Examples of metlin.LineInfo

    final String token = parameters.getParameter(
        MetLinParameters.SECURITY_TOKEN).getValue();


    MetaboliteSearchRequest searchParams = new MetaboliteSearchRequest(
        token, searchMass, adduct, searchTolerance, "Da");
    LineInfo resultsData[][];
    try {
      resultsData = serv.metaboliteSearch(searchParams);
    } catch (AxisFault e) {
      // For some reason, the METLIN SOAP gateway throws AxisFault caused
      // by ArrayStoreException if no result is found. I suspect their
      // SOAP response is malformed and Axis does not like it.
      resultsData = new LineInfo[1][0];
    }


    if (resultsData.length == 0) {
      throw (new IOException("Results could not be retrieved from METLIN"));


    }
    final int totalResults = Math.min(resultsData[0].length, numOfResults);
    String metlinIDs[] = new String[totalResults];


    for (int i = 0; i < totalResults; i++) {
      LineInfo metlinEntry = resultsData[0][i];
      String metlinID = metlinEntry.getMolid();
      retrievedMolecules.put(metlinID, metlinEntry);
      metlinIDs[i] = metlinID;
    }


    return metlinIDs;

  public DBCompound getCompound(String ID, ParameterSet parameters)
      throws IOException {


    URL entryURL = new URL(metLinEntryAddress + ID);


    LineInfo metlinEntry = retrievedMolecules.get(ID);


    if (metlinEntry == null) {
      throw new IOException("Unknown ID " + ID);
    }


    String compoundName = metlinEntry.getName();


    if (compoundName == null) {
      throw (new IOException(
          "Could not parse compound name for compound " + ID));
    }


    String compoundFormula = metlinEntry.getFormula();


    URL structure2DURL = new URL(metLinStructureAddress1 + ID
        + metLinStructureAddress2);


    URL structure3DURL = null;

Examples of metlin.LineInfo

Related Classes of metlin.LineInfo