Package de.unirostock.sems.bives.sbml.parser

Class SBMLRateRule

java.lang.Object

de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

de.unirostock.sems.bives.sbml.parser.SBMLSBase

de.unirostock.sems.bives.sbml.parser.SBMLRule

de.unirostock.sems.bives.sbml.parser.SBMLRateRule

All Implemented Interfaces:

de.unirostock.sems.bives.algorithm.DiffReporter

public class SBMLRateRule
extends SBMLRule

The Class SBMLRateRule used to express equations that determine the rates of change of variables.

Author:

Martin Scharm

Field Summary

Fields inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

documentNode, sbmlModel

Fields inherited from class de.unirostock.sems.bives.sbml.parser.SBMLRule

ALGEBRAIC_RULE, ASSIGNMENT_RULE, math, RATE_RULE, type

Constructor Summary

Constructors

Constructor	Description
SBMLRateRule(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel)	Instantiates a new SBML rate rule.

Method Summary

Modifier and Type	Method	Description
SBMLSBase	getVariable()	Gets the variable of interest.
de.unirostock.sems.bives.markup.MarkupElement	reportDelete()
de.unirostock.sems.bives.markup.MarkupElement	reportInsert()
de.unirostock.sems.bives.markup.MarkupElement	reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt, de.unirostock.sems.bives.algorithm.DiffReporter docA, de.unirostock.sems.bives.algorithm.DiffReporter docB)

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.sbml.parser.SBMLGenericObject

getDocumentNode, getModel

Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLRule

getMath, getRuleType, resolveVariable

Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLSBase

addOntologyLink, flagMetaModifcations, getAnnotation, getMetaId, getNotes, getOntologyLinks, getSBOTerm

Constructor Detail

SBMLRateRule

public SBMLRateRule(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode,
                    SBMLModel sbmlModel)
             throws BivesSBMLParseException

Instantiates a new SBML rate rule.

Parameters:

documentNode - the document node in the corresponding XML tree

sbmlModel - the SBML model

Throws:

BivesSBMLParseException - the bives sbml parse exception

Method Detail

getVariable

public SBMLSBase getVariable()

Gets the variable of interest.

Returns:

the variable

reportModification

public de.unirostock.sems.bives.markup.MarkupElement reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt,
                                                                        de.unirostock.sems.bives.algorithm.DiffReporter docA,
                                                                        de.unirostock.sems.bives.algorithm.DiffReporter docB)

reportInsert

public de.unirostock.sems.bives.markup.MarkupElement reportInsert()

reportDelete

public de.unirostock.sems.bives.markup.MarkupElement reportDelete()