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java.lang.Objectorg.biojava.utils.AbstractChangeable
cytoscape.data.ontology.Ontology
public class Ontology
General Ontology class which implements
This class representes a general and simple ontology class. This
implementation uses
CyNetwork and CyAttributes for its actual data storage.
org.biojava.ontology
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava.ontology.Ontology |
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org.biojava.ontology.Ontology.Impl |
Field Summary | |
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static String |
IS_ONTOLOGY
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Fields inherited from interface org.biojava.ontology.Ontology |
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TERM, TRIPLE |
Constructor Summary | |
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Ontology(String name)
Constructor. |
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Ontology(String name,
String curator,
String description,
CyNetwork dag)
Constructor. |
Method Summary | |
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void |
add(OntologyTerm newTerm)
Add a new ontology term to the DAG. |
boolean |
containsTerm(String id)
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boolean |
containsTriple(org.biojava.ontology.Term subject,
org.biojava.ontology.Term object,
org.biojava.ontology.Term predicate)
See if a triple exists in this ontology. |
org.biojava.ontology.Term |
createTerm(String name,
String description)
Create a new term in this ontology. |
org.biojava.ontology.Term |
createTerm(String arg0,
String arg1,
Object[] arg2)
DOCUMENT ME! |
org.biojava.ontology.Triple |
createTriple(org.biojava.ontology.Term subject,
org.biojava.ontology.Term object,
org.biojava.ontology.Term predicate,
String name,
String description)
DOCUMENT ME! |
org.biojava.ontology.Variable |
createVariable(String arg0,
String arg1)
DOCUMENT ME! |
void |
deleteTerm(org.biojava.ontology.Term arg0)
Delete a term from DAG (CyNetwork) |
String |
getCurator()
|
String |
getDescription()
DOCUMENT ME! |
String |
getName()
Returns name (actually, an ID). |
org.biojava.ontology.OntologyOps |
getOps()
DOCUMENT ME! |
OntologyTerm |
getTerm(String id)
Fetch the term with the specified name. |
Set |
getTerms()
Return all the terms in this ontology. |
Set |
getTriples(org.biojava.ontology.Term arg0,
org.biojava.ontology.Term arg1,
org.biojava.ontology.Term arg2)
returns set of Triples. |
org.biojava.ontology.Term |
importTerm(org.biojava.ontology.Term arg0,
String arg1)
DOCUMENT ME! |
int |
size()
|
String |
toString()
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Methods inherited from class org.biojava.utils.AbstractChangeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
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public static final String IS_ONTOLOGY
Constructor Detail |
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public Ontology(String name)
Creates null network for this ontology.
name
- Name of this ontology. Will be used as ID.
URISyntaxException
public Ontology(String name, String curator, String description, CyNetwork dag)
Takes CyNetwork as its DAG.
name
- curator
- description
- dag
-
URISyntaxException
URISyntaxException
Method Detail |
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public String getName()
getName
in interface org.biojava.ontology.Ontology
public String getCurator()
public void add(OntologyTerm newTerm)
newTerm
- public int size()
public Set getTerms()
getTerms
in interface org.biojava.ontology.Ontology
public boolean containsTerm(String id)
containsTerm
in interface org.biojava.ontology.Ontology
public OntologyTerm getTerm(String id)
getTerm
in interface org.biojava.ontology.Ontology
name
NoSuchElementException
- if no term exists with that namepublic String toString()
toString
in class Object
public boolean containsTriple(org.biojava.ontology.Term subject, org.biojava.ontology.Term object, org.biojava.ontology.Term predicate)
containsTriple
in interface org.biojava.ontology.Ontology
public org.biojava.ontology.Term createTerm(String name, String description) throws org.biojava.ontology.AlreadyExistsException, org.biojava.utils.ChangeVetoException, IllegalArgumentException
createTerm
in interface org.biojava.ontology.Ontology
org.biojava.ontology.AlreadyExistsException
org.biojava.utils.ChangeVetoException
IllegalArgumentException
public org.biojava.ontology.Term createTerm(String arg0, String arg1, Object[] arg2) throws org.biojava.ontology.AlreadyExistsException, org.biojava.utils.ChangeVetoException, IllegalArgumentException
createTerm
in interface org.biojava.ontology.Ontology
arg0
- DOCUMENT ME!arg1
- DOCUMENT ME!arg2
- DOCUMENT ME!
org.biojava.ontology.AlreadyExistsException
- DOCUMENT ME!
org.biojava.utils.ChangeVetoException
- DOCUMENT ME!
IllegalArgumentException
- DOCUMENT ME!public org.biojava.ontology.Triple createTriple(org.biojava.ontology.Term subject, org.biojava.ontology.Term object, org.biojava.ontology.Term predicate, String name, String description) throws org.biojava.ontology.AlreadyExistsException, org.biojava.utils.ChangeVetoException
createTriple
in interface org.biojava.ontology.Ontology
subject
- DOCUMENT ME!object
- DOCUMENT ME!predicate
- DOCUMENT ME!name
- DOCUMENT ME!description
- DOCUMENT ME!
org.biojava.ontology.AlreadyExistsException
- DOCUMENT ME!
org.biojava.utils.ChangeVetoException
- DOCUMENT ME!public org.biojava.ontology.Variable createVariable(String arg0, String arg1) throws org.biojava.ontology.AlreadyExistsException, org.biojava.utils.ChangeVetoException, IllegalArgumentException
createVariable
in interface org.biojava.ontology.Ontology
arg0
- DOCUMENT ME!arg1
- DOCUMENT ME!
org.biojava.ontology.AlreadyExistsException
- DOCUMENT ME!
org.biojava.utils.ChangeVetoException
- DOCUMENT ME!
IllegalArgumentException
- DOCUMENT ME!public void deleteTerm(org.biojava.ontology.Term arg0) throws org.biojava.utils.ChangeVetoException
deleteTerm
in interface org.biojava.ontology.Ontology
org.biojava.utils.ChangeVetoException
public String getDescription()
getDescription
in interface org.biojava.ontology.Ontology
public org.biojava.ontology.OntologyOps getOps()
getOps
in interface org.biojava.ontology.Ontology
public Set getTriples(org.biojava.ontology.Term arg0, org.biojava.ontology.Term arg1, org.biojava.ontology.Term arg2)
getTriples
in interface org.biojava.ontology.Ontology
public org.biojava.ontology.Term importTerm(org.biojava.ontology.Term arg0, String arg1) throws org.biojava.utils.ChangeVetoException, IllegalArgumentException
importTerm
in interface org.biojava.ontology.Ontology
arg0
- DOCUMENT ME!arg1
- DOCUMENT ME!
org.biojava.utils.ChangeVetoException
- DOCUMENT ME!
IllegalArgumentException
- DOCUMENT ME!
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