Class SBMLSingle


  • public class SBMLSingle
    extends de.unirostock.sems.bives.api.Single
    The Class SBMLSingle to study single SBML documents.
    Author:
    Martin Scharm
    • Constructor Detail

      • SBMLSingle

        public SBMLSingle​(File file)
                   throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
                          IOException,
                          org.jdom2.JDOMException,
                          BivesSBMLParseException,
                          de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
        Instantiates a new object to study single SBML documents.
        Parameters:
        file - the file containing the model
        Throws:
        de.unirostock.sems.xmlutils.exception.XmlDocumentParseException - the xml document parse exception
        IOException - Signals that an I/O exception has occurred.
        org.jdom2.JDOMException - the jDOM exception
        BivesSBMLParseException - the bives sbml parse exception
        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception
      • SBMLSingle

        public SBMLSingle​(String xml)
                   throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
                          IOException,
                          org.jdom2.JDOMException,
                          BivesSBMLParseException,
                          de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
        Instantiates a new object to study single SBML documents.
        Parameters:
        xml - the encoded the model
        Throws:
        de.unirostock.sems.xmlutils.exception.XmlDocumentParseException - the xml document parse exception
        IOException - Signals that an I/O exception has occurred.
        org.jdom2.JDOMException - the jDOM exception
        BivesSBMLParseException - the bives sbml parse exception
        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception
      • SBMLSingle

        public SBMLSingle​(de.unirostock.sems.xmlutils.ds.TreeDocument td)
                   throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
                          IOException,
                          org.jdom2.JDOMException,
                          BivesSBMLParseException,
                          de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
        Instantiates a new object.
        Parameters:
        td - the tree document
        Throws:
        de.unirostock.sems.xmlutils.exception.XmlDocumentParseException - the xml document parse exception
        IOException - Signals that an I/O exception has occurred.
        org.jdom2.JDOMException - the jDOM exception
        BivesSBMLParseException - the bives sbml parse exception
        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception
      • SBMLSingle

        public SBMLSingle​(SBMLDocument doc)
        Instantiates a new object to study single SBML documents.
        Parameters:
        doc - the document
    • Method Detail

      • getReactionsGraphML

        public String getReactionsGraphML()
        Specified by:
        getReactionsGraphML in class de.unirostock.sems.bives.api.Single
      • getReactionsGraph

        public Object getReactionsGraph​(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
                                 throws Exception
        Specified by:
        getReactionsGraph in class de.unirostock.sems.bives.api.Single
        Throws:
        Exception
      • getReactionsDotGraph

        public String getReactionsDotGraph()
        Specified by:
        getReactionsDotGraph in class de.unirostock.sems.bives.api.Single
      • getReactionsJsonGraph

        public String getReactionsJsonGraph()
        Specified by:
        getReactionsJsonGraph in class de.unirostock.sems.bives.api.Single
      • getHierarchyGraph

        public Object getHierarchyGraph​(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
                                 throws de.unirostock.sems.bives.exception.BivesUnsupportedException
        Specified by:
        getHierarchyGraph in class de.unirostock.sems.bives.api.Single
        Throws:
        de.unirostock.sems.bives.exception.BivesUnsupportedException
      • getHierarchyGraphML

        public String getHierarchyGraphML()
                                   throws de.unirostock.sems.bives.exception.BivesUnsupportedException
        Specified by:
        getHierarchyGraphML in class de.unirostock.sems.bives.api.Single
        Throws:
        de.unirostock.sems.bives.exception.BivesUnsupportedException
      • getHierarchyDotGraph

        public String getHierarchyDotGraph()
                                    throws de.unirostock.sems.bives.exception.BivesUnsupportedException
        Specified by:
        getHierarchyDotGraph in class de.unirostock.sems.bives.api.Single
        Throws:
        de.unirostock.sems.bives.exception.BivesUnsupportedException
      • getHierarchyJsonGraph

        public String getHierarchyJsonGraph()
                                     throws de.unirostock.sems.bives.exception.BivesUnsupportedException
        Specified by:
        getHierarchyJsonGraph in class de.unirostock.sems.bives.api.Single
        Throws:
        de.unirostock.sems.bives.exception.BivesUnsupportedException
      • flatten

        public String flatten()
                       throws Exception
        Specified by:
        flatten in class de.unirostock.sems.bives.api.Single
        Throws:
        Exception