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

Class SBMLReaction

java.lang.Object

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

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

de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject

de.unirostock.sems.bives.sbml.parser.SBMLReaction

All Implemented Interfaces:

de.unirostock.sems.bives.algorithm.DiffReporter

public class SBMLReaction
extends SBMLGenericIdNameObject
implements de.unirostock.sems.bives.algorithm.DiffReporter

The Class SBMLReaction represents any kind of process that can change the quantity of one or more species in a model.

Author:

Martin Scharm

Field Summary

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

id, name

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

documentNode, sbmlModel

Constructor Summary

Constructors

Constructor	Description
SBMLReaction(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel)	Instantiates a new SBML reaction.

Method Summary

Modifier and Type	Method	Description
SBMLCompartment	getCompartment()	Gets the compartment.
SBMLKineticLaw	getKineticLaw()	Gets the kinetic law.
SBMLListOf	getListOfModifiersNode()	Gets the list of modifiers node.
SBMLListOf	getListOfProductsNode()	Gets the list of products node.
SBMLListOf	getListOfReactantsNode()	Gets the list of reactants node.
List<SBMLSimpleSpeciesReference>	getModifiers()	Gets the modifiers.
List<SBMLSpeciesReference>	getProducts()	Gets the products.
List<SBMLSpeciesReference>	getReactants()	Gets the reactants.
boolean	isFast()	Checks if this reaction is fast.
boolean	isReversible()	Checks if this reaction is reversible.
void	report(de.unirostock.sems.bives.markup.MarkupElement me, boolean insert)	Typeset this reaction.
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.SBMLGenericIdNameObject

getID, getName, getNameAndId, getNameOrId

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

getDocumentNode, getModel

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

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

Constructor Detail

SBMLReaction

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

Instantiates a new SBML reaction.

Parameters:

documentNode - the document node encoding this entity in the corresponding XML tree

sbmlModel - the SBML model

Throws:

BivesSBMLParseException - the bives sbml parse exception

Method Detail

getCompartment

public SBMLCompartment getCompartment()

Gets the compartment.

Returns:

the compartment

isReversible

public boolean isReversible()

Checks if this reaction is reversible.

Returns:

true, if it is reversible

isFast

public boolean isFast()

Checks if this reaction is fast.

Returns:

true, if it is fast

getKineticLaw

public SBMLKineticLaw getKineticLaw()

Gets the kinetic law.

Returns:

the kinetic law

getListOfReactantsNode

public SBMLListOf getListOfReactantsNode()

Gets the list of reactants node.

Returns:

the list of reactants node

getListOfProductsNode

public SBMLListOf getListOfProductsNode()

Gets the list of products node.

Returns:

the list of products node

getListOfModifiersNode

public SBMLListOf getListOfModifiersNode()

Gets the list of modifiers node.

Returns:

the list of modifiers node

getReactants

public List<SBMLSpeciesReference> getReactants()

Gets the reactants.

Returns:

the reactants

getProducts

public List<SBMLSpeciesReference> getProducts()

Gets the products.

Returns:

the products

getModifiers

public List<SBMLSimpleSpeciesReference> getModifiers()

Gets the modifiers.

Returns:

the modifiers

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)

Specified by:

reportModification in interface de.unirostock.sems.bives.algorithm.DiffReporter

reportInsert

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

Specified by:

reportInsert in interface de.unirostock.sems.bives.algorithm.DiffReporter

reportDelete

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

Specified by:

reportDelete in interface de.unirostock.sems.bives.algorithm.DiffReporter

report

public void report(de.unirostock.sems.bives.markup.MarkupElement me,
                   boolean insert)

Typeset this reaction.

Parameters:

me - the markup element

insert - is that an insert? otherwise we report a delete