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

[mothur.git] / slayer.h

diff --git a/slayer.h b/slayer.h
deleted file mode 100644 (file)
index eeefc62..0000000
--- a/slayer.h
+++ /dev/null
@@ -1,64 +0,0 @@
-#ifndef SLAYER_H
-#define SLAYER_H
-/*
- *  slayer.h
- *  Mothur
- *
- *  Created by westcott on 9/25/09.
- *  Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
- 
-#include "sequence.hpp"
-#include "chimera.h"
-
-/***********************************************************************/
-//This class was modeled after the chimeraSlayer written by the Broad Institute
-/***********************************************************************/
-struct snps { 
-       char queryChar;
-       char parentAChar;
-       char parentBChar;
-};
-
-/***********************************************************************/
-
-
-class Slayer {
-
-       public:
-               
-               Slayer(int, int, int, float, int, int, int);
-               ~Slayer() {};
-               
-               string getResults(Sequence, vector<Sequence>);
-               vector<data_struct> getOutput()  {      return outputResults;                   }
-               
-                               
-       private:
-               
-               int windowSize, windowStep, parentFragmentThreshold, iters, percentSNPSample, minBS;
-               float divRThreshold; 
-               vector<data_struct>  outputResults;
-               vector< map<int, int> > baseSpots;
-               Sequence myQuery;
-               
-               map<int, int> verticalFilter(Sequence&, Sequence&, Sequence&);
-               float computePercentID(string, string, int, int);
-               
-               vector<data_struct> runBellerophon(Sequence, Sequence, Sequence, map<int, int>&);
-               vector<snps> getSNPS(string, string, string, int, int);
-               int bootstrapSNPS(vector<snps>, vector<snps>, float&, float&, int);
-               float snpQA(vector<snps>);
-               float snpQB(vector<snps>);
-               float snpAB(vector<snps>);
-               MothurOut* m;
-                               
-};
-
-/***********************************************************************/
-
-#endif
-
-