Package org.biopax.paxtools.io.pathwayCommons

Examples of org.biopax.paxtools.io.pathwayCommons.PathwayCommonsIOHandler

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    {
      try
      {
        main.lockWithMessage("Querying Pathway Commons Database ...");

        PathwayCommonsIOHandler ioHandler = new PathwayCommonsIOHandler(new SimpleIOHandler());
        Map<String, String> pathToID = new HashMap<String, String>();
        List<String> resultPathways = new ArrayList<String>();

        XRef xr = XRef.getFirstRef(refs,
          new String[]{XRef.CPATH, XRef.ENTREZ_GENE, XRef.UNIPROT});

        refs.clear();
        if (xr != null)
        {
          refs.add(xr);
        }
        else
        {
          MessageDialog.openError(main.getShell(), "No Reference ID",
            "No CPATH, Entrez Gene or UniProt ID found to query.");
        }

       
        for (XRef ref : refs)
        {
          if (ref.getDb().equalsIgnoreCase(XRef.CPATH))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.CPATH_ID);
          }
          else if (ref.getDb().equalsIgnoreCase(XRef.UNIPROT))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.UNIPROT);
          }
          else if (ref.getDb().equalsIgnoreCase(XRef.ENTREZ_GENE))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.ENTREZ_GENE);
          }
          else
          {
            continue;
          }

          System.out.println("Querying pathways for " + ref);

          List<List<String>> resultList = ioHandler.getPathways(ref.getRef());
          main.unlock();

          if (resultList.get(0).get(0).contains("xml"))
          {
            MessageDialog.openError(main.getShell(), "Error!", "Unexpected error!");
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    if (!refs.isEmpty())
    {
      try
      {
        main.lockWithMessage("Querying Pathway Commons Database ...");
        PathwayCommonsIOHandler ioHandler = new PathwayCommonsIOHandler();

        // Names of new pathways for the neighborhood
        Map<XRef, String> ref2pname = new HashMap<XRef, String>();

        // Query for only one xref

        XRef xr = XRef.getFirstRef(refs,
          new String[]{XRef.CPATH, XRef.ENTREZ_GENE, XRef.UNIPROT});

        refs.clear();
        if (xr != null)
        {
          refs.add(xr);
        }
        else
        {
          MessageDialog.openError(main.getShell(), "No Reference ID",
            "No CPATH, Entrez Gene or UniProt ID found to query.");
        }

        for (XRef ref : refs)
        {
          if ((db == null || db.equals(XRef.CPATH)) &&
            ref.getDb().equalsIgnoreCase(XRef.CPATH))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.CPATH_ID);
          }
          else if ((db == null || db.equals(XRef.UNIPROT)) &&
            ref.getDb().equalsIgnoreCase(XRef.UNIPROT))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.UNIPROT);
          }
          else if ((db == null || db.equals(XRef.ENTREZ_GENE)) &&
            ref.getDb().equalsIgnoreCase(XRef.ENTREZ_GENE))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.ENTREZ_GENE);
          }
          else
          {
            continue;
          }

          System.out.println("Querying neighbors for " + ref);
          Model resultModel = ioHandler.getNeighbors(ref.getRef());

          main.unlock();
         
          if (resultModel != null && !resultModel.getIdMap().keySet().isEmpty())
          {
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       *   This is particularly useful when giving the users a long list of pathways and letting them choose which pathway to
       *   visualize on the spot, which can be very useful in JWS deployment.  */
      else if (filename.matches("\\d*")){
        try {
          BioPAXIOHandler reader = new SimpleIOHandler();
          PathwayCommonsIOHandler pcIOHandler  = new PathwayCommonsIOHandler(reader);
          Model model = pcIOHandler.retrieveByID(filename);
          LoadBioPaxModelAction action = new LoadBioPaxModelAction(window, model);
          window.firstAction = action;
         
