org.biomage.BioMaterial
Class BioSource

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.BioMaterial.BioMaterial
                  extended by org.biomage.BioMaterial.BioSource
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, java.lang.Comparable, HasAuditTrail, HasCharacteristics, HasDescriptions, HasMaterialType, HasPropertySets, HasQualityControlStatistics, HasSecurity, HasSourceContact, HasTopBioMaterial, HasTreatments

public class BioSource
extends BioMaterial
implements java.io.Serializable, HasSourceContact, java.lang.Comparable

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/interfaces inherited from interface org.biomage.Interface.HasSourceContact
HasSourceContact.SourceContact_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasTreatments
HasTreatments.Treatments_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasCharacteristics
HasCharacteristics.Characteristics_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasQualityControlStatistics
HasQualityControlStatistics.QualityControlStatistics_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasTopBioMaterial
HasTopBioMaterial.TopLevelBioMaterials_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.util.List 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, copied, imported, materialType, ojbConcreteClass, qualityControlStatistics, topLevelBioMaterials, treatments
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BioSource()
          Default constructor.
BioSource(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToSourceContact(Contact contact)
          Method to add Contact to SourceContact_list
 void addToSourceContact(int position, Contact contact)
          Method to add Contact at position to SourceContact_list
 int compareTo(java.lang.Object o)
          equal method to be used by a set for comparison.
 boolean emptyMAGEobject()
           
 Contact getFromSourceContact(int position)
          Method to get Contact from SourceContact_list
 java.lang.String getModelClassName()
           
 HasSourceContact.SourceContact_list getSourceContact()
          Get method for sourceContact
 void removeElementAtFromSourceContact(int position)
          Method to remove by position from SourceContact_list
 void removeFromSourceContact(Contact contact)
          Method to remove first Contact from SourceContact_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setSourceContact(HasSourceContact.SourceContact_list 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, addToTopLevelBioMaterials, addToTopLevelBioMaterials, addToTreatments, addToTreatments, getCharacteristics, getCopied, getFromCharacteristics, getFromQualityControlStatistics, getFromTopLevelBioMaterials, getFromTreatments, getImported, getMaterialType, getQualityControlStatistics, getTopLevelBioMaterials, getTreatments, removeElementAtFromCharacteristics, removeElementAtFromQualityControlStatistics, removeElementAtFromTopLevelBioMaterials, removeElementAtFromTreatments, removeFromCharacteristics, removeFromQualityControlStatistics, removeFromTopLevelBioMaterials, removeFromTreatments, setCharacteristics, setCopied, setImported, setMaterialType, setQualityControlStatistics, setTopLevelBioMaterials, setTreatments
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

sourceContact

protected java.util.List 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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class BioMaterial

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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class BioMaterial

setSourceContact

public void setSourceContact(HasSourceContact.SourceContact_list sourceContact)
Set method for sourceContact

Specified by:
setSourceContact in interface HasSourceContact
Parameters:
value - to set

getSourceContact

public HasSourceContact.SourceContact_list getSourceContact()
Get method for sourceContact

Specified by:
getSourceContact in interface HasSourceContact
Returns:
value of the attribute

addToSourceContact

public void addToSourceContact(Contact contact)
Method to add Contact to SourceContact_list

Specified by:
addToSourceContact in interface HasSourceContact

addToSourceContact

public void addToSourceContact(int position,
                               Contact contact)
Method to add Contact at position to SourceContact_list

Specified by:
addToSourceContact in interface HasSourceContact

getFromSourceContact

public Contact getFromSourceContact(int position)
Method to get Contact from SourceContact_list

Specified by:
getFromSourceContact in interface HasSourceContact

removeElementAtFromSourceContact

public void removeElementAtFromSourceContact(int position)
Method to remove by position from SourceContact_list

Specified by:
removeElementAtFromSourceContact in interface HasSourceContact

removeFromSourceContact

public void removeFromSourceContact(Contact contact)
Method to remove first Contact from SourceContact_list

Specified by:
removeFromSourceContact in interface HasSourceContact

compareTo

public int compareTo(java.lang.Object o)
equal method to be used by a set for comparison. same id is assumed to be same object.

Specified by:
compareTo in interface java.lang.Comparable