org.biomage.BioMaterial
Class BioSample

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.BioSample
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, java.lang.Comparable, HasAuditTrail, HasCharacteristics, HasDescriptions, HasMaterialType, HasPropertySets, HasQualityControlStatistics, HasSecurity, HasTopBioMaterial, HasTreatments, HasType

public class BioSample
extends BioMaterial
implements java.io.Serializable, HasType, java.lang.Comparable

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.

See Also:
Serialized Form

Nested Class Summary
 
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  OntologyEntry type
          The Type attribute describes the role the BioSample holds in the treatment hierarchy.
 
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
BioSample()
          Default constructor.
BioSample(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 int compareTo(java.lang.Object o)
          equal method to be used by a set for comparison.
 boolean emptyMAGEobject()
           
 java.lang.String getModelClassName()
           
 OntologyEntry getType()
          Get method for type
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setType(OntologyEntry type)
          Set method for type
 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

type

protected 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.


BioSample

public BioSample(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

setType

public void setType(OntologyEntry type)
Set method for type

Specified by:
setType in interface HasType
Parameters:
value - to set

getType

public OntologyEntry getType()
Get method for type

Specified by:
getType in interface HasType
Returns:
value of the attribute

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