- final FastaReader fr = new FastaReader(confilename);
- final List<FastaSequence> seqs = new ArrayList<FastaSequence>();
- String newprotein = "";
- while (fr.hasNext()) {
- final FastaSequence fs = fr.next();
- if (fs.getId().equals("QUERY") || fs.getId().equals(id))
- newprotein = fs.getSequence().replaceAll("\n", "");
- else
- seqs.add(fs);
- }
- if (newprotein.equals("")) {
- countUnclearFASTAid++;
- } else {
- SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
- String dateInString1 = table[0].substring(0, table[0].indexOf(":"));
- long dateWork1 = 0;
- try {
- Date dat1 = formatter.parse(dateInString1);
- dateWork1 = dat1.getTime();
- } catch (ParseException e) {
- e.printStackTrace();
- }
- cc.InsertData(dateWork1, table[0], table[1], table[2], id, "OK", "OK", newprotein, seqs);
- ++countinsertions;
- // flush every 100 insertions
- if (0 == countinsertions % 100) {
- cc.flushData();
- }
- }
- } catch (IOException e) {