public class SBMLSingle
extends de.unirostock.sems.bives.api.Single
Modifier and Type | Field and Description |
---|---|
protected SBMLDocument |
doc
The doc.
|
protected SBMLGraphProducer |
graphProducer
The graph producer.
|
Constructor and Description |
---|
SBMLSingle(File file)
Instantiates a new object to study single SBML documents.
|
SBMLSingle(SBMLDocument doc)
Instantiates a new object to study single SBML documents.
|
SBMLSingle(String xml)
Instantiates a new object to study single SBML documents.
|
Modifier and Type | Method and Description |
---|---|
String |
getCRNDotGraph() |
Object |
getCRNGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt) |
String |
getCRNGraphML() |
String |
getCRNJsonGraph() |
String |
getHierarchyDotGraph() |
Object |
getHierarchyGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt) |
String |
getHierarchyGraphML() |
String |
getHierarchyJsonGraph() |
protected SBMLDocument doc
protected SBMLGraphProducer graphProducer
public SBMLSingle(File file) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, FileNotFoundException, ParserConfigurationException, SAXException, IOException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException, BivesSBMLParseException
file
- the file containing the modelde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionFileNotFoundException
- the file not found exceptionParserConfigurationException
- the parser configuration exceptionSAXException
- the sAX exceptionIOException
- Signals that an I/O exception has occurred.de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionBivesSBMLParseException
- the bives sbml parse exceptionpublic SBMLSingle(String xml) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, FileNotFoundException, ParserConfigurationException, SAXException, IOException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException, BivesSBMLParseException
xml
- the encoded the modelde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionFileNotFoundException
- the file not found exceptionParserConfigurationException
- the parser configuration exceptionSAXException
- the sAX exceptionIOException
- Signals that an I/O exception has occurred.de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionBivesSBMLParseException
- the bives sbml parse exceptionpublic SBMLSingle(SBMLDocument doc) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, FileNotFoundException, ParserConfigurationException, SAXException, IOException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
doc
- the documentde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionFileNotFoundException
- the file not found exceptionParserConfigurationException
- the parser configuration exceptionSAXException
- the sAX exceptionIOException
- Signals that an I/O exception has occurred.de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionpublic String getCRNGraphML() throws ParserConfigurationException
getCRNGraphML
in class de.unirostock.sems.bives.api.Single
ParserConfigurationException
public Object getCRNGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt) throws Exception
getCRNGraph
in class de.unirostock.sems.bives.api.Single
Exception
public String getCRNDotGraph()
getCRNDotGraph
in class de.unirostock.sems.bives.api.Single
public String getCRNJsonGraph()
getCRNJsonGraph
in class de.unirostock.sems.bives.api.Single
public Object getHierarchyGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
getHierarchyGraph
in class de.unirostock.sems.bives.api.Single
public String getHierarchyGraphML() throws ParserConfigurationException
getHierarchyGraphML
in class de.unirostock.sems.bives.api.Single
ParserConfigurationException
public String getHierarchyDotGraph()
getHierarchyDotGraph
in class de.unirostock.sems.bives.api.Single
public String getHierarchyJsonGraph()
getHierarchyJsonGraph
in class de.unirostock.sems.bives.api.Single
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