sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / classifytreecommand.h

diff --git a/classifytreecommand.h b/classifytreecommand.h
index 026e4bae414d227dab7750d623999b86d4aa4a73..ef180babdf12e2a3640ea6157d64b91fe4cc9268 100644 (file)
--- a/classifytreecommand.h
+++ b/classifytreecommand.h
@@ -12,6 +12,7 @@
 #include "command.hpp"
 #include "readtree.h"
 #include "treemap.h"
+#include "counttable.h"
 
 class ClassifyTreeCommand : public Command {
 public:
@@ -22,7 +23,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "classify.tree";                               }
        string getCommandCategory()             { return "Phylotype Analysis";          }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Classify.tree"; }
        string getDescription()         { return "Find the consensus taxonomy for the descendant of each tree node"; }
     
@@ -30,21 +33,18 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       ReadTree* read;
-    TreeMap* tmap;
-       string treefile, taxonomyfile, groupfile, namefile, outputDir;
+       string treefile, taxonomyfile, groupfile, namefile, countfile, outputDir;
        bool abort;
        vector<string> outputNames;
     int numUniquesInName, cutoff;
     map<string, string> nameMap;
     map<string, int> nameCount;
     map<string, string> taxMap;
+    CountTable* ct;
        
        int getClassifications(Tree*&);
        map<string, set<string> > getDescendantList(Tree*&, int, map<int, map<string, set<string> > >);
     string getTaxonomy(set<string>, int&);
-    int readNamesFile(); 
-    int readTaxonomyFile();
        
 };