X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.h;h=6d43dcb9dd2067bab91f46d42ff8afa238a4a191;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=acee70c5cb474dee4e25eea4a6dcf6b5bd55fa06;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index acee70c..6d43dcb 100644
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -41,6 +41,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "classify.seqs";		}
 	string getCommandCategory()		{ return "Phylotype Analysis";	}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
 	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"; }
@@ -61,6 +62,7 @@ private:
 	vector<linePair*> lines;
 	vector<string> fastaFileNames;
 	vector<string> namefileNames;
+    vector<string> countfileNames;
 	vector<string> groupfileNames;
 	vector<string> outputNames;
 	map<string, vector<string> > nameMap;
@@ -69,13 +71,12 @@ private:
 	Classify* classify;
 	ReferenceDB* rdb;
 	
-	string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
+	string fastaFileName, templateFileName, countfile, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
 	int processors, kmerSize, numWanted, cutoff, iters;
 	float match, misMatch, gapOpen, gapExtend;
-	bool abort, probs, save, flip;
+	bool abort, probs, save, flip, hasName, hasCount;
 	
 	int driver(linePair*, string, string, string, string);
-	void appendTaxFiles(string, string);
 	int createProcesses(string, string, string, string); 
 	string addUnclassifieds(string, int);