Class SBMLReaction
- java.lang.Object
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- de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
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- de.unirostock.sems.bives.sbml.parser.SBMLSBase
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- de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
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- de.unirostock.sems.bives.sbml.parser.SBMLReaction
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- 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
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Field Summary
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Fields inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
id, name
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Fields inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
documentNode, sbmlModel
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Constructor Summary
Constructors Constructor Description SBMLReaction(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel)
Instantiates a new SBML reaction.
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Method Summary
All Methods Instance Methods Concrete Methods 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)
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Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
getID, getName, getNameAndId, getNameOrId
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Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLSBase
addOntologyLink, flagMetaModifcations, getAnnotation, getMetaId, getNotes, getOntologyLinks, getSBOTerm
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Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
getDocumentNode, getModel
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Constructor Detail
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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 treesbmlModel
- the SBML model- Throws:
BivesSBMLParseException
- the bives sbml parse exception
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Method Detail
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getCompartment
public SBMLCompartment getCompartment()
Gets the compartment.- Returns:
- the compartment
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isReversible
public boolean isReversible()
Checks if this reaction is reversible.- Returns:
- true, if it is reversible
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isFast
public boolean isFast()
Checks if this reaction is fast.- Returns:
- true, if it is fast
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getKineticLaw
public SBMLKineticLaw getKineticLaw()
Gets the kinetic law.- Returns:
- the kinetic law
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getListOfReactantsNode
public SBMLListOf getListOfReactantsNode()
Gets the list of reactants node.- Returns:
- the list of reactants node
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getListOfProductsNode
public SBMLListOf getListOfProductsNode()
Gets the list of products node.- Returns:
- the list of products node
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getListOfModifiersNode
public SBMLListOf getListOfModifiersNode()
Gets the list of modifiers node.- Returns:
- the list of modifiers node
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getReactants
public List<SBMLSpeciesReference> getReactants()
Gets the reactants.- Returns:
- the reactants
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getProducts
public List<SBMLSpeciesReference> getProducts()
Gets the products.- Returns:
- the products
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getModifiers
public List<SBMLSimpleSpeciesReference> getModifiers()
Gets the modifiers.- Returns:
- the modifiers
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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 interfacede.unirostock.sems.bives.algorithm.DiffReporter
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reportInsert
public de.unirostock.sems.bives.markup.MarkupElement reportInsert()
- Specified by:
reportInsert
in interfacede.unirostock.sems.bives.algorithm.DiffReporter
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reportDelete
public de.unirostock.sems.bives.markup.MarkupElement reportDelete()
- Specified by:
reportDelete
in interfacede.unirostock.sems.bives.algorithm.DiffReporter
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report
public void report(de.unirostock.sems.bives.markup.MarkupElement me, boolean insert)
Typeset this reaction.- Parameters:
me
- the markup elementinsert
- is that an insert? otherwise we report a delete
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