org.biomage.BQS
Class BibliographicReference

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.BQS.BibliographicReference
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAccessions, HasAuditTrail, HasDescriptions, HasParameters, HasPropertySets, HasSecurity

public class BibliographicReference
extends Describable
implements java.io.Serializable, HasAccessions, HasParameters

Attributes for the most common criteria and association with OntologyEntry allows criteria to be specified for searching for a Bibliographic reference.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAccessions
HasAccessions.Accessions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasParameters
HasParameters.Parameters_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 accessions
          References in publications, eg Medline and PubMed, for this BibliographicReference.
protected  java.util.List parameters
          Criteria that can be used to look up the reference in a repository.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BibliographicReference()
          Default constructor.
BibliographicReference(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToAccessions(DatabaseEntry databaseEntry)
          Method to add DatabaseEntry to Accessions_list
 void addToAccessions(int position, DatabaseEntry databaseEntry)
          Method to add DatabaseEntry at position to Accessions_list
 void addToParameters(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Parameters_list
 void addToParameters(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Parameters_list
 boolean emptyMAGEobject()
           
 HasAccessions.Accessions_list getAccessions()
          Get method for accessions
 java.lang.String getAuthors()
          Get method for authors
 java.lang.String getEditor()
          Get method for editor
 DatabaseEntry getFromAccessions(int position)
          Method to get DatabaseEntry from Accessions_list
 OntologyEntry getFromParameters(int position)
          Method to get OntologyEntry from Parameters_list
 java.lang.String getIssue()
          Get method for issue
 java.lang.String getModelClassName()
           
 java.lang.String getPages()
          Get method for pages
 HasParameters.Parameters_list getParameters()
          Get method for parameters
 java.lang.String getPublication()
          Get method for publication
 java.lang.String getPublisher()
          Get method for publisher
 java.lang.String getTitle()
          Get method for title
 java.lang.String getURI()
          Get method for URI
 java.lang.String getVolume()
          Get method for volume
 java.util.Date getYear()
          Get method for year
 void removeElementAtFromAccessions(int position)
          Method to remove by position from Accessions_list
 void removeElementAtFromParameters(int position)
          Method to remove by position from Parameters_list
 void removeFromAccessions(DatabaseEntry databaseEntry)
          Method to remove first DatabaseEntry from Accessions_list
 void removeFromParameters(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Parameters_list
 void setAccessions(HasAccessions.Accessions_list accessions)
          Set method for accessions
 void setAuthors(java.lang.String authors)
          Set method for authors
 void setEditor(java.lang.String editor)
          Set method for editor
 void setIssue(java.lang.String issue)
          Set method for issue
 void setPages(java.lang.String pages)
          Set method for pages
 void setParameters(HasParameters.Parameters_list parameters)
          Set method for parameters
 void setPublication(java.lang.String publication)
          Set method for publication
 void setPublisher(java.lang.String publisher)
          Set method for publisher
 void setTitle(java.lang.String title)
          Set method for title
 void setURI(java.lang.String URI)
          Set method for URI
 void setVolume(java.lang.String volume)
          Set method for volume
 void setYear(java.util.Date year)
          Set method for year
 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

parameters

protected java.util.List parameters
Criteria that can be used to look up the reference in a repository.


accessions

protected java.util.List accessions
References in publications, eg Medline and PubMed, for this BibliographicReference.

Constructor Detail

BibliographicReference

public BibliographicReference()
Default constructor.


