org.biomage.BioMaterial
Class BioSample

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioMaterial.BioMaterial
                          |
                          +--org.biomage.BioMaterial.BioSample

All Implemented Interfaces:

HasAuditTrail, HasCharacteristics, HasDescriptions, HasMaterialType, HasPropertySets, HasQualityControlStatistics, HasSecurity, HasTreatments, HasType, java.io.Serializable

public class BioSample

extends BioMaterial

implements java.io.Serializable, 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.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biomage.Interface.HasTreatments

HasTreatments.Treatments_list

Nested classes inherited from class org.biomage.Interface.HasCharacteristics

HasCharacteristics.Characteristics_list

Nested classes inherited from class org.biomage.Interface.HasQualityControlStatistics

HasQualityControlStatistics.QualityControlStatistics_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected OntologyEntry

type The Type attribute describes the role the BioSample holds in the treatment hierarchy.

Fields inherited from class org.biomage.BioMaterial.BioMaterial

characteristics, materialType, qualityControlStatistics, treatments

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

BioSample()
Default constructor.

BioSample(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

OntologyEntry	getType() Get method for type
void	setType(OntologyEntry type) Set method for type
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.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

protected 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

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 BioMaterial

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 BioMaterial

java.io.IOException

setType

public void setType(OntologyEntry type)

Set method for type

Specified by:

setType in interface HasType

getType

public OntologyEntry getType()

Get method for type

Specified by:

getType in interface HasType

Returns:

value of the attribute