org.biomage.BioMaterial
Class BioSource

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

All Implemented Interfaces:

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

public class BioSource

extends BioMaterial

implements java.io.Serializable, HasSourceContact

The BioSource is the original source material before any treatment events. It is also a top node of the directed acyclic graph generated by treatments. The association to OntologyEntry allows enumeration of a BioSource's inherent properties.

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 Contact

sourceContact The BioSource's source is the provider of the biological material (a cell line, strain, etc...).

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

BioSource()
Default constructor.

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

Method Summary

Contact	getSourceContact() Get method for sourceContact
void	setSourceContact(Contact sourceContact) Set method for sourceContact
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

sourceContact

protected Contact sourceContact

The BioSource's source is the provider of the biological material (a cell line, strain, etc...). This could be the ATTC (American Tissue Type Collection).

Constructor Detail

BioSource

public BioSource()

Default constructor.

BioSource

public BioSource(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

setSourceContact

public void setSourceContact(Contact sourceContact)

Set method for sourceContact

Specified by:

setSourceContact in interface HasSourceContact

getSourceContact

public Contact getSourceContact()

Get method for sourceContact

Specified by:

getSourceContact in interface HasSourceContact

Returns:

value of the attribute