org.biomage.BioAssayData
Class CompositeSequenceDimension

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.CompositeSequenceDimension
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasCompositeSequences, HasDescriptions, HasPropertySets, HasSecurity

public class CompositeSequenceDimension
extends DesignElementDimension
implements java.io.Serializable, HasCompositeSequences

Specialized DesignElementDimension to hold CompositeSequences.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasCompositeSequences
HasCompositeSequences.CompositeSequences_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 compositeSequences
          The CompositeSequences 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
CompositeSequenceDimension()
          Default constructor.
CompositeSequenceDimension(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToCompositeSequences(CompositeSequence compositeSequence)
          Method to add CompositeSequence to CompositeSequences_list
 void addToCompositeSequences(int position, CompositeSequence compositeSequence)
          Method to add CompositeSequence at position to CompositeSequences_list
 boolean emptyMAGEobject()
           
 HasCompositeSequences.CompositeSequences_list getCompositeSequences()
          Get method for compositeSequences
 CompositeSequence getFromCompositeSequences(int position)
          Method to get CompositeSequence from CompositeSequences_list
 java.lang.String getModelClassName()
           
 void removeElementAtFromCompositeSequences(int position)
          Method to remove by position from CompositeSequences_list
 void removeFromCompositeSequences(CompositeSequence compositeSequence)
          Method to remove first CompositeSequence from CompositeSequences_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setCompositeSequences(HasCompositeSequences.CompositeSequences_list compositeSequences)
          Set method for compositeSequences
 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

compositeSequences

protected java.util.List compositeSequences
The CompositeSequences for this Dimension.

Constructor Detail

CompositeSequenceDimension

public CompositeSequenceDimension()
Default constructor.


CompositeSequenceDimension

public CompositeSequenceDimension(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

setCompositeSequences

public void setCompositeSequences(HasCompositeSequences.CompositeSequences_list compositeSequences)
Set method for compositeSequences

Specified by:
setCompositeSequences in interface HasCompositeSequences
Parameters:
value - to set

getCompositeSequences

public HasCompositeSequences.CompositeSequences_list getCompositeSequences()
Get method for compositeSequences

Specified by:
getCompositeSequences in interface HasCompositeSequences
Returns:
value of the attribute

addToCompositeSequences

public void addToCompositeSequences(CompositeSequence compositeSequence)
Method to add CompositeSequence to CompositeSequences_list

Specified by:
addToCompositeSequences in interface HasCompositeSequences

addToCompositeSequences

public void addToCompositeSequences(int position,
                                    CompositeSequence compositeSequence)
Method to add CompositeSequence at position to CompositeSequences_list

Specified by:
addToCompositeSequences in interface HasCompositeSequences

getFromCompositeSequences

public CompositeSequence getFromCompositeSequences(int position)
Method to get CompositeSequence from CompositeSequences_list

Specified by:
getFromCompositeSequences in interface HasCompositeSequences

removeElementAtFromCompositeSequences

public void removeElementAtFromCompositeSequences(int position)
Method to remove by position from CompositeSequences_list

Specified by:
removeElementAtFromCompositeSequences in interface HasCompositeSequences

removeFromCompositeSequences

public void removeFromCompositeSequences(CompositeSequence compositeSequence)
Method to remove first CompositeSequence from CompositeSequences_list

Specified by:
removeFromCompositeSequences in interface HasCompositeSequences