Class SBMLSBase

    • Constructor Detail

      • 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 tree
        sbmlModel - the SBML model
        Throws:
        BivesSBMLParseException - the bives sbml parse exception
    • Method Detail

      • 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
      • getOntologyLinks

        public HashMap<String,​List<String>> getOntologyLinks()
        Gets the links that point to an ontology.
        Returns:
        the ontology links
      • addOntologyLink

        public void addOntologyLink​(String qualifier,
                                    String link)
        Adds an link into an ontology.
        Parameters:
        qualifier - the qualifier
        link - the link
      • getSBOTerm

        public de.unirostock.sems.bives.ds.ontology.SBOTerm getSBOTerm()
        Gets the SBO term.
        Returns:
        the SBO term
      • getMetaId

        public String getMetaId()
        Gets the meta id.
        Returns:
        the meta id
      • getNotes

        public de.unirostock.sems.bives.ds.Xhtml getNotes()
        Gets the notes.
        Returns:
        the notes
      • getAnnotation

        public de.unirostock.sems.xmlutils.ds.DocumentNode getAnnotation()
        Gets the annotation.
        Returns:
        the annotation