working on pam

[mothur.git] / collect.h

diff --git a/collect.h b/collect.h
index aca4ccd40069cf5fdcdb9fed05b17cabe447f567..51712331401747192b62a9198ca6fa3cda8f4cef 100644 (file)
--- a/collect.h
+++ b/collect.h
@@ -1,9 +1,6 @@
 #ifndef COLLECT_H
 #define COLLECT_H
 
-using namespace std;
-
-
 #include "collectorscurvedata.h"
 #include "display.h"
 #include "ordervector.hpp"
@@ -11,7 +8,7 @@ using namespace std;
 #include "rabundvector.hpp"
 #include "sharedordervector.h"
 #include "datavector.hpp"
-#include "globaldata.hpp"
+#include "mothurout.h"
 
 /***********************************************************************/
 
@@ -19,17 +16,16 @@ class Collect {
        
 public:
        Collect(OrderVector* order, vector<Display*> disp) :
-                                       numSeqs(order->getNumSeqs()), order(order), displays(disp), label(order->getLabel())  {};
+                                       numSeqs(order->getNumSeqs()), order(order), displays(disp), label(order->getLabel())  { m = MothurOut::getInstance(); };
        Collect(SharedOrderVector* sharedorder, vector<Display*> disp) :
-                                       numSeqs(sharedorder->getNumSeqs()), sharedorder(sharedorder), displays(disp), label(sharedorder->getLabel())  {};
+                                       numSeqs(sharedorder->getNumSeqs()), sharedorder(sharedorder), displays(disp), label(sharedorder->getLabel())  { m = MothurOut::getInstance(); }
 
        ~Collect(){             };
-       void getCurve(int);
-       void getSharedCurve(int);
+       int getCurve(float);
+       int getSharedCurve(float);
        
 private:
        SharedOrderVector* sharedorder;
-       GlobalData* globaldata;
        OrderVector* order;
        vector<Display*> displays;
        int numSeqs, numGroupComb, totalNumSeq;
@@ -37,6 +33,7 @@ private:
        void getGroupComb();
        vector<string> groupComb;
        bool validGroup(vector<string>, string);
+       MothurOut* m;
 };