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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:

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

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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.

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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.

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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

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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

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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

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setType

public void setType(org.biomage.Description.OntologyEntry type)

Set method for type

Specified by:

setType in interface org.biomage.Interface.HasType

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getType

public org.biomage.Description.OntologyEntry getType()

Get method for type

Specified by:

getType in interface org.biomage.Interface.HasType

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioMaterial overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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