org.biomage.BioMaterial
Class BioSample
java.lang.Object
org.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioMaterial.BioMaterial
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
Field Summary |
protected OntologyEntry |
type
The Type attribute describes the role the BioSample holds in the
treatment hierarchy. |
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.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 |
type
protected OntologyEntry type
- The Type attribute describes the role the BioSample holds in the
treatment hierarchy. This type can be an extract.
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.
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