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Searched refs:taxonomyFileName (Results 1 – 6 of 6) sorted by relevance

/dports/biology/mothur/mothur-1.46.1/source/commands/
H A Dphylotypecommand.cpp96 taxonomyFileName = validParameter.validFile(parameters, "taxonomy"); in PhylotypeCommand()
97 if (taxonomyFileName == "not found") { in PhylotypeCommand()
98 taxonomyFileName = current->getTaxonomyFile(); in PhylotypeCommand()
99 …if (taxonomyFileName != "") { m->mothurOut("Using " + taxonomyFileName + " as input file for the … in PhylotypeCommand()
104 }else if (taxonomyFileName == "not open") { taxonomyFileName = ""; abort = true; } in PhylotypeCommand()
105 else { current->setTaxonomyFile(taxonomyFileName); } in PhylotypeCommand()
117 if (outputdir == ""){ outputdir += util.hasPath(taxonomyFileName); } in PhylotypeCommand()
134 vector<string> files; files.push_back(taxonomyFileName); in PhylotypeCommand()
155 TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff, outputdir); in execute()
177 string fileroot = outputdir + util.getRootName(util.getSimpleName(taxonomyFileName)); in execute()
H A Dclassifyseqscommand.cpp207 taxonomyFileName = validParameter.validFile(parameters, "taxonomy"); in ClassifySeqsCommand()
208 …if (taxonomyFileName == "not found") { m->mothurOut("[ERROR]: The taxonomy parameter is a require… in ClassifySeqsCommand()
209 }else if (taxonomyFileName == "not open") { abort = true; } in ClassifySeqsCommand()
307 …if(method == "wang"){ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize… in execute()
308 …else if(method == "knn"){ classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize,… in execute()
311 …if (search == "kmer") { classify = new KmerTree(templateFileName, taxonomyFileName, kmerSize, cu… in execute()
312 else { classify = new AlignTree(templateFileName, taxonomyFileName, cutoff); } in execute()
316 …classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, util.… in execute()
323 string baseTName = util.getSimpleName(taxonomyFileName); in execute()
467 string search, taxonomyFileName, templateFileName, method, filename; member
H A Dphylotypecommand.h39 string taxonomyFileName, label, namefile, countfile; variable
H A Dclassifyseqscommand.h61 …ateFileName, countfile, distanceFileName, namefile, search, method, taxonomyFileName, groupfile, o… variable
/dports/biology/mothur/mothur-1.46.1/source/classifier/
H A Daligntree.cpp14 AlignTree::AlignTree(string referenceFileName, string taxonomyFileName, int cutoff) : Classify(), c… in AlignTree() argument
21 readTaxonomy(taxonomyFileName); in AlignTree()
H A Dkmertree.cpp14 KmerTree::KmerTree(string referenceFileName, string taxonomyFileName, int k, int cutoff) : Classify… in KmerTree() argument
24 readTaxonomy(taxonomyFileName); in KmerTree()