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;
}
