Class SBMLSimpleSpeciesReference
- 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.SBMLSimpleSpeciesReference
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- Direct Known Subclasses:
SBMLSpeciesReference
public class SBMLSimpleSpeciesReference extends SBMLSBase
The Class SBMLSimpleSpeciesReference representing a link to a species (mainly for modifiers, parent class for substrates and products).- Author:
- Martin Scharm
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Field Summary
Fields Modifier and Type Field Description protected String
id
The id of this species reference.protected String
name
The name.protected SBMLSpecies
species
The species it is linking to.-
Fields inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
documentNode, sbmlModel
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Constructor Summary
Constructors Constructor Description SBMLSimpleSpeciesReference(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel)
Instantiates a new SBML simple species reference.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description SBMLSpecies
getSpecies()
Gets the corresponding species.String
report()
Typeset this reference.String
reportDelete()
Report a delete.String
reportInsert()
Report an insert.String
reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt, SBMLSimpleSpeciesReference a, SBMLSimpleSpeciesReference b)
Report modification between two versions of this species reference.-
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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Field Detail
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id
protected String id
The id of this species reference.
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name
protected String name
The name.
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species
protected SBMLSpecies species
The species it is linking to.
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Constructor Detail
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SBMLSimpleSpeciesReference
public SBMLSimpleSpeciesReference(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel) throws BivesSBMLParseException
Instantiates a new SBML simple species reference.- 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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getSpecies
public SBMLSpecies getSpecies()
Gets the corresponding species.- Returns:
- the species
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reportModification
public String reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt, SBMLSimpleSpeciesReference a, SBMLSimpleSpeciesReference b)
Report modification between two versions of this species reference.- Parameters:
conMgmt
- the connection managera
- the original referenceb
- the modified reference- Returns:
- the textual representation of this modification
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reportInsert
public String reportInsert()
Report an insert.- Returns:
- the string
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reportDelete
public String reportDelete()
Report a delete.- Returns:
- the string
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report
public String report()
Typeset this reference.- Returns:
- the string
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