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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.BQS.BibliographicReference
public class BibliographicReference
Attributes for the most common criteria and association with OntologyEntry allows criteria to be specified for searching for a Bibliographic reference.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasAccessions |
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HasAccessions.Accessions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasParameters |
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HasParameters.Parameters_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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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 |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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BibliographicReference()
Default constructor. |
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BibliographicReference(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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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 |
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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 |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId, toString |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected java.util.List parameters
protected java.util.List accessions
Constructor Detail |
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public BibliographicReference()
public BibliographicReference(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Describable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Describable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Describable
java.io.IOException
public void setTitle(java.lang.String title)
value
- to setpublic java.lang.String getTitle()
public void setAuthors(java.lang.String authors)
value
- to setpublic java.lang.String getAuthors()
public void setPublication(java.lang.String publication)
value
- to setpublic java.lang.String getPublication()
public void setPublisher(java.lang.String publisher)
value
- to setpublic java.lang.String getPublisher()
public void setEditor(java.lang.String editor)
value
- to setpublic java.lang.String getEditor()
public void setYear(java.util.Date year)
value
- to setpublic java.util.Date getYear()
public void setVolume(java.lang.String volume)
value
- to setpublic java.lang.String getVolume()
public void setIssue(java.lang.String issue)
value
- to setpublic java.lang.String getIssue()
public void setPages(java.lang.String pages)
value
- to setpublic java.lang.String getPages()
public void setURI(java.lang.String URI)
value
- to setpublic java.lang.String getURI()
public java.lang.String getModelClassName()
getModelClassName
in class Describable
public void setParameters(HasParameters.Parameters_list parameters)
setParameters
in interface HasParameters
value
- to setpublic HasParameters.Parameters_list getParameters()
getParameters
in interface HasParameters
public void addToParameters(OntologyEntry ontologyEntry)
addToParameters
in interface HasParameters
public void addToParameters(int position, OntologyEntry ontologyEntry)
addToParameters
in interface HasParameters
public OntologyEntry getFromParameters(int position)
getFromParameters
in interface HasParameters
public void removeElementAtFromParameters(int position)
removeElementAtFromParameters
in interface HasParameters
public void removeFromParameters(OntologyEntry ontologyEntry)
removeFromParameters
in interface HasParameters
public void setAccessions(HasAccessions.Accessions_list accessions)
setAccessions
in interface HasAccessions
value
- to setpublic HasAccessions.Accessions_list getAccessions()
getAccessions
in interface HasAccessions
public void addToAccessions(DatabaseEntry databaseEntry)
addToAccessions
in interface HasAccessions
public void addToAccessions(int position, DatabaseEntry databaseEntry)
addToAccessions
in interface HasAccessions
public DatabaseEntry getFromAccessions(int position)
getFromAccessions
in interface HasAccessions
public void removeElementAtFromAccessions(int position)
removeElementAtFromAccessions
in interface HasAccessions
public void removeFromAccessions(DatabaseEntry databaseEntry)
removeFromAccessions
in interface HasAccessions
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