Package de.unirostock.sems.bives.cellml.api

Class CellMLSingle

java.lang.Object

de.unirostock.sems.bives.api.Single

de.unirostock.sems.bives.cellml.api.CellMLSingle

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

The Class CellMLSingle to study single CellML documents.

Author:

Martin Scharm

Field Summary

Fields

Modifier and Type	Field	Description
protected CellMLGraphProducer	graphProducer	The graph producer.

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

tree

Constructor Summary

Constructors

Constructor	Description
CellMLSingle(CellMLDocument doc)	Instantiates a new object.
CellMLSingle(de.unirostock.sems.xmlutils.ds.TreeDocument td)	Instantiates a new object.
CellMLSingle(File file)	Instantiates a new object.
CellMLSingle(String xml)	Instantiates a new object.

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

graphProducer

protected CellMLGraphProducer graphProducer

The graph producer.

Constructor Detail

CellMLSingle

public CellMLSingle(File file)
             throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
                    IOException,
                    org.jdom2.JDOMException,
                    BivesCellMLParseException,
                    de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                    de.unirostock.sems.bives.exception.BivesLogicalException,
                    de.unirostock.sems.bives.exception.BivesImportException,
                    URISyntaxException

Instantiates a new object.

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

BivesCellMLParseException - the bives cell ml parse exception

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

de.unirostock.sems.bives.exception.BivesLogicalException - the bives logical exception

de.unirostock.sems.bives.exception.BivesImportException - the bives import exception

URISyntaxException - the uRI syntax exception

CellMLSingle

public CellMLSingle(String xml)
             throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
                    IOException,
                    org.jdom2.JDOMException,
                    BivesCellMLParseException,
                    de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                    de.unirostock.sems.bives.exception.BivesLogicalException,
                    de.unirostock.sems.bives.exception.BivesImportException,
                    URISyntaxException

Instantiates a new object.

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

BivesCellMLParseException - the bives cell ml parse exception

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

de.unirostock.sems.bives.exception.BivesLogicalException - the bives logical exception

de.unirostock.sems.bives.exception.BivesImportException - the bives import exception

URISyntaxException - the uRI syntax exception

CellMLSingle

public CellMLSingle(de.unirostock.sems.xmlutils.ds.TreeDocument td)
             throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
                    IOException,
                    org.jdom2.JDOMException,
                    BivesCellMLParseException,
                    de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                    de.unirostock.sems.bives.exception.BivesLogicalException,
                    de.unirostock.sems.bives.exception.BivesImportException,
                    URISyntaxException

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

BivesCellMLParseException - the bives cell ml parse exception

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

de.unirostock.sems.bives.exception.BivesLogicalException - the bives logical exception

de.unirostock.sems.bives.exception.BivesImportException - the bives import exception

URISyntaxException - the uRI syntax exception

CellMLSingle

public CellMLSingle(CellMLDocument doc)

Instantiates a new object.

Parameters:

doc - the CellML document

Method Detail

getReactionsGraphML

public String getReactionsGraphML()

Specified by:

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

getHierarchyGraph

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

Specified by:

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

Throws:

Exception

getHierarchyGraphML

public String getHierarchyGraphML()

Specified by:

getHierarchyGraphML 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

getHierarchyDotGraph

public String getHierarchyDotGraph()

Specified by:

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

getHierarchyJsonGraph

public String getHierarchyJsonGraph()

Specified by:

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

flatten

public String flatten()
               throws Exception

Specified by:

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

Throws:

Exception