|
||||||||||
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.Description.Description
public class Description
A free text description of an object.
Nested Class Summary |
---|
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDatabaseReferences |
---|
HasDatabaseReferences.DatabaseReferences_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBibliographicReferences |
---|
HasBibliographicReferences.BibliographicReferences_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAnnotations |
---|
HasAnnotations.Annotations_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 |
annotations
Allows specification of ontology entries related to the instance being described. |
protected java.util.List |
bibliographicReferences
References to existing literature. |
protected java.util.List |
databaseReferences
References to entries in databases. |
protected ExternalReference |
externalReference
Specifies where the described instance was originally obtained from. |
Fields inherited from class org.biomage.Common.Describable |
---|
security |
Fields inherited from class org.biomage.Common.Extendable |
---|
editable, id, securedElementId |
Constructor Summary | |
---|---|
Description()
Default constructor. |
|
Description(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
---|---|
void |
addToAnnotations(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Annotations_list |
void |
addToAnnotations(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Annotations_list |
void |
addToBibliographicReferences(BibliographicReference bibliographicReference)
Method to add BibliographicReference to BibliographicReferences_list |
void |
addToBibliographicReferences(int position,
BibliographicReference bibliographicReference)
Method to add BibliographicReference at position to BibliographicReferences_list |
void |
addToDatabaseReferences(DatabaseEntry databaseEntry)
Method to add DatabaseEntry to DatabaseReferences_list |
void |
addToDatabaseReferences(int position,
DatabaseEntry databaseEntry)
Method to add DatabaseEntry at position to DatabaseReferences_list |
boolean |
emptyMAGEobject()
|
HasAnnotations.Annotations_list |
getAnnotations()
Get method for annotations |
HasBibliographicReferences.BibliographicReferences_list |
getBibliographicReferences()
Get method for bibliographicReferences |
HasDatabaseReferences.DatabaseReferences_list |
getDatabaseReferences()
Get method for databaseReferences |
ExternalReference |
getExternalReference()
Get method for externalReference |
OntologyEntry |
getFromAnnotations(int position)
Method to get OntologyEntry from Annotations_list |
BibliographicReference |
getFromBibliographicReferences(int position)
Method to get BibliographicReference from BibliographicReferences_list |
DatabaseEntry |
getFromDatabaseReferences(int position)
Method to get DatabaseEntry from DatabaseReferences_list |
java.lang.String |
getModelClassName()
|
java.lang.String |
getText()
Get method for text |
java.lang.String |
getURI()
Get method for URI |
void |
removeElementAtFromAnnotations(int position)
Method to remove by position from Annotations_list |
void |
removeElementAtFromBibliographicReferences(int position)
Method to remove by position from BibliographicReferences_list |
void |
removeElementAtFromDatabaseReferences(int position)
Method to remove by position from DatabaseReferences_list |
void |
removeFromAnnotations(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Annotations_list |
void |
removeFromBibliographicReferences(BibliographicReference bibliographicReference)
Method to remove first BibliographicReference from BibliographicReferences_list |
void |
removeFromDatabaseReferences(DatabaseEntry databaseEntry)
Method to remove first DatabaseEntry from DatabaseReferences_list |
void |
setAnnotations(HasAnnotations.Annotations_list annotations)
Set method for annotations |
void |
setBibliographicReferences(HasBibliographicReferences.BibliographicReferences_list bibliographicReferences)
Set method for bibliographicReferences |
void |
setDatabaseReferences(HasDatabaseReferences.DatabaseReferences_list databaseReferences)
Set method for databaseReferences |
void |
setExternalReference(ExternalReference externalReference)
Set method for externalReference |
void |
setText(java.lang.String text)
Set method for text |
void |
setURI(java.lang.String URI)
Set method for URI |
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.Describable |
---|
addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAttributes, 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, toString |
Methods inherited from class java.lang.Object |
---|
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
---|
protected ExternalReference externalReference
protected java.util.List annotations
protected java.util.List databaseReferences
protected java.util.List bibliographicReferences
Constructor Detail |
---|
public Description()
public Description(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
---|
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Describable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Describable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Describable
java.io.IOException
public void setText(java.lang.String text)
value
- to setpublic java.lang.String getText()
public void setURI(java.lang.String URI)
value
- to setpublic java.lang.String getURI()
public java.lang.String getModelClassName()
getModelClassName
in class Describable
public void setExternalReference(ExternalReference externalReference)
setExternalReference
in interface HasExternalReference
value
- to setpublic ExternalReference getExternalReference()
getExternalReference
in interface HasExternalReference
public void setAnnotations(HasAnnotations.Annotations_list annotations)
setAnnotations
in interface HasAnnotations
value
- to setpublic HasAnnotations.Annotations_list getAnnotations()
getAnnotations
in interface HasAnnotations
public void addToAnnotations(OntologyEntry ontologyEntry)
addToAnnotations
in interface HasAnnotations
public void addToAnnotations(int position, OntologyEntry ontologyEntry)
addToAnnotations
in interface HasAnnotations
public OntologyEntry getFromAnnotations(int position)
getFromAnnotations
in interface HasAnnotations
public void removeElementAtFromAnnotations(int position)
removeElementAtFromAnnotations
in interface HasAnnotations
public void removeFromAnnotations(OntologyEntry ontologyEntry)
removeFromAnnotations
in interface HasAnnotations
public void setDatabaseReferences(HasDatabaseReferences.DatabaseReferences_list databaseReferences)
setDatabaseReferences
in interface HasDatabaseReferences
value
- to setpublic HasDatabaseReferences.DatabaseReferences_list getDatabaseReferences()
getDatabaseReferences
in interface HasDatabaseReferences
public void addToDatabaseReferences(DatabaseEntry databaseEntry)
addToDatabaseReferences
in interface HasDatabaseReferences
public void addToDatabaseReferences(int position, DatabaseEntry databaseEntry)
addToDatabaseReferences
in interface HasDatabaseReferences
public DatabaseEntry getFromDatabaseReferences(int position)
getFromDatabaseReferences
in interface HasDatabaseReferences
public void removeElementAtFromDatabaseReferences(int position)
removeElementAtFromDatabaseReferences
in interface HasDatabaseReferences
public void removeFromDatabaseReferences(DatabaseEntry databaseEntry)
removeFromDatabaseReferences
in interface HasDatabaseReferences
public void setBibliographicReferences(HasBibliographicReferences.BibliographicReferences_list bibliographicReferences)
setBibliographicReferences
in interface HasBibliographicReferences
value
- to setpublic HasBibliographicReferences.BibliographicReferences_list getBibliographicReferences()
getBibliographicReferences
in interface HasBibliographicReferences
public void addToBibliographicReferences(BibliographicReference bibliographicReference)
addToBibliographicReferences
in interface HasBibliographicReferences
public void addToBibliographicReferences(int position, BibliographicReference bibliographicReference)
addToBibliographicReferences
in interface HasBibliographicReferences
public BibliographicReference getFromBibliographicReferences(int position)
getFromBibliographicReferences
in interface HasBibliographicReferences
public void removeElementAtFromBibliographicReferences(int position)
removeElementAtFromBibliographicReferences
in interface HasBibliographicReferences
public void removeFromBibliographicReferences(BibliographicReference bibliographicReference)
removeFromBibliographicReferences
in interface HasBibliographicReferences
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |