|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioMaterial.BioMaterial
org.biomage.BioMaterial.BioSource
public class BioSource
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/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.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 |
---|
protected java.util.List sourceContact
Constructor Detail |
---|
public BioSource()
public BioSource(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
---|
public void setAttributes(org.xml.sax.Attributes atts)
setAttributes
in class BioMaterial
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class BioMaterial
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class BioMaterial
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class BioMaterial
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class BioMaterial
public void setSourceContact(HasSourceContact.SourceContact_list sourceContact)
setSourceContact
in interface HasSourceContact
value
- to setpublic HasSourceContact.SourceContact_list getSourceContact()
getSourceContact
in interface HasSourceContact
public void addToSourceContact(Contact contact)
addToSourceContact
in interface HasSourceContact
public void addToSourceContact(int position, Contact contact)
addToSourceContact
in interface HasSourceContact
public Contact getFromSourceContact(int position)
getFromSourceContact
in interface HasSourceContact
public void removeElementAtFromSourceContact(int position)
removeElementAtFromSourceContact
in interface HasSourceContact
public void removeFromSourceContact(Contact contact)
removeFromSourceContact
in interface HasSourceContact
public int compareTo(java.lang.Object o)
compareTo
in interface java.lang.Comparable
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |