#include "phylotree.h"
#include "phylosummary.h"
#include "knn.h"
+#include "kmertree.h"
+#include "aligntree.h"
-//KNN and Bayesian methods modeled from algorithms in
+//KNN and Wang methods modeled from algorithms in
//Naı¨ve Bayesian Classifier for Rapid Assignment of rRNA Sequences
//into the New Bacterial Taxonomy†
//Qiong Wang,1 George M. Garrity,1,2 James M. Tiedje,1,2 and James R. Cole1*
//make classify
Classify* myclassify;
+ string outputMethodTag = pDataArray->method + ".";
if(pDataArray->method == "bayesian"){ myclassify = new Bayesian(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->cutoff, pDataArray->iters, pDataArray->threadID, pDataArray->flip, pDataArray->writeShortcuts); }
else if(pDataArray->method == "knn"){ myclassify = new Knn(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->numWanted, pDataArray->threadID); }
+ else if(pDataArray->method == "zap"){
+ outputMethodTag = pDataArray->search + "_" + outputMethodTag;
+ if (pDataArray->search == "kmer") { myclassify = new KmerTree(pDataArray->templateFileName, pDataArray->taxonomyFileName, pDataArray->kmerSize, pDataArray->cutoff); }
+ else { myclassify = new AlignTree(pDataArray->templateFileName, pDataArray->taxonomyFileName, pDataArray->cutoff); }
+ }
else {
pDataArray->m->mothurOut(pDataArray->search + " is not a valid method option. I will run the command using bayesian.");
pDataArray->m->mothurOutEndLine();