moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / bayesian.h

diff --git a/bayesian.h b/bayesian.h
deleted file mode 100644 (file)
index 7c88433..0000000
--- a/bayesian.h
+++ /dev/null
@@ -1,50 +0,0 @@
-#ifndef BAYESIAN_H
-#define BAYESIAN_H
-
-/*
- *  bayesian.h
- *  Mothur
- *
- *  Created by westcott on 11/3/09.
- *  Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "classify.h"
-
-/**************************************************************************************************/
-
-class Bayesian : public Classify {
-       
-public:
-       Bayesian(string, string, string, int, int, int, int, bool);
-       ~Bayesian();
-       
-       string getTaxonomy(Sequence*);
-       
-private:
-       vector< vector<float> > wordGenusProb;  //vector of maps from genus to probability
-                                                                               //wordGenusProb[0][392] = probability that a sequence within genus that's index in the tree is 392 would contain kmer 0;
-       
-       vector<int> genusTotals;
-       vector<int> genusNodes;  //indexes in phyloTree where genus' are located
-       
-       vector<diffPair> WordPairDiffArr; 
-       
-       int kmerSize, numKmers, confidenceThreshold, iters;
-       
-       string bootstrapResults(vector<int>, int, int);
-       int getMostProbableTaxonomy(vector<int>);
-       void readProbFile(ifstream&, ifstream&, string, string);
-       bool checkReleaseDate(ifstream&, ifstream&, ifstream&, ifstream&);
-       bool isReversed(vector<int>&);
-       vector<int> createWordIndexArr(Sequence*);
-       int generateWordPairDiffArr();
-       
-};
-
-/**************************************************************************************************/
-
-#endif
-