Class SBMLConnectorPreprocessor


  • public class SBMLConnectorPreprocessor
    extends de.unirostock.sems.bives.algorithm.Connector
    The Class SBMLConnectorPreprocessor to pre-compute a mapping.
    Author:
    Martin Scharm
    • Constructor Detail

      • SBMLConnectorPreprocessor

        public SBMLConnectorPreprocessor​(SBMLDocument sbmlDocA,
                                         SBMLDocument sbmlDocB,
                                         boolean allowDifferentIds,
                                         boolean careAboutNames,
                                         boolean stricterNames)
        Instantiates a new sBML connector preprocessor.
        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
      • SBMLConnectorPreprocessor

        public SBMLConnectorPreprocessor​(SBMLDocument sbmlDocA,
                                         SBMLDocument sbmlDocB)
        Instantiates a new sBML connector preprocessor. 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
      • SBMLConnectorPreprocessor

        public SBMLConnectorPreprocessor​(de.unirostock.sems.bives.algorithm.Connector preprocessor,
                                         boolean allowDifferentIds,
                                         boolean careAboutNames,
                                         boolean stricterNames)
        Instantiates a new sBML connector preprocessor.
        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
      • SBMLConnectorPreprocessor

        public SBMLConnectorPreprocessor​(de.unirostock.sems.bives.algorithm.Connector preprocessor)
        Instantiates a new sBML connector preprocessor. 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()
                        throws de.unirostock.sems.bives.exception.BivesConnectionException
        Specified by:
        connect in class de.unirostock.sems.bives.algorithm.Connector
        Throws:
        de.unirostock.sems.bives.exception.BivesConnectionException