Class SBMLSingle
- java.lang.Object
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- de.unirostock.sems.bives.api.Single
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- de.unirostock.sems.bives.sbml.api.SBMLSingle
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public class SBMLSingle extends de.unirostock.sems.bives.api.Single
The Class SBMLSingle to study single SBML documents.- Author:
- Martin Scharm
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Field Summary
Fields Modifier and Type Field Description protected SBMLDocument
doc
The doc.protected SBMLGraphProducer
graphProducer
The graph producer.
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Constructor Summary
Constructors Constructor Description SBMLSingle(SBMLDocument doc)
Instantiates a new object to study single SBML documents.SBMLSingle(de.unirostock.sems.xmlutils.ds.TreeDocument td)
Instantiates a new object.SBMLSingle(File file)
Instantiates a new object to study single SBML documents.SBMLSingle(String xml)
Instantiates a new object to study single SBML documents.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
flatten()
String
getHierarchyDotGraph()
Object
getHierarchyGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
String
getHierarchyGraphML()
String
getHierarchyJsonGraph()
String
getReactionsDotGraph()
Object
getReactionsGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
String
getReactionsGraphML()
String
getReactionsJsonGraph()
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Field Detail
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doc
protected SBMLDocument doc
The doc.
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graphProducer
protected SBMLGraphProducer graphProducer
The graph producer.
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Constructor Detail
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SBMLSingle
public SBMLSingle(File file) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, IOException, org.jdom2.JDOMException, BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
Instantiates a new object to study single SBML documents.- Parameters:
file
- the file containing the model- Throws:
de.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 exception
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SBMLSingle
public SBMLSingle(String xml) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, IOException, org.jdom2.JDOMException, BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
Instantiates a new object to study single SBML documents.- Parameters:
xml
- the encoded the model- Throws:
de.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 exception
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SBMLSingle
public 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
Instantiates a new object.- Parameters:
td
- the tree document- Throws:
de.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 exception
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SBMLSingle
public SBMLSingle(SBMLDocument doc)
Instantiates a new object to study single SBML documents.- Parameters:
doc
- the document
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Method Detail
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getReactionsGraphML
public String getReactionsGraphML()
- Specified by:
getReactionsGraphML
in classde.unirostock.sems.bives.api.Single
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getReactionsGraph
public Object getReactionsGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt) throws Exception
- Specified by:
getReactionsGraph
in classde.unirostock.sems.bives.api.Single
- Throws:
Exception
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getReactionsDotGraph
public String getReactionsDotGraph()
- Specified by:
getReactionsDotGraph
in classde.unirostock.sems.bives.api.Single
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getReactionsJsonGraph
public String getReactionsJsonGraph()
- Specified by:
getReactionsJsonGraph
in classde.unirostock.sems.bives.api.Single
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getHierarchyGraph
public Object getHierarchyGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt) throws de.unirostock.sems.bives.exception.BivesUnsupportedException
- Specified by:
getHierarchyGraph
in classde.unirostock.sems.bives.api.Single
- Throws:
de.unirostock.sems.bives.exception.BivesUnsupportedException
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getHierarchyGraphML
public String getHierarchyGraphML() throws de.unirostock.sems.bives.exception.BivesUnsupportedException
- Specified by:
getHierarchyGraphML
in classde.unirostock.sems.bives.api.Single
- Throws:
de.unirostock.sems.bives.exception.BivesUnsupportedException
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getHierarchyDotGraph
public String getHierarchyDotGraph() throws de.unirostock.sems.bives.exception.BivesUnsupportedException
- Specified by:
getHierarchyDotGraph
in classde.unirostock.sems.bives.api.Single
- Throws:
de.unirostock.sems.bives.exception.BivesUnsupportedException
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getHierarchyJsonGraph
public String getHierarchyJsonGraph() throws de.unirostock.sems.bives.exception.BivesUnsupportedException
- Specified by:
getHierarchyJsonGraph
in classde.unirostock.sems.bives.api.Single
- Throws:
de.unirostock.sems.bives.exception.BivesUnsupportedException
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