m->mothurOut("The name parameter allows you add a names file with your taxonomy file.\n");
m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n");
m->mothurOut("The default value for label is all labels in your inputfile.\n");
m->mothurOut("The name parameter allows you add a names file with your taxonomy file.\n");
m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n");
m->mothurOut("The default value for label is all labels in your inputfile.\n");
- m->mothurOut("The cutoff parameter allows you to specify a concensus confidence threshold for your taxonomy. The default is 51, meaning 51%. Cutoff cannot be below 51.\n");
- m->mothurOut("The probs parameter shuts off the outputting of the concensus confidence results. The default is true, meaning you want the confidence to be shown.\n");
+ m->mothurOut("The cutoff parameter allows you to specify a consensus confidence threshold for your taxonomy. The default is 51, meaning 51%. Cutoff cannot be below 51.\n");
+ m->mothurOut("The probs parameter shuts off the outputting of the consensus confidence results. The default is true, meaning you want the confidence to be shown.\n");
m->mothurOut("The classify.otu command should be in the following format: classify.otu(taxonomy=yourTaxonomyFile, list=yourListFile, name=yourNamesFile, label=yourLabels).\n");
m->mothurOut("Example classify.otu(taxonomy=abrecovery.silva.full.taxonomy, list=abrecovery.fn.list, label=0.10).\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
m->mothurOut("The classify.otu command should be in the following format: classify.otu(taxonomy=yourTaxonomyFile, list=yourListFile, name=yourNamesFile, label=yourLabels).\n");
m->mothurOut("Example classify.otu(taxonomy=abrecovery.silva.full.taxonomy, list=abrecovery.fn.list, label=0.10).\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
it = taxMap.find(names[i]);
if (it == taxMap.end()) { //this name is not in taxonomy file, skip it
it = taxMap.find(names[i]);
if (it == taxMap.end()) { //this name is not in taxonomy file, skip it
it2 = nameMap.find(names[i]);
if (it2 == nameMap.end()) { //this name is not in name file, skip it
it2 = nameMap.find(names[i]);
if (it2 == nameMap.end()) { //this name is not in name file, skip it