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org.biomage.ArrayDesign
Class DesignElementGroup  view DesignElementGroup download DesignElementGroup.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.ArrayDesign.DesignElementGroup
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasSpecies, org.biomage.Interface.HasTypes, java.io.Serializable
Direct Known Subclasses:
CompositeGroup, FeatureGroup, ReporterGroup

public abstract class DesignElementGroup
extends org.biomage.Common.Identifiable
implements java.io.Serializable, org.biomage.Interface.HasSpecies, org.biomage.Interface.HasTypes

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


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasTypes
org.biomage.Interface.HasTypes.Types_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.Description.OntologyEntry species
          The organism from which the biosequences of this group are from.
private  org.biomage.Interface.HasTypes.Types_list types
          The specific type of a feature, reporter, or composite.
 
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
DesignElementGroup()
          Default constructor.
DesignElementGroup(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToTypes(int position, org.biomage.Description.OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Types_list
 void addToTypes(org.biomage.Description.OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Types_list
 org.biomage.Description.OntologyEntry getFromTypes(int position)
          Method to get OntologyEntry from Types_list
 org.biomage.Description.OntologyEntry getSpecies()
          Get method for species
 org.biomage.Interface.HasTypes.Types_list getTypes()
          Get method for types
 void removeElementAtFromTypes(int position)
          Method to remove by position from Types_list
 void removeFromTypes(org.biomage.Description.OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Types_list
 void setSpecies(org.biomage.Description.OntologyEntry species)
          Set method for species
 void setTypes(org.biomage.Interface.HasTypes.Types_list types)
          Set method for types
 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

species

private org.biomage.Description.OntologyEntry species
The organism from which the biosequences of this group are from.


types

private org.biomage.Interface.HasTypes.Types_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.

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

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.


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.


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.


setSpecies

public void setSpecies(org.biomage.Description.OntologyEntry species)
Set method for species

Specified by:
setSpecies in interface org.biomage.Interface.HasSpecies

getSpecies

public org.biomage.Description.OntologyEntry getSpecies()
Get method for species

Specified by:
getSpecies in interface org.biomage.Interface.HasSpecies

setTypes

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

Specified by:
setTypes in interface org.biomage.Interface.HasTypes

getTypes

public org.biomage.Interface.HasTypes.Types_list getTypes()
Get method for types

Specified by:
getTypes in interface org.biomage.Interface.HasTypes

addToTypes

public void addToTypes(org.biomage.Description.OntologyEntry ontologyEntry)
Method to add OntologyEntry to Types_list

Specified by:
addToTypes in interface org.biomage.Interface.HasTypes

addToTypes

public void addToTypes(int position,
                       org.biomage.Description.OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Types_list

Specified by:
addToTypes in interface org.biomage.Interface.HasTypes

getFromTypes

public org.biomage.Description.OntologyEntry getFromTypes(int position)
Method to get OntologyEntry from Types_list

Specified by:
getFromTypes in interface org.biomage.Interface.HasTypes

removeElementAtFromTypes

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

Specified by:
removeElementAtFromTypes in interface org.biomage.Interface.HasTypes

removeFromTypes

public void removeFromTypes(org.biomage.Description.OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Types_list

Specified by:
removeFromTypes in interface org.biomage.Interface.HasTypes