public class BioPAX
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
baseString |
static java.lang.String |
biopaxFileString
Standard BioPAX v.3 prefix
|
OntModel |
biopaxmodel
BioPAX OWL as com.hp.hpl.jena.ontology.OntModel
|
static java.lang.String |
biopaxString
Standard BioPAX v.3 prefix
|
static java.lang.String |
idName
Some identifier for this BioPAX
|
static java.lang.String |
importString
Standard BioPAX v.3 prefix
|
Model |
model
BioPAX OWL as com.hp.hpl.jena.rdf.Model
|
static java.lang.String |
namespaceFileString
Standard BioPAX v.3 prefix
|
static java.lang.String |
namespaceString
Standard BioPAX v.3 prefix
|
Ontology |
ontology
com.hp.hpl.jena.ontology.Ontology object
|
static java.lang.String[] |
reactionEdgeTypes |
static java.lang.String[] |
reactionNodeTypes |
Constructor and Description |
---|
BioPAX() |
BioPAX(java.lang.String _biopaxString,
java.lang.String _namespaceString,
java.lang.String _modelnamespaceString)
Non-standard constructor with some prefixes
|
Modifier and Type | Method and Description |
---|---|
ControlledVocabulary |
addGOTerm(java.lang.String id,
java.lang.String name)
Adds to OWL model an openControlledVocabulary term
|
CellularLocationVocabulary |
getCompartment(java.lang.String name) |
void |
loadBioPAX(java.io.InputStream is)
Loads BioPAX content from InputStream is
|
void |
loadBioPAX(java.lang.String fn)
Loads BioPAX content from file fn
|
void |
loadBioPAXFromString(java.lang.String text)
Loads BioPAX content from String
|
void |
makeCompartments()
Adds some standard compartments
|
static void |
printDump(Model model)
Prints the content of the BioPAX Model object as readable text
|
static void |
saveToFile(java.lang.String fileName,
Model model)
Save Model object to file
|
static void |
saveToFile(java.lang.String fileName,
OntModel model)
Save an OntModel object to file
|
public static java.lang.String[] reactionNodeTypes
public static java.lang.String[] reactionEdgeTypes
public static java.lang.String biopaxString
public static java.lang.String biopaxFileString
public static java.lang.String namespaceString
public static java.lang.String namespaceFileString
public static java.lang.String importString
public static java.lang.String baseString
public static java.lang.String idName
public OntModel biopaxmodel
public Model model
public Ontology ontology
public BioPAX()
public BioPAX(java.lang.String _biopaxString, java.lang.String _namespaceString, java.lang.String _modelnamespaceString)
_biopaxString
- _namespaceString
- _modelnamespaceString
- public static void saveToFile(java.lang.String fileName, OntModel model)
fileName
- model
- public static void saveToFile(java.lang.String fileName, Model model)
fileName
- model
- public static void printDump(Model model)
public ControlledVocabulary addGOTerm(java.lang.String id, java.lang.String name) throws java.lang.Exception
id
- is the GO idname
- is the standard name for this idjava.lang.Exception
public void makeCompartments()
public CellularLocationVocabulary getCompartment(java.lang.String name)
name
- public void loadBioPAX(java.lang.String fn) throws java.lang.Exception
fn
- java.lang.Exception
public void loadBioPAX(java.io.InputStream is) throws java.lang.Exception
input
- streamjava.lang.Exception
public void loadBioPAXFromString(java.lang.String text) throws java.lang.Exception
text
- java.lang.Exception