Revert to previous commit

[mothur.git] / classifytreecommand.h

diff --git a/classifytreecommand.h b/classifytreecommand.h
new file mode 100644 (file)
index 0000000..30957af
--- /dev/null
+++ b/classifytreecommand.h
@@ -0,0 +1,51 @@
+#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