m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
string baseTName = m->getSimpleName(taxonomyFileName);
- if (taxonomyFileName == "saved") {baseTName = rdb->getSavedTaxonomy(); }
+ if (taxonomyFileName == "saved") { baseTName = rdb->getSavedTaxonomy(); }
//set rippedTaxName to
string RippedTaxName = "";
}
outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
- outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
outputNames.push_back(taxSummary); outputTypes["taxsummary"].push_back(taxSummary);
int start = time(NULL);
}
#endif
- if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur suspects some of your sequences may be reversed, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); }
+ if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur suspects some of your sequences may be reversed, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine();
+ outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
+ }else { m->mothurRemove(newaccnosFile); }
m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
#ifdef USE_MPI
}
#endif
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
- m->mothurOutEndLine();
}
+ delete classify;
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
//set taxonomy file as new current taxonomyfile
string current = "";
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
}
- delete classify;
+
return 0;
}