Package org.gvt.util

Examples of org.gvt.util.BioPAXReader.readXMLFile()

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      }
     
      merger.merge(target, sources.toArray(new Model[sources.size()]));

      BioPAXReader reader = new BioPAXReader(target);
      BioPAXGraph graph = (BioPAXGraph) reader.readXMLFile(null);

      if (createNewPathway)
      {
        List<String> intids = getInteractionIDs(model);
        newPathwayName = graph.createPathway(
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      }
     
      merger.merge(target, sources.toArray(new Model[sources.size()]));

      BioPAXReader reader = new BioPAXReader(target);
      BioPAXGraph graph = (BioPAXGraph) reader.readXMLFile(null);

      if (createNewPathway)
      {
        List<String> intids = getInteractionIDs(model);
        newPathwayName = graph.createPathway(
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        if (root == null)
        {
          File xmlfile = filename == null ? null : new File(filename);
          BioPAXReader reader = model == null ?
            new BioPAXReader(): new BioPAXReader(model);
          root = (BioPAXGraph) reader.readXMLFile(xmlfile);
        }

        if (root != null)
        {
          if (!root.modelConstainsPathway() || pathwayName != null)
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        if (root == null)
        {
          File xmlfile = filename == null ? null : new File(filename);
          BioPAXReader reader = model == null ?
            new BioPAXReader(main.getJenaIOHandler()): new BioPAXReader(model);
          root = (BioPAXGraph) reader.readXMLFile(xmlfile);
        }

        if (root != null)
        {
          if (!root.modelConstainsPathway())
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