org.biomage.BQS
Class BibliographicReference

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.BQS.BibliographicReference

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasParameters, HasPropertySets, HasSecurity, java.io.Serializable

public class BibliographicReference

extends Describable

implements java.io.Serializable, 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 inherited from class org.biomage.Interface.HasParameters

HasParameters.Parameters_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected HasParameters.Parameters_list

parameters Criteria that can be used to look up the reference in a repository.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

BibliographicReference()
Default constructor.

BibliographicReference(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

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
java.lang.String	getAuthors() Get method for authors
java.lang.String	getEditor() Get method for editor
OntologyEntry	getFromParameters(int position) Method to get OntologyEntry from Parameters_list
java.lang.String	getIssue() Get method for issue
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	removeElementAtFromParameters(int position) Method to remove by position from Parameters_list
void	removeFromParameters(OntologyEntry ontologyEntry) Method to remove first OntologyEntry from Parameters_list
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, 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

parameters

protected HasParameters.Parameters_list parameters

Criteria that can be used to look up the reference in a repository.

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

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

java.io.IOException

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

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

java.io.IOException

setTitle

public void setTitle(java.lang.String title)

Set method for title

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

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

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

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

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

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

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

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

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

getURI

public java.lang.String getURI()

Get method for URI

Returns:

value of the attribute

setParameters

public void setParameters(HasParameters.Parameters_list parameters)

Set method for parameters

Specified by:

setParameters in interface HasParameters

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