private String getProteaseInformation( BufferedReader bReader, String proteaseName, CsDatabaseEntry csdatabase, ProteaseDatabaseEntry proteasedatabase, String commentS) throws IOException { String line; String commentP = null; proteasedatabase.setP_NL_Name(proteaseName); proteasedatabase.setP_Name("to check"); proteasedatabase.setP_EC_Number("to check"); proteasedatabase.setP_UniprotID("to check"); while ((line = bReader.readLine()) != null) { String splitarray[] = line.split("\t"); String naturallanguage = splitarray[0]; naturallanguage = naturallanguage.replaceAll("\"", ""); naturallanguage = naturallanguage.replaceAll(",", ""); naturallanguage = naturallanguage.replaceAll(";", ""); if (naturallanguage.equalsIgnoreCase(proteaseName)) { String proteaseSymbol = splitarray[1]; proteaseSymbol = proteaseSymbol.replaceAll("sept-0", "SEPT"); String proteaseUniprot = splitarray[2]; String proteaseBrenda = splitarray[3]; if (proteaseUniprot.contains("n.d")) { proteasedatabase.setP_Name("n.d."); proteasedatabase.setP_UniprotID(proteaseUniprot); proteasedatabase.setP_EC_Number(proteaseBrenda); csdatabase.setProtease(proteasedatabase); } else { String UniprotURL = "http://www.uniprot.org/uniprot/" + proteaseUniprot + ".xml"; NodeList entries = getEntries("/uniprot/entry", parseUniprot(UniprotURL)); for (int i = 0; i < entries.getLength(); i++) { getUniProteasepproteinname(entries, i, proteasedatabase); String genename = getUniProteasegenename(entries, i, proteasedatabase); } commentP = commentS + ";-"; proteasedatabase.setP_UniprotID(proteaseUniprot); proteasedatabase.setP_EC_Number(proteaseBrenda); csdatabase.setProtease(proteasedatabase); System.out.println(proteaseUniprot); System.out.println(proteaseBrenda); } } } return commentP; }
private void getUniProteasepproteinname( NodeList entries, int i, ProteaseDatabaseEntry proteasedatabase) { // GET SUBSTRATE PROTEIN NAME using getInformation method LinkedList<String> protnamelist = getInformation("./protein/recommendedName/fullName/text()", entries.item(i)); String protname = null; if (!protnamelist.isEmpty()) { protname = protnamelist.getFirst(); protname = protname.replaceAll(",", ""); System.out.println(protname); proteasedatabase.setP_Name(protname); } }