- distcalculator = new ignoreGaps();
- decalc = new DeCalculator();
-
- decalc->setMask(seqMask);
-
- //mask querys
- for (int i = 0; i < querySeqs.size(); i++) {
- decalc->runMask(querySeqs[i]);
- }
-
- //mask templates
- for (int i = 0; i < templateSeqs.size(); i++) {
- decalc->runMask(templateSeqs[i]);
- }
-
-for (int i = 0; i < lines.size(); i++) { cout << "line pair " << i << " = " << lines[i]->start << '\t' << lines[i]->end << endl; }
-
- if (processors == 1) {
- mothurOut("Finding closest sequence in template to each sequence... "); cout.flush();
- bestfit = findPairs(lines[0]->start, lines[0]->end);
-
- //ex.align matches from wigeon
-for (int m = 0; m < templateSeqs.size(); m++) {
- if (templateSeqs[m]->getName() == "159481") { bestfit[17] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "100137") { bestfit[16] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "112956") { bestfit[15] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "102326") { bestfit[14] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "66229") { bestfit[13] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "206276") { bestfit[12] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "63607") { bestfit[11] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "7056") { bestfit[10] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "7088") { bestfit[9] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "17553") { bestfit[8] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "131723") { bestfit[7] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "69013") { bestfit[6] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "24543") { bestfit[5] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "27824") { bestfit[4] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "1456") { bestfit[3] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "1456") { bestfit[2] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "141312") { bestfit[1] = *(templateSeqs[m]); }
- if (templateSeqs[m]->getName() == "141312") { bestfit[0] = *(templateSeqs[m]); }
-
-
-}
-
- for (int j = 0; j < bestfit.size(); j++) {
- //chops off beginning and end of sequences so they both start and end with a base
- decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]);
- }
- mothurOut("Done."); mothurOutEndLine();
-
- mothurOut("Finding window breaks... "); cout.flush();
- for (int i = lines[0]->start; i < lines[0]->end; i++) {
- it = trimmed[i].begin();
-//cout << "trimmed = " << it->first << '\t' << it->second << endl;
- vector<int> win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
- windowsForeachQuery[i] = win;
- }
- mothurOut("Done."); mothurOutEndLine();
-
- }else { createProcessesSpots(); }
-
- //find P
- mothurOut("Getting conservation... "); cout.flush();