Docjar: A Java Source and Docuemnt Enginecom.*    java.*    javax.*    org.*    all    new    plug-in

Quick Search    Search Deep

org.biomage.BQS
Class BibliographicReference  view BibliographicReference download BibliographicReference.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.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

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.


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

authors

java.lang.String authors

publication

java.lang.String publication

publisher

java.lang.String publisher

editor

java.lang.String editor

year

java.util.Date year

volume

java.lang.String volume

issue

java.lang.String issue

pages

java.lang.String pages

URI

java.lang.String URI

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.


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.


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.


setTitle

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


getTitle

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


setAuthors

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


getAuthors

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


setPublication

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


getPublication

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


setPublisher

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


getPublisher

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


setEditor

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


getEditor

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


setYear

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


getYear

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


setVolume

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


getVolume

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


setIssue

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


getIssue

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


setPages

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


getPages

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


setURI

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


getURI

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


setParameters

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

Specified by:
setParameters in interface org.biomage.Interface.HasParameters

getParameters

public org.biomage.Interface.HasParameters.Parameters_list getParameters()
Get method for parameters

Specified by:
getParameters in interface org.biomage.Interface.HasParameters

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

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

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

removeElementAtFromParameters

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

Specified by:
removeElementAtFromParameters in interface org.biomage.Interface.HasParameters

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