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[mothur.git] / 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 bayesian, knn.  */
+
+#include "mothur.h"
+#include "database.hpp"
+#include "phylotree.h"
+
+
+class Sequence;
+
+
+/**************************************************************************************************/
+
+class Classify {
+
+public:
+       Classify();
+       virtual ~Classify(){};
+       virtual string getTaxonomy(Sequence*) = 0;
+       virtual string getSimpleTax()  { return simpleTax;      }
+       virtual bool getFlipped()  { return flipped;    }
+       virtual void generateDatabaseAndNames(string, string, string, int, float, float, float, float);
+       virtual void setDistName(string s) {} //for knn, so if distance method is selected with knn you can create the smallest distance file in the right place.
+       
+protected:
+
+       map<string, string> taxonomy;  //name maps to taxonomy
+       //map<string, int> genusCount;  //maps genus to count - in essence a list of how many seqs are in each taxonomy
+       map<string, int>::iterator itTax;
+       map<string, string>::iterator it;
+       Database* database;
+       PhyloTree* phyloTree;
+       
+       string taxFile, templateFile, simpleTax;
+       vector<string> names;
+       int threadID;
+       bool flip, flipped;
+       
+       int readTaxonomy(string);
+       vector<string> parseTax(string);
+       MothurOut* m;
+       
+};
+
+/**************************************************************************************************/
+
+#endif
+