        } catch (IOException e) {
          e.printStackTrace();
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    {
      try
      {
        main.lockWithMessage("Querying Pathway Commons Database ...");

        PathwayCommonsIOHandler ioHandler = new PathwayCommonsIOHandler();
        Map<String, String> pathToID = new HashMap<String, String>();
        List<String> resultPathways = new ArrayList<String>();

        XRef xr = XRef.getFirstRef(refs,
          new String[]{XRef.CPATH, XRef.ENTREZ_GENE, XRef.UNIPROT});

        refs.clear();
        if (xr != null)
        {
          refs.add(xr);
        }
        else
        {
          MessageDialog.openError(main.getShell(), "No Reference ID",
            "No CPATH, Entrez Gene or UniProt ID found to query.");
        }

       
        for (XRef ref : refs)
        {
          if (ref.getDb().equalsIgnoreCase(XRef.CPATH))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.CPATH_ID);
          }
          else if (ref.getDb().equalsIgnoreCase(XRef.UNIPROT))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.UNIPROT);
          }
          else if (ref.getDb().equalsIgnoreCase(XRef.ENTREZ_GENE))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.ENTREZ_GENE);
          }
          else
          {
            continue;
          }

          System.out.println("Querying pathways for " + ref);

          List<List<String>> resultList = ioHandler.getPathways(ref.getRef());
          main.unlock();

          if (resultList.get(0).get(0).contains("xml"))
          {
            MessageDialog.openError(main.getShell(), "Error!", "Unexpected error!");
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    if (!refs.isEmpty())
    {
      try
      {
        main.lockWithMessage("Querying Pathway Commons Database ...");
        PathwayCommonsIOHandler ioHandler = new PathwayCommonsIOHandler(new SimpleIOHandler());

        // Names of new pathways for the neighborhood
        Map<XRef, String> ref2pname = new HashMap<XRef, String>();

        // Query for only one xref

        XRef xr = XRef.getFirstRef(refs,
          new String[]{XRef.CPATH, XRef.ENTREZ_GENE, XRef.UNIPROT});

        refs.clear();
        if (xr != null)
        {
          refs.add(xr);
        }
        else
        {
          MessageDialog.openError(main.getShell(), "No Reference ID",
            "No CPATH, Entrez Gene or UniProt ID found to query.");
        }

        for (XRef ref : refs)
        {
          if ((db == null || db.equals(XRef.CPATH)) &&
            ref.getDb().equalsIgnoreCase(XRef.CPATH))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.CPATH_ID);
          }
          else if ((db == null || db.equals(XRef.UNIPROT)) &&
            ref.getDb().equalsIgnoreCase(XRef.UNIPROT))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.UNIPROT);
          }
          else if ((db == null || db.equals(XRef.ENTREZ_GENE)) &&
            ref.getDb().equalsIgnoreCase(XRef.ENTREZ_GENE))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.ENTREZ_GENE);
          }
          else
          {
            continue;
          }

          System.out.println("Querying neighbors for " + ref);
          Model resultModel = ioHandler.getNeighbors(ref.getRef());

          main.unlock();
         
          if (resultModel != null && !resultModel.getObjects().isEmpty())
          {
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    if (id != null)
    {
      try
      {
        main.lockWithMessage("Querying Internal PC Database ...");
        PathwayCommonsIOHandler ioHandler = new PathwayCommonsIOHandler(new SimpleIOHandler());

        System.out.println("Querying neighbors for " + id);
        Model resultModel = ioHandler.getNeighbors(id); // TODO: implement to query internal PC hibernate DB

        main.unlock();

        if (resultModel != null && !resultModel.getObjects().isEmpty())
        {
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Related Classes of org.biopax.paxtools.io.pathwayCommons.PathwayCommonsIOHandler

  • org.gvt.action.QueryNeighborsAction
  • org.gvt.action.QueryPathwaysAction
  • org.gvt.action.QueryPCInternalNeighborsAction
  • org.gvt.ChisioMain
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