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

---

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:

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

---

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

---