Package de.unirostock.sems.bives.sbml.api

Class SBMLSingle

java.lang.Object

de.unirostock.sems.bives.api.Single

de.unirostock.sems.bives.sbml.api.SBMLSingle

public class SBMLSingle
extends de.unirostock.sems.bives.api.Single

The Class SBMLSingle to study single SBML documents.

Author:

Martin Scharm

Field Summary

Fields

Modifier and Type	Field	Description
protected SBMLDocument	doc	The doc.
protected SBMLGraphProducer	graphProducer	The graph producer.

Fields inherited from class de.unirostock.sems.bives.api.Single

tree

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.

Method Summary

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()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from class de.unirostock.sems.bives.api.Single

getCRNDotGraph, getCRNGraph, getCRNGraphML, getCRNJsonGraph

Field Detail

doc

protected SBMLDocument doc

The doc.

graphProducer

protected SBMLGraphProducer graphProducer

The graph producer.

Constructor Detail

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 exception

IOException - Signals that an I/O exception has occurred.

org.jdom2.JDOMException - the jDOM exception

BivesSBMLParseException - the bives sbml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

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 exception

IOException - Signals that an I/O exception has occurred.

org.jdom2.JDOMException - the jDOM exception

BivesSBMLParseException - the bives sbml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

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 exception

IOException - Signals that an I/O exception has occurred.

org.jdom2.JDOMException - the jDOM exception

BivesSBMLParseException - the bives sbml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

SBMLSingle

public SBMLSingle(SBMLDocument doc)

Instantiates a new object to study single SBML documents.

Parameters:

doc - the document

Method Detail

getReactionsGraphML

public String getReactionsGraphML()

Specified by:

getReactionsGraphML in class de.unirostock.sems.bives.api.Single

getReactionsGraph

public Object getReactionsGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
                         throws Exception

Specified by:

getReactionsGraph in class de.unirostock.sems.bives.api.Single

Throws:

Exception

getReactionsDotGraph

public String getReactionsDotGraph()

Specified by:

getReactionsDotGraph in class de.unirostock.sems.bives.api.Single

getReactionsJsonGraph

public String getReactionsJsonGraph()

Specified by:

getReactionsJsonGraph in class de.unirostock.sems.bives.api.Single

getHierarchyGraph

public Object getHierarchyGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
                         throws de.unirostock.sems.bives.exception.BivesUnsupportedException

Specified by:

getHierarchyGraph in class de.unirostock.sems.bives.api.Single

Throws:

de.unirostock.sems.bives.exception.BivesUnsupportedException

getHierarchyGraphML

public String getHierarchyGraphML()
                           throws de.unirostock.sems.bives.exception.BivesUnsupportedException

Specified by:

getHierarchyGraphML in class de.unirostock.sems.bives.api.Single

Throws:

de.unirostock.sems.bives.exception.BivesUnsupportedException

getHierarchyDotGraph

public String getHierarchyDotGraph()
                            throws de.unirostock.sems.bives.exception.BivesUnsupportedException

Specified by:

getHierarchyDotGraph in class de.unirostock.sems.bives.api.Single

Throws:

de.unirostock.sems.bives.exception.BivesUnsupportedException

getHierarchyJsonGraph

public String getHierarchyJsonGraph()
                             throws de.unirostock.sems.bives.exception.BivesUnsupportedException

Specified by:

getHierarchyJsonGraph in class de.unirostock.sems.bives.api.Single

Throws:

de.unirostock.sems.bives.exception.BivesUnsupportedException

flatten

public String flatten()
               throws Exception

Specified by:

flatten in class de.unirostock.sems.bives.api.Single

Throws:

Exception