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.
|
SBMLSingle(de.unirostock.sems.xmlutils.ds.TreeDocument td)
Instantiates a new object.
|
Modifier and Type | Method and Description |
---|---|
String |
flatten() |
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, IOException, org.jdom2.JDOMException, BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
file
- the file containing the modelde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionIOException
- Signals that an I/O exception has occurred.org.jdom2.JDOMException
- the jDOM exceptionBivesSBMLParseException
- the bives sbml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionpublic SBMLSingle(String xml) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, IOException, org.jdom2.JDOMException, BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
xml
- the encoded the modelde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionIOException
- Signals that an I/O exception has occurred.org.jdom2.JDOMException
- the jDOM exceptionBivesSBMLParseException
- the bives sbml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionpublic SBMLSingle(de.unirostock.sems.xmlutils.ds.TreeDocument td) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, IOException, org.jdom2.JDOMException, BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
td
- the tree documentde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionIOException
- Signals that an I/O exception has occurred.org.jdom2.JDOMException
- the jDOM exceptionBivesCellMLParseException
- the bives cell ml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionBivesLogicalException
- the bives logical exceptionBivesImportException
- the bives import exceptionURISyntaxException
- the uRI syntax exceptionBivesSBMLParseException
public SBMLSingle(SBMLDocument doc)
doc
- the documentpublic String getCRNGraphML()
getCRNGraphML
in class de.unirostock.sems.bives.api.Single
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) throws de.unirostock.sems.bives.exception.BivesUnsupportedException
getHierarchyGraph
in class de.unirostock.sems.bives.api.Single
de.unirostock.sems.bives.exception.BivesUnsupportedException
public String getHierarchyGraphML() throws de.unirostock.sems.bives.exception.BivesUnsupportedException
getHierarchyGraphML
in class de.unirostock.sems.bives.api.Single
de.unirostock.sems.bives.exception.BivesUnsupportedException
public String getHierarchyDotGraph() throws de.unirostock.sems.bives.exception.BivesUnsupportedException
getHierarchyDotGraph
in class de.unirostock.sems.bives.api.Single
de.unirostock.sems.bives.exception.BivesUnsupportedException
public String getHierarchyJsonGraph() throws de.unirostock.sems.bives.exception.BivesUnsupportedException
getHierarchyJsonGraph
in class de.unirostock.sems.bives.api.Single
de.unirostock.sems.bives.exception.BivesUnsupportedException
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