org.biomage.ArrayDesign
Class DesignElementGroup

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.ArrayDesign.DesignElementGroup
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasPropertySets, HasSecurity, HasSpecies, HasTypes
Direct Known Subclasses:
CompositeGroup, FeatureGroup, ReporterGroup

public abstract class DesignElementGroup
extends Identifiable
implements java.io.Serializable, HasSpecies, HasTypes

The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasTypes
HasTypes.Types_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.lang.String ojbConcreteClass
           
protected  OntologyEntry species
          The organism from which the biosequences of this group are from.
protected  java.util.List types
          The specific type of a feature, reporter, or composite.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
DesignElementGroup()
          Default constructor.
DesignElementGroup(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToTypes(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Types_list
 void addToTypes(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Types_list
 OntologyEntry getFromTypes(int position)
          Method to get OntologyEntry from Types_list
 java.lang.String getModelClassName()
           
 OntologyEntry getSpecies()
          Get method for species
 HasTypes.Types_list getTypes()
          Get method for types
 void removeElementAtFromTypes(int position)
          Method to remove by position from Types_list
 void removeFromTypes(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Types_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setSpecies(OntologyEntry species)
          Set method for species
 void setTypes(HasTypes.Types_list types)
          Set method for types
 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

ojbConcreteClass

protected java.lang.String ojbConcreteClass

types

protected java.util.List types
The specific type of a feature, reporter, or composite. A composite type might be a gene while a reporter type might be a cDNA clone or an oligo.


species

protected OntologyEntry species
The organism from which the biosequences of this group are from.

Constructor Detail

DesignElementGroup

public DesignElementGroup()
Default constructor.


DesignElementGroup

public DesignElementGroup(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 Identifiable

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 Identifiable
Throws:
java.io.IOException

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 Identifiable
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 Identifiable
Throws:
java.io.IOException

getModelClassName

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

setTypes

public void setTypes(HasTypes.Types_list types)
Set method for types

Specified by:
setTypes in interface HasTypes
Parameters:
value - to set

getTypes

public HasTypes.Types_list getTypes()
Get method for types

Specified by:
getTypes in interface HasTypes
Returns:
value of the attribute

addToTypes

public void addToTypes(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Types_list

Specified by:
addToTypes in interface HasTypes

addToTypes

public void addToTypes(int position,
                       OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Types_list

Specified by:
addToTypes in interface HasTypes

getFromTypes

public OntologyEntry getFromTypes(int position)
Method to get OntologyEntry from Types_list

Specified by:
getFromTypes in interface HasTypes

removeElementAtFromTypes

public void removeElementAtFromTypes(int position)
Method to remove by position from Types_list

Specified by:
removeElementAtFromTypes in interface HasTypes

removeFromTypes

public void removeFromTypes(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Types_list

Specified by:
removeFromTypes in interface HasTypes

setSpecies

public void setSpecies(OntologyEntry species)
Set method for species

Specified by:
setSpecies in interface HasSpecies
Parameters:
value - to set

getSpecies

public OntologyEntry getSpecies()
Get method for species

Specified by:
getSpecies in interface HasSpecies
Returns:
value of the attribute