major change to the tree class to use the count table class instead of tree map....

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
index d1c173490ac3778e485bcb58334047f4757d6a1e..45e377c3cbe1ac1ad735cd9c4f47d4c4c37c30a5 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 {
@@ -25,6 +26,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "classify.otu";                }
        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 getDescription()         { return "find the concensus taxonomy for each OTU"; }
@@ -33,10 +35,11 @@ public:
        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
@@ -44,9 +47,6 @@ private:
        map<string, string> nameMap;
        map<string, string> taxMap;
 
-       int readNamesFile();
-       int readTaxonomyFile();
-       void removeConfidences(string&);
        int process(ListVector*);
        string addUnclassifieds(string, int);
        vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&);  // returns the name of the "representative" taxonomy of given bin