X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.h;fp=classify.h;h=4e0354782e5063e2a52268e88a1412b40db3c28e;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;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 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
+