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 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;
}
