moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / classifytreecommand.h

diff --git a/classifytreecommand.h b/classifytreecommand.h
deleted file mode 100644 (file)
index 30957af..0000000
--- a/classifytreecommand.h
+++ /dev/null
@@ -1,51 +0,0 @@
-#ifndef Mothur_classifytreecommand_h
-#define Mothur_classifytreecommand_h
-
-//
-//  classifytreecommand.h
-//  Mothur
-//
-//  Created by Sarah Westcott on 2/20/12.
-//  Copyright (c) 2012 Schloss Lab. All rights reserved.
-//
-
-#include "command.hpp"
-#include "readtree.h"
-#include "treemap.h"
-
-class ClassifyTreeCommand : public Command {
-public:
-       ClassifyTreeCommand(string);
-       ClassifyTreeCommand();
-       ~ClassifyTreeCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "classify.tree";                               }
-       string getCommandCategory()             { return "Phylotype Analysis";          }
-       string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Classify.tree"; }
-       string getDescription()         { return "Find the consensus taxonomy for the descendant of each tree node"; }
-    
-       int execute();
-       void help() { m->mothurOut(getHelpString()); }  
-       
-private:
-       string treefile, taxonomyfile, groupfile, namefile, outputDir;
-       bool abort;
-       vector<string> outputNames;
-    int numUniquesInName, cutoff;
-    map<string, string> nameMap;
-    map<string, int> nameCount;
-    map<string, string> taxMap;
-       
-       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();
-       
-};
-
-
-
-#endif