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org.biomage.BQS
Class BibliographicReference  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Common.Describable
          org.biomage.BQS.BibliographicReference

All Implemented Interfaces:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasParameters, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable

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public class BibliographicReference

extends org.biomage.Common.Describable

implements java.io.Serializable, org.biomage.Interface.HasParameters

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

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Nested Class Summary

 

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

org.biomage.Interface.HasParameters.Parameters_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
(package private)  java.lang.String	authors
(package private)  java.lang.String	editor
(package private)  java.lang.String	issue
(package private)  java.lang.String	pages
private  org.biomage.Interface.HasParameters.Parameters_list	parameters           Criteria that can be used to look up the reference in a repository.
(package private)  java.lang.String	publication
(package private)  java.lang.String	publisher
(package private)  java.lang.String	title
(package private)  java.lang.String	URI
(package private)  java.lang.String	volume
(package private)  java.util.Date	year

 

Fields inherited from class org.biomage.Common.Describable

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

BibliographicReference()           Default constructor.

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

 

Method Summary
void	addToParameters(int position, org.biomage.Description.OntologyEntry ontologyEntry)           Method to add OntologyEntry at position to Parameters_list
void	addToParameters(org.biomage.Description.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
org.biomage.Description.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
org.biomage.Interface.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(org.biomage.Description.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(org.biomage.Interface.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
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

title

java.lang.String title

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authors

java.lang.String authors

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publication

java.lang.String publication

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publisher

java.lang.String publisher

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editor

java.lang.String editor

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year

java.util.Date year

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volume

java.lang.String volume

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issue

java.lang.String issue

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pages

java.lang.String pages

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URI

java.lang.String URI

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parameters

private org.biomage.Interface.HasParameters.Parameters_list parameters

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

Constructor Detail

BibliographicReference

public BibliographicReference()

Default constructor.

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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.

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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.

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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.

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setTitle

public void setTitle(java.lang.String title)

Set method for title

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getTitle

public java.lang.String getTitle()

Get method for title

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setAuthors

public void setAuthors(java.lang.String authors)

Set method for authors

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getAuthors

public java.lang.String getAuthors()

Get method for authors

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setPublication

public void setPublication(java.lang.String publication)

Set method for publication

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getPublication

public java.lang.String getPublication()

Get method for publication

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setPublisher

public void setPublisher(java.lang.String publisher)

Set method for publisher

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getPublisher

public java.lang.String getPublisher()

Get method for publisher

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setEditor

public void setEditor(java.lang.String editor)

Set method for editor

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getEditor

public java.lang.String getEditor()

Get method for editor

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setYear

public void setYear(java.util.Date year)

Set method for year

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getYear

public java.util.Date getYear()

Get method for year

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setVolume

public void setVolume(java.lang.String volume)

Set method for volume

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getVolume

public java.lang.String getVolume()

Get method for volume

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setIssue

public void setIssue(java.lang.String issue)

Set method for issue

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getIssue

public java.lang.String getIssue()

Get method for issue

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setPages

public void setPages(java.lang.String pages)

Set method for pages

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getPages

public java.lang.String getPages()

Get method for pages

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setURI

public void setURI(java.lang.String URI)

Set method for URI

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getURI

public java.lang.String getURI()

Get method for URI

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setParameters

public void setParameters(org.biomage.Interface.HasParameters.Parameters_list parameters)

Set method for parameters

Specified by:

setParameters in interface org.biomage.Interface.HasParameters

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getParameters

public org.biomage.Interface.HasParameters.Parameters_list getParameters()

Get method for parameters

Specified by:

getParameters in interface org.biomage.Interface.HasParameters

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addToParameters

public void addToParameters(org.biomage.Description.OntologyEntry ontologyEntry)

Method to add OntologyEntry to Parameters_list

Specified by:

addToParameters in interface org.biomage.Interface.HasParameters

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addToParameters

public void addToParameters(int position,
                            org.biomage.Description.OntologyEntry ontologyEntry)

Method to add OntologyEntry at position to Parameters_list

Specified by:

addToParameters in interface org.biomage.Interface.HasParameters

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getFromParameters

public org.biomage.Description.OntologyEntry getFromParameters(int position)

Method to get OntologyEntry from Parameters_list

Specified by:

getFromParameters in interface org.biomage.Interface.HasParameters

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removeElementAtFromParameters

public void removeElementAtFromParameters(int position)

Method to remove by position from Parameters_list

Specified by:

removeElementAtFromParameters in interface org.biomage.Interface.HasParameters

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removeFromParameters

public void removeFromParameters(org.biomage.Description.OntologyEntry ontologyEntry)

Method to remove first OntologyEntry from Parameters_list

Specified by:

removeFromParameters in interface org.biomage.Interface.HasParameters

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BQS overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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