Examples of BioPAXReader

org.gvt.util.BioPAXReader
GraphML reader class for loading graphml files @author Ozgun BaburCopyright: Bilkent Center for Bioinformatics, 2007 - present

Examples of org.gvt.util.BioPAXReader

        merger = new Merger(SimpleEditorMap.get(target.getLevel()));
      }
      
      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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Examples of org.gvt.util.BioPAXReader

    }
  }


  private void updateRoot()
  {
    BioPAXGraph root = (BioPAXGraph) new BioPAXReader(main.getOwlModel()).readXMLFile(null);
    main.setRootGraph(root);
  }

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Examples of org.gvt.util.BioPAXReader

        merger = new Merger(new JenaEditorMap(BioPAXLevel.L2));
      }
      
      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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Examples of org.gvt.util.BioPAXReader

    }
  }


  private void updateRoot()
  {
    BioPAXGraph root = (BioPAXGraph) new BioPAXReader(main.getOwlModel()).readXMLFile(null);
    main.setRootGraph(root);
  }

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Examples of org.gvt.util.BioPAXReader

        BioPAXGraph root = this.graph;


        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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Examples of org.gvt.util.BioPAXReader

        BioPAXGraph root = this.graph;


        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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Examples of org.gvt.util.BioPAXReader

    }
  }


  private void updateRoot()
  {
    BioPAXGraph root = (BioPAXGraph) new BioPAXReader(main.getOwlModel()).readXMLFile(null);
    main.setRootGraph(root);
  }

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