Class SBMLSpecies
- 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.SBMLSpecies
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- All Implemented Interfaces:
de.unirostock.sems.bives.algorithm.DiffReporter
public class SBMLSpecies extends SBMLGenericIdNameObject implements de.unirostock.sems.bives.algorithm.DiffReporter
The Class SBMLSpecies representing a species in an SBML document.- 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 SBMLSpecies(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel)
Instantiates a new SBML species.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
canBeReactantOrProduct()
Can this species take part in a reaction as a reactant or product?boolean
canHaveAssignmentRule()
Is this species allowed to have an assignment rule.SBMLCompartment
getCompartment()
Gets the compartment that hosts this species.double
getInitialAmount()
Returns the initial amount of this species or null if not defined.double
getInitialConcentration()
Returns the initial concentration of this species or null if not defined.boolean
hasBoundaryCondition()
Checks for a boundary condition.boolean
hasOnlySubstanceUnits()
Checks if this species has only substance units.boolean
isConstant()
Checks if this species is constant.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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SBMLSpecies
public SBMLSpecies(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel) throws BivesSBMLParseException
Instantiates a new SBML species.- 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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getInitialAmount
public double getInitialAmount()
Returns the initial amount of this species or null if not defined.- Returns:
- the initial amount
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getInitialConcentration
public double getInitialConcentration()
Returns the initial concentration of this species or null if not defined.- Returns:
- the initial concentration
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getCompartment
public SBMLCompartment getCompartment()
Gets the compartment that hosts this species.- Returns:
- the compartment
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canHaveAssignmentRule
public boolean canHaveAssignmentRule()
Is this species allowed to have an assignment rule.- Returns:
- true, if allowed
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canBeReactantOrProduct
public boolean canBeReactantOrProduct()
Can this species take part in a reaction as a reactant or product?- Returns:
- true, if that is possible
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isConstant
public boolean isConstant()
Checks if this species is constant.- Returns:
- true, if it is constant
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hasBoundaryCondition
public boolean hasBoundaryCondition()
Checks for a boundary condition.- Returns:
- true, if successful
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hasOnlySubstanceUnits
public boolean hasOnlySubstanceUnits()
Checks if this species has only substance units.- Returns:
- true, if it has only substance units
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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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