started work on classify.seqs command. changed the database class so that it does...

[mothur.git] / classify.h

diff --git a/classify.h b/classify.h
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+#ifndef CLASSIFY_H
+#define CLASSIFY_H
+
+/*
+ *  classify.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/3/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+/* This class is a parent to phylotyp, bayesian, knn.  */
+
+#include "mothur.h"
+#include "database.hpp"
+
+
+
+class Sequence;
+
+/**************************************************************************************************/
+
+class Classify {
+
+public:
+       Classify(string, string, string, int, int, int, int, int);
+       Classify(){};
+       
+       virtual ~Classify(){};
+       virtual string getTaxonomy(Sequence*) = 0;
+       
+protected:
+
+       map<string, string> taxonomy;  //name maps to taxonomy
+       map<string, string>::iterator it;
+       Database* database;
+       
+       string taxFile, templateFile;
+       vector<string> names;
+       
+       void readTaxonomy(string);
+               
+};
+
+/**************************************************************************************************/
+
+#endif
+