public class SBMLSpecies extends SBMLGenericIdNameObject implements de.unirostock.sems.bives.algorithm.DiffReporter
id, name
documentNode, sbmlModel
Constructor and Description |
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SBMLSpecies(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode,
SBMLModel sbmlModel)
Instantiates a new SBML species.
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Modifier and Type | Method and Description |
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boolean |
canBeReactantOrProduct()
Can this species take part in a reaction as a reactant or product?
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boolean |
canHaveAssignmentRule()
Is this species allowed to have an assignment rule.
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SBMLCompartment |
getCompartment()
Gets the compartment that hosts this species.
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double |
getInitialAmount()
Returns the initial amount of this species or null if not defined.
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double |
getInitialConcentration()
Returns the initial concentration of this species or null if not defined.
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boolean |
hasBoundaryCondition()
Checks for a boundary condition.
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boolean |
hasOnlySubstanceUnits()
Checks if this species has only substance units.
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boolean |
isConstant()
Checks if this species is constant.
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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) |
getID, getName, getNameAndId, getNameOrId
addOntologyLink, getAnnotation, getMetaId, getNotes, getOntologyLinks, getSBOTerm
getDocumentNode, getModel
public SBMLSpecies(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel) throws BivesSBMLParseException
documentNode
- the document node encoding this entity in the corresponding XML treesbmlModel
- the SBML modelBivesSBMLParseException
- the bives sbml parse exceptionpublic double getInitialAmount()
public double getInitialConcentration()
public SBMLCompartment getCompartment()
public boolean canHaveAssignmentRule()
public boolean canBeReactantOrProduct()
public boolean isConstant()
public boolean hasBoundaryCondition()
public boolean hasOnlySubstanceUnits()
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)
reportModification
in interface de.unirostock.sems.bives.algorithm.DiffReporter
public de.unirostock.sems.bives.markup.MarkupElement reportInsert()
reportInsert
in interface de.unirostock.sems.bives.algorithm.DiffReporter
public de.unirostock.sems.bives.markup.MarkupElement reportDelete()
reportDelete
in interface de.unirostock.sems.bives.algorithm.DiffReporter
Copyright © 2016 SEMS project @ University of Rostock. All rights reserved.