sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / slayer.h

diff --git a/slayer.h b/slayer.h
index e898989b17fa73020a367fef11fa1d3b0f688565..eeefc62392b64cdb0eb5797cba1c994b27058f50 100644 (file)
--- a/slayer.h
+++ b/slayer.h
@@ -11,18 +11,17 @@
 
  
 #include "sequence.hpp"
+#include "chimera.h"
 
 /***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
-struct data_struct { //not right needs work...
-       int regionStart;
-       int regionEnd;
-       string parent;
-       float queryToParent;
-       float queryToParentLocal;
-       float divR;
+struct snps { 
+       char queryChar;
+       char parentAChar;
+       char parentBChar;
 };
+
 /***********************************************************************/
 
 
@@ -30,24 +29,31 @@ class Slayer {
 
        public:
                
-               Slayer(int, int, int, float);
+               Slayer(int, int, int, float, int, int, int);
                ~Slayer() {};
                
-               void getResults(Sequence*, vector<Sequence*>);
-               //float getPercentID() {        return percentIdenticalQueryChimera;    }
-               //vector<results> getOutput()  {        return outputResults;                   }
+               string getResults(Sequence, vector<Sequence>);
+               vector<data_struct> getOutput()  {      return outputResults;                   }
                
                                
        private:
                
-               int windowSize, windowStep, parentFragmentThreshold;
+               int windowSize, windowStep, parentFragmentThreshold, iters, percentSNPSample, minBS;
                float divRThreshold; 
+               vector<data_struct>  outputResults;
+               vector< map<int, int> > baseSpots;
+               Sequence myQuery;
                
-               void verticalFilter(vector<Sequence*>);
+               map<int, int> verticalFilter(Sequence&, Sequence&, Sequence&);
                float computePercentID(string, string, int, int);
                
-               vector<data_struct> runBellerophon(Sequence*, Sequence*, Sequence*);
-               
+               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;
                                
 };