List of readXMLFile() Examples

Examples of readXMLFile()

Examples of org.biopax.paxtools.io.BioPAXIOHandler.readXMLFile()

      }
      
      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.biopax.paxtools.io.SimpleIOHandler.readXMLFile()

      }
      
      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.readXMLFile()

      }
      
      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.readXMLFile()

      }
      
      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.readXMLFile()

        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.readXMLFile()

        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.SIFReader.readXMLFile()

      genesfile = dialog.getGenefile();
      limit = dialog.getLimit();
      directed = dialog.getDirected();


      SIFReader sifReader = new SIFReader(selectedRuleTypes);
      BasicSIFGraph graph = (BasicSIFGraph) sifReader.readXMLFile(new File(siffile));


      if (graph.getNodes().isEmpty())
      {
        MessageDialog.openInformation(main.getShell(), "Graph empty!",
          "Loaded SIF file does not have any interaction of specified type.");

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


      File xmlfile = new File(filename);


      SIFReader reader = new SIFReader();


      CompoundModel root = reader.readXMLFile(xmlfile);


      if (root != null)
      {
        main.createNewTab(root);

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

      genesfile = dialog.getGenefile();
      limit = dialog.getLimit();
      directed = dialog.getDirected();


      SIFReader sifReader = new SIFReader(selectedRuleTypes);
      BasicSIFGraph graph = (BasicSIFGraph) sifReader.readXMLFile(new File(siffile));


      if (graph.getNodes().isEmpty())
      {
        MessageDialog.openInformation(main.getShell(), "Graph empty!",
          "Loaded SIF file does not have any interaction of specified type.");

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


      File xmlfile = new File(filename);


      SIFReader reader = new SIFReader();


      CompoundModel root = reader.readXMLFile(xmlfile);


      if (root != null)
      {
        main.createNewTab(root);

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