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org.biomage.BioMaterial
Class BioSample  view BioSample download BioSample.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioMaterial.BioMaterial
                  extended byorg.biomage.BioMaterial.BioSample
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasCharacteristics, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasMaterialType, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasQualityControlStatistics, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasTreatments, org.biomage.Interface.HasType, java.io.Serializable

public class BioSample
extends BioMaterial
implements java.io.Serializable, org.biomage.Interface.HasType

BioSamples are products of treatments that are of interest. BioSamples are often used as the sources for other biosamples. The Type attribute describes the role the BioSample holds in the treatment hierarchy. This type can be an extract.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasTreatments
org.biomage.Interface.HasTreatments.Treatments_list
 
Nested classes inherited from class org.biomage.Interface.HasCharacteristics
org.biomage.Interface.HasCharacteristics.Characteristics_list
 
Nested classes inherited from class org.biomage.Interface.HasQualityControlStatistics
org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_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 type
          The Type attribute describes the role the BioSample holds in the treatment hierarchy.
 
Fields inherited from class org.biomage.BioMaterial.BioMaterial
 
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
BioSample()
          Default constructor.
BioSample(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 org.biomage.Description.OntologyEntry getType()
          Get method for type
 void setType(org.biomage.Description.OntologyEntry type)
          Set method for type
 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.BioMaterial.BioMaterial
addToCharacteristics, addToCharacteristics, addToQualityControlStatistics, addToQualityControlStatistics, addToTreatments, addToTreatments, getCharacteristics, getFromCharacteristics, getFromQualityControlStatistics, getFromTreatments, getMaterialType, getQualityControlStatistics, getTreatments, removeElementAtFromCharacteristics, removeElementAtFromQualityControlStatistics, removeElementAtFromTreatments, removeFromCharacteristics, removeFromQualityControlStatistics, removeFromTreatments, setCharacteristics, setMaterialType, setQualityControlStatistics, setTreatments
 
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

type

private org.biomage.Description.OntologyEntry type
The Type attribute describes the role the BioSample holds in the treatment hierarchy. This type can be an extract.

Constructor Detail

BioSample

public BioSample()
Default constructor.


BioSample

public BioSample(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 BioMaterial

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 BioMaterial

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 BioMaterial

setType

public void setType(org.biomage.Description.OntologyEntry type)
Set method for type

Specified by:
setType in interface org.biomage.Interface.HasType

getType

public org.biomage.Description.OntologyEntry getType()
Get method for type

Specified by:
getType in interface org.biomage.Interface.HasType