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org.biomage.BioMaterial
Class BioSource  view BioSource download BioSource.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.BioSource
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.HasSourceContact, org.biomage.Interface.HasTreatments, java.io.Serializable

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


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.AuditAndSecurity.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
 
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
BioSource()
          Default constructor.
BioSource(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 org.biomage.AuditAndSecurity.Contact getSourceContact()
          Get method for sourceContact
 void setSourceContact(org.biomage.AuditAndSecurity.Contact sourceContact)
          Set method for sourceContact
 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

sourceContact

private org.biomage.AuditAndSecurity.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

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

setSourceContact

public void setSourceContact(org.biomage.AuditAndSecurity.Contact sourceContact)
Set method for sourceContact

Specified by:
setSourceContact in interface org.biomage.Interface.HasSourceContact

getSourceContact

public org.biomage.AuditAndSecurity.Contact getSourceContact()
Get method for sourceContact

Specified by:
getSourceContact in interface org.biomage.Interface.HasSourceContact