Class SBMLSpeciesReference
- 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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- de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference
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public class SBMLSpeciesReference extends SBMLSimpleSpeciesReference
The Class SBMLSpeciesReference representing a link to a species.- Author:
- Martin Scharm
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Field Summary
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Fields inherited from class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
id, name, species
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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 SBMLSpeciesReference(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel)
Instantiates a new SBML species reference.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
report()
Typeset this reference.String
reportDelete()
Report a delete.String
reportInsert()
Report an insert.String
reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt, SBMLSpeciesReference a, SBMLSpeciesReference b)
Report the modifications of this species reference.-
Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
getSpecies, reportModification
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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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SBMLSpeciesReference
public SBMLSpeciesReference(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel) throws BivesSBMLParseException
Instantiates a new SBML species reference.- Parameters:
documentNode
- the document node encoding this entity in the corresponding XML treesbmlModel
- the corresponding SBML model- Throws:
BivesSBMLParseException
- the bives sbml parse exception
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Method Detail
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reportModification
public String reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt, SBMLSpeciesReference a, SBMLSpeciesReference b)
Report the modifications of this species reference.- Parameters:
conMgmt
- the connection managera
- the original species referenceb
- the modified species reference- Returns:
- the string
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reportInsert
public String reportInsert()
Description copied from class:SBMLSimpleSpeciesReference
Report an insert.- Overrides:
reportInsert
in classSBMLSimpleSpeciesReference
- Returns:
- the string
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reportDelete
public String reportDelete()
Description copied from class:SBMLSimpleSpeciesReference
Report a delete.- Overrides:
reportDelete
in classSBMLSimpleSpeciesReference
- Returns:
- the string
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report
public String report()
Description copied from class:SBMLSimpleSpeciesReference
Typeset this reference.- Overrides:
report
in classSBMLSimpleSpeciesReference
- Returns:
- the string
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