Class SBMLDiff


  • public class SBMLDiff
    extends de.unirostock.sems.bives.api.Diff
    The Class SBMLDiff to compare two SBML models.
    Author:
    Martin Scharm
    • Constructor Detail

      • SBMLDiff

        public SBMLDiff​(File a,
                        File b,
                        de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)
                 throws BivesSBMLParseException,
                        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                        de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
                        IOException,
                        org.jdom2.JDOMException
        Instantiates a new SBML differ.
        Parameters:
        a - the file containing the original SBML model
        b - the file containing the modified SBML model
        diffAnnotator - the diff annotator
        Throws:
        BivesSBMLParseException - the bives sbml parse exception
        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception
        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
      • SBMLDiff

        public SBMLDiff​(String a,
                        String b,
                        de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)
                 throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
                        IOException,
                        org.jdom2.JDOMException,
                        BivesSBMLParseException,
                        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
        Instantiates a new SBML differ.
        Parameters:
        a - the XML code representing the original SBML model
        b - the XML code representing the modified SBML model
        diffAnnotator - the diff annotator
        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
      • SBMLDiff

        public SBMLDiff​(de.unirostock.sems.xmlutils.ds.TreeDocument a,
                        de.unirostock.sems.xmlutils.ds.TreeDocument b,
                        de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)
                 throws BivesSBMLParseException,
                        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
        Instantiates a new SBML differ.
        Parameters:
        a - the tree document representing the original model
        b - the tree document representing the modified model
        diffAnnotator - the diff annotator
        Throws:
        BivesSBMLParseException - the bives sbml parse exception
        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception
      • SBMLDiff

        public SBMLDiff​(SBMLDocument a,
                        SBMLDocument b,
                        de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)
        Instantiates a new SBML differ.
        Parameters:
        a - the original document
        b - the modified document
        diffAnnotator - the diff annotator
      • SBMLDiff

        public SBMLDiff​(File a,
                        File b)
                 throws BivesSBMLParseException,
                        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                        de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
                        IOException,
                        org.jdom2.JDOMException
        Instantiates a new SBML differ.
        Parameters:
        a - the file containing the original SBML model
        b - the file containing the modified SBML model
        Throws:
        BivesSBMLParseException - the bives sbml parse exception
        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception
        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
      • SBMLDiff

        public SBMLDiff​(String a,
                        String b)
                 throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
                        IOException,
                        org.jdom2.JDOMException,
                        BivesSBMLParseException,
                        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
        Instantiates a new SBML differ.
        Parameters:
        a - the XML code representing the original SBML model
        b - the XML code representing the modified SBML 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
      • SBMLDiff

        public SBMLDiff​(de.unirostock.sems.xmlutils.ds.TreeDocument a,
                        de.unirostock.sems.xmlutils.ds.TreeDocument b)
                 throws BivesSBMLParseException,
                        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
        Instantiates a new SBML differ.
        Parameters:
        a - the tree document representing the original model
        b - the tree document representing the modified model
        Throws:
        BivesSBMLParseException - the bives sbml parse exception
        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception
      • SBMLDiff

        public SBMLDiff​(SBMLDocument a,
                        SBMLDocument b)
        Instantiates a new SBML differ.
        Parameters:
        a - the original document
        b - the modified document
    • Method Detail

      • mapTrees

        public boolean mapTrees​(boolean allowDifferentIds,
                                boolean careAboutNames,
                                boolean stricterNames)
                         throws de.unirostock.sems.bives.exception.BivesConnectionException
        Specified by:
        mapTrees in class de.unirostock.sems.bives.api.Diff
        Throws:
        de.unirostock.sems.bives.exception.BivesConnectionException
      • getReactionsGraphML

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

        public String getReport​(de.unirostock.sems.bives.markup.Typesetting ts)
        Specified by:
        getReport in class de.unirostock.sems.bives.api.Diff
      • getMarkDownReport

        public String getMarkDownReport()
        Specified by:
        getMarkDownReport in class de.unirostock.sems.bives.api.Diff
      • getReStructuredTextReport

        public String getReStructuredTextReport()
        Specified by:
        getReStructuredTextReport in class de.unirostock.sems.bives.api.Diff
      • getHTMLReport

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

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

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

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

        public Object getHierarchyGraph​(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
        Specified by:
        getHierarchyGraph in class de.unirostock.sems.bives.api.Diff
      • getHierarchyGraphML

        public String getHierarchyGraphML()
        Specified by:
        getHierarchyGraphML in class de.unirostock.sems.bives.api.Diff
      • getHierarchyDotGraph

        public String getHierarchyDotGraph()
        Specified by:
        getHierarchyDotGraph in class de.unirostock.sems.bives.api.Diff
      • getHierarchyJsonGraph

        public String getHierarchyJsonGraph()
        Specified by:
        getHierarchyJsonGraph in class de.unirostock.sems.bives.api.Diff
      • getReactionsSbgnJsonGraph

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