Revert to previous commit

[mothur.git] / slayer.h

diff --git a/slayer.h b/slayer.h
new file mode 100644 (file)
index 0000000..eeefc62
--- /dev/null
+++ b/slayer.h
@@ -0,0 +1,64 @@
+#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
+
+