Merge remote-tracking branch 'origin/master'

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
index b924775cf5b30436c1783714a758281cf072c32f..2e76057f1219b8c44785a5be9b6962043bbb68af 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -13,6 +13,7 @@
 #include "command.hpp"
 #include "listvector.hpp"
 #include "inputdata.h"
+#include "counttable.h"
 
 
 class ClassifyOtuCommand : public Command {
@@ -27,17 +28,18 @@ public:
        string getCommandCategory()             { return "Phylotype Analysis";  }
        string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Classify.otu"; }
+       string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nhttp://www.mothur.org/wiki/Classify.otu"; }
        string getDescription()         { return "find the concensus taxonomy for each OTU"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
 
 private:
-
+    GroupMap* groupMap;
+    CountTable* ct;
        ListVector* list;
        InputData* input;
-       string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
+       string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis, countfile;
        bool abort, allLines, probs;
        int cutoff;
        set<string> labels; //holds labels to be used