Package net.sf.mzmine.modules.peaklistmethods.identification.dbsearch

Examples of net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.DBCompound

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

    DBCompound newCompound = new DBCompound(OnlineDatabase.MASSBANK, ID,
        compoundName, compoundFormula, databaseURL, structure2DURL,
        structure3DURL);

    return newCompound;
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      name = ERROR_MESSAGE;
      formula = null;
    }

    // Create and return the compound record.
    return new DBCompound(OnlineDatabase.CHEMSPIDER, ID, name, formula,
        new URL(STRUCTURE_URL_PATTERN.replaceFirst("CSID", ID)),
        new URL(STRUCTURE2D_URL_PATTERN.replaceFirst("CSID", ID)),
        new URL(STRUCTURE3D_URL_PATTERN.replaceFirst("CSID", ID)));
  }
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    URL structure2DURL = new URL(metLinStructureAddress1 + ID
        + metLinStructureAddress2);

    URL structure3DURL = null;

    DBCompound newCompound = new DBCompound(OnlineDatabase.METLIN, ID,
        compoundName, compoundFormula, entryURL, structure2DURL,
        structure3DURL);

    return newCompound;
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    if (ID3DMet != null) {
      structure3DURL = new URL(met3DStructureAddress1 + ID3DMet
          + met3DStructureAddress2);
    }

    DBCompound newCompound = new DBCompound(OnlineDatabase.KEGG, ID,
        compoundName, compoundFormula, entryURL, structure2DURL,
        structure3DURL);

    return newCompound;
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    if (compoundName == null) {
      throw (new IOException("Invalid compound ID " + ID));
    }

    DBCompound newCompound = new DBCompound(OnlineDatabase.PLANTCYC, ID,
        compoundName, compoundFormula, entryURL, structure2DURL,
        structure3DURL);

    return newCompound;
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    URL entryURL = new URL(pubchemEntryAddress + CID);
    URL structure2DURL = new URL(pubchem2DStructureAddress + CID);
    URL structure3DURL = new URL(pubchem3DStructureAddress + CID);

    DBCompound newCompound = new DBCompound(OnlineDatabase.PubChem, CID,
        compoundName, compoundFormula, entryURL, structure2DURL,
        structure3DURL);

    return newCompound;
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    if (compoundName == null) {
      throw (new IOException("Could not parse compound name"));
    }

    DBCompound newCompound = new DBCompound(OnlineDatabase.HMDB, ID,
        compoundName, compoundFormula, entryURL, structure2DURL,
        structure3DURL);

    return newCompound;
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    String compoundFormula = fields[3];
    URL structure2DURL = new URL(lipidMapsStructureAddress + ID);
    URL structure3DURL = null;
    URL databaseURL = new URL(lipidMapsDetailsAddress + ID);

    DBCompound newCompound = new DBCompound(OnlineDatabase.LIPIDMAPS, ID,
        compoundName, compoundFormula, databaseURL, structure2DURL,
        structure3DURL);

    return newCompound;
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    if (compoundName == null) {
      throw (new IOException("Could not parse compound name"));
    }

    DBCompound newCompound = new DBCompound(OnlineDatabase.YMDB, ID,
        compoundName, compoundFormula, entryURL, structure2DURL,
        structure3DURL);

    return newCompound;
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Related Classes of net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.DBCompound

  • net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.databases.ChemSpiderGateway
  • net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.databases.HMDBGateway
  • net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.databases.KEGGGateway
  • net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.databases.LipidMapsGateway
  • net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.databases.MassBankGateway
  • net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.databases.MetLinGateway
  • net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.databases.PlantCycGateway
  • net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.databases.PubChemGateway
  • net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.databases.YMDBGateway
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