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SUMMARY: JavaDoc of org.biomage.Description.Description JAVADOC | Sourc code of org.biomage.Description.Description SOURCE | Download org.biomage.Description.Description DOWNLOAD | NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD

org.biomage.Description
Class Description  view Description download Description.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Description.Description
All Implemented Interfaces:
org.biomage.Interface.HasAnnotations, org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBibliographicReferences, org.biomage.Interface.HasDatabaseReferences, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasExternalReference, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable
public class Description
extends org.biomage.Common.Describable
implements java.io.Serializable, org.biomage.Interface.HasDatabaseReferences, org.biomage.Interface.HasBibliographicReferences, org.biomage.Interface.HasExternalReference, org.biomage.Interface.HasAnnotations

A free text description of an object.

Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasDatabaseReferences
org.biomage.Interface.HasDatabaseReferences.DatabaseReferences_list
 
Nested classes inherited from class org.biomage.Interface.HasBibliographicReferences
org.biomage.Interface.HasBibliographicReferences.BibliographicReferences_list
 
Nested classes inherited from class org.biomage.Interface.HasAnnotations
org.biomage.Interface.HasAnnotations.Annotations_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.Interface.HasAnnotations.Annotations_list annotations
          Allows specification of ontology entries related to the instance being described.
private  org.biomage.Interface.HasBibliographicReferences.BibliographicReferences_list bibliographicReferences
          References to existing literature.
private  org.biomage.Interface.HasDatabaseReferences.DatabaseReferences_list databaseReferences
          References to entries in databases.
private  ExternalReference externalReference
          Specifies where the described instance was originally obtained from.
(package private)  java.lang.String text
          The description.
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
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(org.biomage.BQS.BibliographicReference bibliographicReference)
          Method to add BibliographicReference to BibliographicReferences_list
 void addToBibliographicReferences(int position, org.biomage.BQS.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
 org.biomage.Interface.HasAnnotations.Annotations_list getAnnotations()
          Get method for annotations
 org.biomage.Interface.HasBibliographicReferences.BibliographicReferences_list getBibliographicReferences()
          Get method for bibliographicReferences
 org.biomage.Interface.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
 org.biomage.BQS.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 getText()
          Get method for text
 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(org.biomage.BQS.BibliographicReference bibliographicReference)
          Method to remove first BibliographicReference from BibliographicReferences_list
 void removeFromDatabaseReferences(DatabaseEntry databaseEntry)
          Method to remove first DatabaseEntry from DatabaseReferences_list
 void setAnnotations(org.biomage.Interface.HasAnnotations.Annotations_list annotations)
          Set method for annotations
 void setBibliographicReferences(org.biomage.Interface.HasBibliographicReferences.BibliographicReferences_list bibliographicReferences)
          Set method for bibliographicReferences
 void setDatabaseReferences(org.biomage.Interface.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 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.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

text

java.lang.String text
The description.

databaseReferences

private org.biomage.Interface.HasDatabaseReferences.DatabaseReferences_list databaseReferences
References to entries in databases.

bibliographicReferences

private org.biomage.Interface.HasBibliographicReferences.BibliographicReferences_list bibliographicReferences
References to existing literature.

externalReference

private ExternalReference externalReference
Specifies where the described instance was originally obtained from.

annotations

private org.biomage.Interface.HasAnnotations.Annotations_list annotations
Allows specification of ontology entries related to the instance being described.

Constructor Detail

Description

public Description()
Default constructor.

Description

public Description(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.

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.

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.

setText

public void setText(java.lang.String text)
Set method for text

getText

public java.lang.String getText()
Get method for text

setDatabaseReferences

public void setDatabaseReferences(org.biomage.Interface.HasDatabaseReferences.DatabaseReferences_list databaseReferences)
Set method for databaseReferences

Specified by:
setDatabaseReferences in interface org.biomage.Interface.HasDatabaseReferences

getDatabaseReferences

public org.biomage.Interface.HasDatabaseReferences.DatabaseReferences_list getDatabaseReferences()
Get method for databaseReferences

Specified by:
getDatabaseReferences in interface org.biomage.Interface.HasDatabaseReferences

addToDatabaseReferences

public void addToDatabaseReferences(DatabaseEntry databaseEntry)
Method to add DatabaseEntry to DatabaseReferences_list

Specified by:
addToDatabaseReferences in interface org.biomage.Interface.HasDatabaseReferences

addToDatabaseReferences

public void addToDatabaseReferences(int position,
                                    DatabaseEntry databaseEntry)
Method to add DatabaseEntry at position to DatabaseReferences_list

Specified by:
addToDatabaseReferences in interface org.biomage.Interface.HasDatabaseReferences

getFromDatabaseReferences

public DatabaseEntry getFromDatabaseReferences(int position)
Method to get DatabaseEntry from DatabaseReferences_list

