Nested classes inherited from class org.biomage.Interface.HasDescriptions
org.biomage.Interface.HasDescriptions.Descriptions_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  org.biomage.Interface.HasContainedFeatures.ContainedFeatures_list containedFeatures
          The features for this dimension.
 
Fields inherited from class org.biomage.Common.Identifiable
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
FeatureDimension()
          Default constructor.
FeatureDimension(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToContainedFeatures(org.biomage.DesignElement.Feature feature)
          Method to add Feature to ContainedFeatures_list
 void addToContainedFeatures(int position, org.biomage.DesignElement.Feature feature)
          Method to add Feature at position to ContainedFeatures_list
 org.biomage.Interface.HasContainedFeatures.ContainedFeatures_list getContainedFeatures()
          Get method for containedFeatures
 org.biomage.DesignElement.Feature getFromContainedFeatures(int position)
          Method to get Feature from ContainedFeatures_list
 void removeElementAtFromContainedFeatures(int position)
          Method to remove by position from ContainedFeatures_list
 void removeFromContainedFeatures(org.biomage.DesignElement.Feature feature)
          Method to remove first Feature from ContainedFeatures_list
 void setContainedFeatures(org.biomage.Interface.HasContainedFeatures.ContainedFeatures_list containedFeatures)
          Set method for containedFeatures
 void writeAssociations(java.io.Writer out)
          writeAssociations
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName
 
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, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

containedFeatures

private org.biomage.Interface.HasContainedFeatures.ContainedFeatures_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

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 DesignElementDimension

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

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

setContainedFeatures

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

Specified by:
setContainedFeatures in interface org.biomage.Interface.HasContainedFeatures

getContainedFeatures

public org.biomage.Interface.HasContainedFeatures.ContainedFeatures_list getContainedFeatures()
Get method for containedFeatures

Specified by:
getContainedFeatures in interface org.biomage.Interface.HasContainedFeatures

addToContainedFeatures

public void addToContainedFeatures(org.biomage.DesignElement.Feature feature)
Method to add Feature to ContainedFeatures_list

Specified by:
addToContainedFeatures in interface org.biomage.Interface.HasContainedFeatures

addToContainedFeatures

public void addToContainedFeatures(int position,
                                   org.biomage.DesignElement.Feature feature)
Method to add Feature at position to ContainedFeatures_list

Specified by:
addToContainedFeatures in interface org.biomage.Interface.HasContainedFeatures

getFromContainedFeatures

public org.biomage.DesignElement.Feature getFromContainedFeatures(int position)
Method to get Feature from ContainedFeatures_list

Specified by:
getFromContainedFeatures in interface org.biomage.Interface.HasContainedFeatures

removeElementAtFromContainedFeatures

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

Specified by:
removeElementAtFromContainedFeatures in interface org.biomage.Interface.HasContainedFeatures

removeFromContainedFeatures

public void removeFromContainedFeatures(org.biomage.DesignElement.Feature feature)
Method to remove first Feature from ContainedFeatures_list

Specified by:
removeFromContainedFeatures in interface org.biomage.Interface.HasContainedFeatures