sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
index 36a0328aa85bb2d646e14ec37b1d13f8a0581241..c0a822070fa9a8b0b570f05e1ede727e19ead48b 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 {
@@ -25,8 +26,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "classify.otu";                }
        string getCommandCategory()             { return "Phylotype Analysis";  }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        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"; }
        
@@ -34,20 +36,21 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
 
 private:
-
+    GroupMap* groupMap;
+    CountTable* ct;
        ListVector* list;
        InputData* input;
-       string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
-       bool abort, allLines, probs;
+       string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis, countfile;
+       bool abort, allLines, probs, persample;
        int cutoff;
        set<string> labels; //holds labels to be used
-       vector<string> outputNames;
+       vector<string> outputNames, groups;
        map<string, string> nameMap;
        map<string, string> taxMap;
 
        int process(ListVector*);
        string addUnclassifieds(string, int);
-       vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&);  // returns the name of the "representative" taxonomy of given bin
+       vector<string> findConsensusTaxonomy(vector<string>, int&, string&);    // returns the name of the "representative" taxonomy of given bin
        
                                                                                                
 };