Specified by:
getFromDatabaseReferences in interface org.biomage.Interface.HasDatabaseReferences

removeElementAtFromDatabaseReferences

public void removeElementAtFromDatabaseReferences(int position)
Method to remove by position from DatabaseReferences_list

Specified by:
removeElementAtFromDatabaseReferences in interface org.biomage.Interface.HasDatabaseReferences

removeFromDatabaseReferences

public void removeFromDatabaseReferences(DatabaseEntry databaseEntry)
Method to remove first DatabaseEntry from DatabaseReferences_list

Specified by:
removeFromDatabaseReferences in interface org.biomage.Interface.HasDatabaseReferences

setBibliographicReferences

public void setBibliographicReferences(org.biomage.Interface.HasBibliographicReferences.BibliographicReferences_list bibliographicReferences)
Set method for bibliographicReferences

Specified by:
setBibliographicReferences in interface org.biomage.Interface.HasBibliographicReferences

getBibliographicReferences

public org.biomage.Interface.HasBibliographicReferences.BibliographicReferences_list getBibliographicReferences()
Get method for bibliographicReferences

Specified by:
getBibliographicReferences in interface org.biomage.Interface.HasBibliographicReferences

addToBibliographicReferences

public void addToBibliographicReferences(org.biomage.BQS.BibliographicReference bibliographicReference)
Method to add BibliographicReference to BibliographicReferences_list

Specified by:
addToBibliographicReferences in interface org.biomage.Interface.HasBibliographicReferences

addToBibliographicReferences

public void addToBibliographicReferences(int position,
                                         org.biomage.BQS.BibliographicReference bibliographicReference)
Method to add BibliographicReference at position to BibliographicReferences_list

Specified by:
addToBibliographicReferences in interface org.biomage.Interface.HasBibliographicReferences

getFromBibliographicReferences

public org.biomage.BQS.BibliographicReference getFromBibliographicReferences(int position)
Method to get BibliographicReference from BibliographicReferences_list

Specified by:
getFromBibliographicReferences in interface org.biomage.Interface.HasBibliographicReferences

removeElementAtFromBibliographicReferences

public void removeElementAtFromBibliographicReferences(int position)
Method to remove by position from BibliographicReferences_list

Specified by:
removeElementAtFromBibliographicReferences in interface org.biomage.Interface.HasBibliographicReferences

removeFromBibliographicReferences

public void removeFromBibliographicReferences(org.biomage.BQS.BibliographicReference bibliographicReference)
Method to remove first BibliographicReference from BibliographicReferences_list

Specified by:
removeFromBibliographicReferences in interface org.biomage.Interface.HasBibliographicReferences

setExternalReference

public void setExternalReference(ExternalReference externalReference)
Set method for externalReference

Specified by:
setExternalReference in interface org.biomage.Interface.HasExternalReference

getExternalReference

public ExternalReference getExternalReference()
Get method for externalReference

Specified by:
getExternalReference in interface org.biomage.Interface.HasExternalReference

setAnnotations

public void setAnnotations(org.biomage.Interface.HasAnnotations.Annotations_list annotations)
Set method for annotations

Specified by:
setAnnotations in interface org.biomage.Interface.HasAnnotations

getAnnotations

public org.biomage.Interface.HasAnnotations.Annotations_list getAnnotations()
Get method for annotations

Specified by:
getAnnotations in interface org.biomage.Interface.HasAnnotations

addToAnnotations

public void addToAnnotations(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Annotations_list

Specified by:
addToAnnotations in interface org.biomage.Interface.HasAnnotations

addToAnnotations

public void addToAnnotations(int position,
                             OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Annotations_list

Specified by:
addToAnnotations in interface org.biomage.Interface.HasAnnotations

getFromAnnotations

public OntologyEntry getFromAnnotations(int position)
Method to get OntologyEntry from Annotations_list

Specified by:
getFromAnnotations in interface org.biomage.Interface.HasAnnotations

removeElementAtFromAnnotations

public void removeElementAtFromAnnotations(int position)
Method to remove by position from Annotations_list

Specified by:
removeElementAtFromAnnotations in interface org.biomage.Interface.HasAnnotations

removeFromAnnotations

public void removeFromAnnotations(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Annotations_list

Specified by:
removeFromAnnotations in interface org.biomage.Interface.HasAnnotations
Overview  Package   Class  Use  Deprecated  Index 
Home >> All >> org >> biomage >> [ Description overview ]  PREV CLASS  NEXT CLASS
SUMMARY: JavaDoc of org.biomage.Description.Description JAVADOC | Sourc code of org.biomage.Description.Description SOURCE | Download org.biomage.Description.Description DOWNLOAD | NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD