Class SBMLDiffAnnotator


  • public class SBMLDiffAnnotator
    extends de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
    Author:
    Martin Scharm
    • Field Detail

      • functionPath

        public static final Pattern functionPath
        The XPATH to a function definition.
      • eventPath

        public static final Pattern eventPath
        The XPATH to an event definition.
      • rulePath

        public static final Pattern rulePath
        The XPATH to a rule.
      • annotationPath

        public static final Pattern annotationPath
        The XPATH to a machine readable annotation.
      • descriptionPath

        public static final Pattern descriptionPath
        The XPATH to a human readable annotation.
      • speciesPath

        public static final Pattern speciesPath
        The XPATH to a species.
      • reactionsPath

        public static final Pattern reactionsPath
        The XPATH to a reaction.
      • kineticsPath

        public static final Pattern kineticsPath
        The XPATH to a kinetic law.
      • unitsPath

        public static final Pattern unitsPath
        The XPATH to a reaction.
      • parameterPath

        public static final Pattern parameterPath
        The XPATH to a parameter.
      • creationDatePath

        public static final Pattern creationDatePath
        The XPATH to a machine readable annotation.
      • modificationDatePath

        public static final Pattern modificationDatePath
        The XPATH to a machine readable annotation.
      • contributorPath

        public static final Pattern contributorPath
        The XPATH to a machine readable annotation.
      • creatorPath

        public static final Pattern creatorPath
        The XPATH to a machine readable annotation.
      • reactionsSpeciesReference

        public static final Pattern reactionsSpeciesReference
      • reactionsModifierSpeciesReference

        public static final Pattern reactionsModifierSpeciesReference
      • ontologyLink

        public static final Pattern ontologyLink
    • Constructor Detail

      • SBMLDiffAnnotator

        public SBMLDiffAnnotator()
    • Method Detail

      • annotateDeletion

        public de.unirostock.sems.comodi.Change annotateDeletion​(de.unirostock.sems.xmlutils.ds.TreeNode node,
                                                                 org.jdom2.Element diffNode,
                                                                 de.unirostock.sems.comodi.ChangeFactory changeFac)
        Overrides:
        annotateDeletion in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
      • annotateInsertion

        public de.unirostock.sems.comodi.Change annotateInsertion​(de.unirostock.sems.xmlutils.ds.TreeNode node,
                                                                  org.jdom2.Element diffNode,
                                                                  de.unirostock.sems.comodi.ChangeFactory changeFac)
        Overrides:
        annotateInsertion in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
      • annotateMove

        public de.unirostock.sems.comodi.Change annotateMove​(de.unirostock.sems.xmlutils.ds.TreeNode nodeA,
                                                             de.unirostock.sems.xmlutils.ds.TreeNode nodeB,
                                                             org.jdom2.Element diffNode,
                                                             de.unirostock.sems.comodi.ChangeFactory changeFac,
                                                             boolean permutation)
        Overrides:
        annotateMove in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
      • annotateUpdateAttribute

        public de.unirostock.sems.comodi.Change annotateUpdateAttribute​(de.unirostock.sems.xmlutils.ds.TreeNode nodeA,
                                                                        de.unirostock.sems.xmlutils.ds.TreeNode nodeB,
                                                                        String attributeName,
                                                                        org.jdom2.Element diffNode,
                                                                        de.unirostock.sems.comodi.ChangeFactory changeFac)
        Overrides:
        annotateUpdateAttribute in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
      • annotateUpdateText

        public de.unirostock.sems.comodi.Change annotateUpdateText​(de.unirostock.sems.xmlutils.ds.TextNode nodeA,
                                                                   de.unirostock.sems.xmlutils.ds.TextNode nodeB,
                                                                   org.jdom2.Element diffNode,
                                                                   de.unirostock.sems.comodi.ChangeFactory changeFac)
        Overrides:
        annotateUpdateText in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
      • annotatePatch

        public void annotatePatch​(String rootId,
                                  de.unirostock.sems.comodi.ChangeFactory changeFac)
        Overrides:
        annotatePatch in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator