private String getProteaseNameSymbolId( Matcher patternProteaseName, CsDatabaseEntry csdatabase, ProteaseDatabaseEntry proteasedatabase, String proteaseTaxon, String commentS) throws IOException { String commentP = null; if (patternProteaseName.find()) { String proteaseName = patternProteaseName.group(1); proteaseName = proteaseName.trim(); proteaseName = proteaseName.replaceAll(",", ""); proteaseName = proteaseName.replaceAll(";", ""); commentP = mapProteasetoLibrairy( commentS, proteaseTaxon, proteaseName, csdatabase, proteasedatabase); } else { String proteaseName = "n.d."; String proteaseSymbol = "n.d."; String proteaseUniprot = "n.d"; String proteaseBrenda = "n.d."; commentP = commentS + ";-"; proteasedatabase.setP_NL_Name(proteaseName); proteasedatabase.setP_Symbol(proteaseSymbol); proteasedatabase.setP_UniprotID(proteaseUniprot); proteasedatabase.setP_EC_Number(proteaseBrenda); csdatabase.setProtease(proteasedatabase); System.out.println(proteaseName); System.out.println(proteaseSymbol); System.out.println(proteaseUniprot); System.out.println(proteaseBrenda); } return commentP; }
private String getUniProteasegenename( NodeList entries, int i, ProteaseDatabaseEntry proteasedatabase) { // GET SUBSTRATE GENE NAME using getInformation method LinkedList<String> genenamelist = getInformation("./gene/name[@type][1]/text()", entries.item(i)); String genename = null; if (!genenamelist.isEmpty()) { genename = genenamelist.getFirst(); System.out.println(genename); proteasedatabase.setP_Symbol(genename); } return genename; }