X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.h;h=a3328d8dcea09eebe63c641e04e1b816fc92fee1;hb=f12174bc43f9e8ad536f2a37fb3a763b1ac90ba9;hp=0cffec6948a83849a078fbef99b81cb5fe7b4433;hpb=e8e13c129ba8184ec5932a090773f353f3ae3406;p=mothur.git

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 0cffec6..a3328d8 100644
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -43,8 +43,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "classify.seqs";		}
 	string getCommandCategory()		{ return "Phylotype Analysis";	}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ] \nAltschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ] \nDeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ] \nhttp://www.mothur.org/wiki/Classify.seqs"; }
 	string getDescription()		{ return "classify sequences"; }
 	
@@ -166,10 +167,11 @@ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
 		
 		//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 = search + "_" + outputMethodTag;
+            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);  }
         }