+ if (namefile != "") { nameMap = m->readNames(namefile); }
+
+ if (m->control_pressed) { return 0; }
+
+ ifstream in;
+ m->openInputFile(fastafile, in);
+
+ ofstream out;
+ string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("aligncheck");
+ m->openOutputFile(outfile, out);
+
+
+ out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t';
+ out << "loop" << '\t' << "tilde" << '\t' << "total" << '\t' << "numseqs" << endl;
+
+ vector<int> pound;
+ vector<int> dash;
+ vector<int> plus;
+ vector<int> equal;
+ vector<int> loop;
+ vector<int> tilde;
+ vector<int> total;
+
+ int count = 0;
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outfile); return 0; }
+
+ Sequence seq(in); m->gobble(in);
+ if (seq.getName() != "") {
+ statData data = getStats(seq.getAligned());
+
+ if (haderror == 1) { m->control_pressed = true; break; }
+
+ int num = 1;
+ if (namefile != "") {
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = nameMap.find(seq.getName());
+
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + seq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ //for each sequence this sequence represents
+ for (int i = 0; i < num; i++) {
+ pound.push_back(data.pound);
+ dash.push_back(data.dash);
+ plus.push_back(data.plus);
+ equal.push_back(data.equal);
+ loop.push_back(data.loop);
+ tilde.push_back(data.tilde);
+ total.push_back(data.total);
+ }
+ count++;
+
+ out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
+ out << data.loop << '\t' << data.tilde << '\t' << data.total << '\t' << num << endl;
+ }
+ }
+
+ in.close();
+ out.close();
+
+ if (m->control_pressed) { m->mothurRemove(outfile); return 0; }
+
+ sort(pound.begin(), pound.end());
+ sort(dash.begin(), dash.end());
+ sort(plus.begin(), plus.end());
+ sort(equal.begin(), equal.end());
+ sort(loop.begin(), loop.end());
+ sort(tilde.begin(), tilde.end());
+ sort(total.begin(), total.end());
+ int size = pound.size();
+
+ int ptile0_25 = int(size * 0.025);
+ int ptile25 = int(size * 0.250);
+ int ptile50 = int(size * 0.500);
+ int ptile75 = int(size * 0.750);
+ int ptile97_5 = int(size * 0.975);
+ int ptile100 = size - 1;
+
+ if (m->control_pressed) { m->mothurRemove(outfile); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal"); m->mothurOutEndLine();
+ m->mothurOut("Minimum:\t" + toString(pound[0]) + "\t" + toString(dash[0]) + "\t" + toString(plus[0]) + "\t" + toString(equal[0]) + "\t" + toString(loop[0]) + "\t" + toString(tilde[0]) + "\t" + toString(total[0])); m->mothurOutEndLine();
+ m->mothurOut("2.5%-tile:\t" + toString(pound[ptile0_25]) + "\t" + toString(dash[ptile0_25]) + "\t" + toString(plus[ptile0_25]) + "\t" + toString(equal[ptile0_25]) + "\t"+ toString(loop[ptile0_25]) + "\t"+ toString(tilde[ptile0_25]) + "\t"+ toString(total[ptile0_25])); m->mothurOutEndLine();
+ m->mothurOut("25%-tile:\t" + toString(pound[ptile25]) + "\t" + toString(dash[ptile25]) + "\t" + toString(plus[ptile25]) + "\t" + toString(equal[ptile25]) + "\t" + toString(loop[ptile25]) + "\t" + toString(tilde[ptile25]) + "\t" + toString(total[ptile25])); m->mothurOutEndLine();
+ m->mothurOut("Median: \t" + toString(pound[ptile50]) + "\t" + toString(dash[ptile50]) + "\t" + toString(plus[ptile50]) + "\t" + toString(equal[ptile50]) + "\t" + toString(loop[ptile50]) + "\t" + toString(tilde[ptile50]) + "\t" + toString(total[ptile50])); m->mothurOutEndLine();
+ m->mothurOut("75%-tile:\t" + toString(pound[ptile75]) + "\t" + toString(dash[ptile75]) + "\t" + toString(plus[ptile75]) + "\t" + toString(equal[ptile75]) + "\t" + toString(loop[ptile75]) + "\t" + toString(tilde[ptile75]) + "\t" + toString(total[ptile75])); m->mothurOutEndLine();
+ m->mothurOut("97.5%-tile:\t" + toString(pound[ptile97_5]) + "\t" + toString(dash[ptile97_5]) + "\t" + toString(plus[ptile97_5]) + "\t" + toString(equal[ptile97_5]) + "\t" + toString(loop[ptile97_5]) + "\t" + toString(tilde[ptile97_5]) + "\t" + toString(total[ptile97_5])); m->mothurOutEndLine();
+ m->mothurOut("Maximum:\t" + toString(pound[ptile100]) + "\t" + toString(dash[ptile100]) + "\t" + toString(plus[ptile100]) + "\t" + toString(equal[ptile100]) + "\t" + toString(loop[ptile100]) + "\t" + toString(tilde[ptile100]) + "\t" + toString(total[ptile100])); m->mothurOutEndLine();
+ if (namefile == "") { m->mothurOut("# of Seqs:\t" + toString(count)); m->mothurOutEndLine(); }
+ else { m->mothurOut("# of unique seqs:\t" + toString(count)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(size)); m->mothurOutEndLine(); }
+
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(outfile); m->mothurOutEndLine(); outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);
+ m->mothurOutEndLine();