BibliographicReference

public BibliographicReference(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

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 Describable
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 Describable
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 Describable
Throws:
java.io.IOException

setTitle

public void setTitle(java.lang.String title)
Set method for title

Parameters:
value - to set

getTitle

public java.lang.String getTitle()
Get method for title

Returns:
value of the attribute

setAuthors

public void setAuthors(java.lang.String authors)
Set method for authors

Parameters:
value - to set

getAuthors

public java.lang.String getAuthors()
Get method for authors

Returns:
value of the attribute

setPublication

public void setPublication(java.lang.String publication)
Set method for publication

Parameters:
value - to set

getPublication

public java.lang.String getPublication()
Get method for publication

Returns:
value of the attribute

setPublisher

public void setPublisher(java.lang.String publisher)
Set method for publisher

Parameters:
value - to set

getPublisher

public java.lang.String getPublisher()
Get method for publisher

Returns:
value of the attribute

setEditor

public void setEditor(java.lang.String editor)
Set method for editor

Parameters:
value - to set

getEditor

public java.lang.String getEditor()
Get method for editor

Returns:
value of the attribute

setYear

public void setYear(java.util.Date year)
Set method for year

Parameters:
value - to set

getYear

public java.util.Date getYear()
Get method for year

Returns:
value of the attribute

setVolume

public void setVolume(java.lang.String volume)
Set method for volume

Parameters:
value - to set

getVolume

public java.lang.String getVolume()
Get method for volume

Returns:
value of the attribute

setIssue

public void setIssue(java.lang.String issue)
Set method for issue

Parameters:
value - to set

getIssue

public java.lang.String getIssue()
Get method for issue

Returns:
value of the attribute

setPages

public void setPages(java.lang.String pages)
Set method for pages

Parameters:
value - to set

getPages

public java.lang.String getPages()
Get method for pages

Returns:
value of the attribute

setURI

public void setURI(java.lang.String URI)
Set method for URI

Parameters:
value - to set

getURI

public java.lang.String getURI()
Get method for URI

Returns:
value of the attribute

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Describable

setParameters

public void setParameters(HasParameters.Parameters_list parameters)
Set method for parameters

Specified by:
setParameters in interface HasParameters
Parameters:
value - to set

getParameters

public HasParameters.Parameters_list getParameters()
Get method for parameters

Specified by:
getParameters in interface HasParameters
Returns:
value of the attribute

addToParameters

public void addToParameters(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Parameters_list

Specified by:
addToParameters in interface HasParameters

addToParameters

public void addToParameters(int position,
                            OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Parameters_list

Specified by:
addToParameters in interface HasParameters

getFromParameters

public OntologyEntry getFromParameters(int position)
Method to get OntologyEntry from Parameters_list

Specified by:
getFromParameters in interface HasParameters

removeElementAtFromParameters

public void removeElementAtFromParameters(int position)
Method to remove by position from Parameters_list

Specified by:
removeElementAtFromParameters in interface HasParameters

removeFromParameters

public void removeFromParameters(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Parameters_list

Specified by:
removeFromParameters in interface HasParameters

setAccessions

public void setAccessions(HasAccessions.Accessions_list accessions)
Set method for accessions

Specified by:
setAccessions in interface HasAccessions
Parameters:
value - to set

getAccessions

public HasAccessions.Accessions_list getAccessions()
Get method for accessions

Specified by:
getAccessions in interface HasAccessions
Returns:
value of the attribute

addToAccessions

public void addToAccessions(DatabaseEntry databaseEntry)
Method to add DatabaseEntry to Accessions_list

Specified by:
addToAccessions in interface HasAccessions

addToAccessions

public void addToAccessions(int position,
                            DatabaseEntry databaseEntry)
Method to add DatabaseEntry at position to Accessions_list

Specified by:
addToAccessions in interface HasAccessions

getFromAccessions

public DatabaseEntry getFromAccessions(int position)
Method to get DatabaseEntry from Accessions_list

Specified by:
getFromAccessions in interface HasAccessions

removeElementAtFromAccessions

public void removeElementAtFromAccessions(int position)
Method to remove by position from Accessions_list

Specified by:
removeElementAtFromAccessions in interface HasAccessions

removeFromAccessions

public void removeFromAccessions(DatabaseEntry databaseEntry)
Method to remove first DatabaseEntry from Accessions_list

Specified by:
removeFromAccessions in interface HasAccessions