Class SBMLSBase
- 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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- Direct Known Subclasses:
SBMLConstraint
,SBMLEvent
,SBMLEventAssignment
,SBMLEventDelay
,SBMLEventPriority
,SBMLEventTrigger
,SBMLGenericIdNameObject
,SBMLInitialAssignment
,SBMLKineticLaw
,SBMLListOf
,SBMLModel
,SBMLRule
,SBMLSimpleSpeciesReference
,SBMLUnit
public abstract class SBMLSBase extends SBMLGenericObject
The Class SBMLSBase. This base type is designed to allow a modeler or a software package to attach arbitrary information to each major element or list in an SBML model.- Author:
- Martin Scharm
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Field Summary
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Fields inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
documentNode, sbmlModel
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addOntologyLink(String qualifier, String link)
Adds an link into an ontology.boolean
flagMetaModifcations(de.unirostock.sems.bives.markup.MarkupElement me)
Flags occuring modifcations of the meta information (notes, annotations) to the given MarkupElement.de.unirostock.sems.xmlutils.ds.DocumentNode
getAnnotation()
Gets the annotation.String
getMetaId()
Gets the meta id.de.unirostock.sems.bives.ds.Xhtml
getNotes()
Gets the notes.HashMap<String,List<String>>
getOntologyLinks()
Gets the links that point to an ontology.de.unirostock.sems.bives.ds.ontology.SBOTerm
getSBOTerm()
Gets the SBO term.-
Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
getDocumentNode, getModel
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Constructor Detail
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SBMLSBase
public SBMLSBase(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel) throws BivesSBMLParseException
Instantiates a new SBMLS base.- 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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flagMetaModifcations
public boolean flagMetaModifcations(de.unirostock.sems.bives.markup.MarkupElement me)
Flags occuring modifcations of the meta information (notes, annotations) to the given MarkupElement.- Parameters:
me
- the MarkupElement that should be flagged- Returns:
- true, if flagged
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getOntologyLinks
public HashMap<String,List<String>> getOntologyLinks()
Gets the links that point to an ontology.- Returns:
- the ontology links
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addOntologyLink
public void addOntologyLink(String qualifier, String link)
Adds an link into an ontology.- Parameters:
qualifier
- the qualifierlink
- the link
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getSBOTerm
public de.unirostock.sems.bives.ds.ontology.SBOTerm getSBOTerm()
Gets the SBO term.- Returns:
- the SBO term
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getMetaId
public String getMetaId()
Gets the meta id.- Returns:
- the meta id
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getNotes
public de.unirostock.sems.bives.ds.Xhtml getNotes()
Gets the notes.- Returns:
- the notes
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getAnnotation
public de.unirostock.sems.xmlutils.ds.DocumentNode getAnnotation()
Gets the annotation.- Returns:
- the annotation
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