Class SBMLConnector


  • public class SBMLConnector
    extends de.unirostock.sems.bives.algorithm.Connector
    The Class SBMLConnector to connect SBML documents.
    Author:
    Martin Scharm
    • Field Summary

      • Fields inherited from class de.unirostock.sems.bives.algorithm.Connector

        allowDifferentIds, careAboutNames, conMgmt, docA, docB, stricterNames
    • Constructor Summary

      Constructors 
      Constructor Description
      SBMLConnector​(de.unirostock.sems.bives.algorithm.Connector preprocessor)
      Instantiates a new SBML connector.
      SBMLConnector​(de.unirostock.sems.bives.algorithm.Connector preprocessor, boolean allowDifferentIds, boolean careAboutNames, boolean stricterNames)
      Instantiates a new SBML connector.
      SBMLConnector​(SBMLDocument sbmlDocA, SBMLDocument sbmlDocB)
      Instantiates a new SBML connector.
      SBMLConnector​(SBMLDocument sbmlDocA, SBMLDocument sbmlDocB, boolean allowDifferentIds, boolean careAboutNames, boolean stricterNames)
      Instantiates a new SBML connector.
    • Constructor Detail

      • SBMLConnector

        public SBMLConnector​(SBMLDocument sbmlDocA,
                             SBMLDocument sbmlDocB,
                             boolean allowDifferentIds,
                             boolean careAboutNames,
                             boolean stricterNames)
        Instantiates a new SBML connector.
        Parameters:
        sbmlDocA - the original document
        sbmlDocB - the modified document
        allowDifferentIds - may mapped entities have different ids? see Diff.ALLOW_DIFFERENT_IDS
        careAboutNames - should we care about names? see Diff.CARE_ABOUT_NAMES
        stricterNames - should we handle the names very strictly? see Diff.STRICTER_NAMES
      • SBMLConnector

        public SBMLConnector​(SBMLDocument sbmlDocA,
                             SBMLDocument sbmlDocB)
        Instantiates a new SBML connector. Uses default values for the mapping, see Diff.ALLOW_DIFFERENT_IDS, Diff.CARE_ABOUT_NAMES, and Diff.STRICTER_NAMES.
        Parameters:
        sbmlDocA - the original document
        sbmlDocB - the modified document
      • SBMLConnector

        public SBMLConnector​(de.unirostock.sems.bives.algorithm.Connector preprocessor,
                             boolean allowDifferentIds,
                             boolean careAboutNames,
                             boolean stricterNames)
        Instantiates a new SBML connector.
        Parameters:
        preprocessor - the preprocessor
        allowDifferentIds - may mapped entities have different ids? see Diff.ALLOW_DIFFERENT_IDS
        careAboutNames - should we care about names? see Diff.CARE_ABOUT_NAMES
        stricterNames - should we handle the names very strictly? see Diff.STRICTER_NAMES
      • SBMLConnector

        public SBMLConnector​(de.unirostock.sems.bives.algorithm.Connector preprocessor)
        Instantiates a new SBML connector. Uses default values for the mapping, see Diff.ALLOW_DIFFERENT_IDS, Diff.CARE_ABOUT_NAMES, and Diff.STRICTER_NAMES.
        Parameters:
        preprocessor - the preprocessor
    • Method Detail

      • init

        protected void init()
                     throws de.unirostock.sems.bives.exception.BivesConnectionException
        Specified by:
        init in class de.unirostock.sems.bives.algorithm.Connector
        Throws:
        de.unirostock.sems.bives.exception.BivesConnectionException
      • connect

        protected void connect()
        Specified by:
        connect in class de.unirostock.sems.bives.algorithm.Connector