X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.h;fp=classify.h;h=2926800284ce00cbb7ceb2768bfbe35f28a44a80;hb=63e089e0b3aad1741bab60119ed7ccc784dce347;hp=0000000000000000000000000000000000000000;hpb=f5023c911c377e5320c5110c78af98dd8841ef58;p=mothur.git

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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
+