changes while testing

[mothur.git] / rarefact.h

diff --git a/rarefact.h b/rarefact.h
index fc1e8d13e4b289851c65e72a1ebd1804edfbd44d..f6bc35551f50858e47a7999ce198145bcb81a4bb 100644 (file)
--- a/rarefact.h
+++ b/rarefact.h
@@ -1,8 +1,6 @@
 #ifndef RAREFACT_H
 #define RAREFACT_H
 
-using namespace std;
-
 #include "rarefactioncurvedata.h"
 #include "raredisplay.h"
 #include "ordervector.hpp"
@@ -12,24 +10,28 @@ using namespace std;
 class Rarefact {
        
 public:
-       Rarefact(OrderVector* o, vector<Display*> disp) :
-                       numSeqs(o->getNumSeqs()), order(o), displays(disp), label(o->getLabel())  {};
-       Rarefact(SharedOrderVector* sharedorder, vector<Display*> disp) :
-                                       numSeqs(sharedorder->getNumSeqs()), sharedorder(sharedorder), displays(disp), label(sharedorder->getLabel())  {};
+       Rarefact(OrderVector* o, vector<Display*> disp, int p, set<int> en) :
+                       numSeqs(o->getNumSeqs()), order(o), displays(disp), label(o->getLabel()), processors(p), ends(en)  { m = MothurOut::getInstance(); }
+       Rarefact(vector<SharedRAbundVector*> shared, vector<Display*> disp) :
+                                        lookup(shared), displays(disp) {  m = MothurOut::getInstance(); }
 
        ~Rarefact(){};
-       void getCurve(int, int);
-       void getSharedCurve(int, int);
+       int getCurve(float, int);
+       int getSharedCurve(float, int);
        
 private:
-       SharedOrderVector* sharedorder;
-       GlobalData* globaldata;
+       
        OrderVector* order;
        vector<Display*> displays;
-       int numSeqs, numGroupComb;
+       int numSeqs, numGroupComb, processors;
        string label;
+    set<int> ends;
        void mergeVectors(SharedRAbundVector*, SharedRAbundVector*);
        vector<SharedRAbundVector*> lookup; 
+       MothurOut* m;
+       
+       int createProcesses(vector<int>&, RarefactionCurveData*, int);
+       int driver(RarefactionCurveData*, int, int);
 
 };