sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / readcluster.h

diff --git a/readcluster.h b/readcluster.h
index bcd910cb1c032e06df74aae9acfd55e7b3be2142..7ea579c2fc1a250bba3500f7d6dc59d3ebed26f8 100644 (file)
--- a/readcluster.h
+++ b/readcluster.h
@@ -13,7 +13,7 @@
 #include "mothur.h"
 #include "nameassignment.hpp"
 #include "listvector.hpp"
-#include "globaldata.hpp"
+#include "counttable.h"
 
 
 /******************************************************/
@@ -21,21 +21,24 @@
 class ReadCluster {
        
 public:
-       ReadCluster(string, float);
+       ReadCluster(string, float, string, bool);
        ~ReadCluster();
-       void read(NameAssignment*);
+       int read(NameAssignment*&);
+    int read(CountTable*&);
        string getOutputFile() { return OutPutFile; }
        void setFormat(string f) { format = f;  }
        ListVector* getListVector()             {       return list;    }
        
 private:
-       GlobalData* globaldata;
-       string distFile;
+       string distFile, outputDir;
        string OutPutFile, format;
        ListVector* list;
        float cutoff;
+       MothurOut* m;
+       bool sortWanted;
        
-       void convertPhylip2Column(NameAssignment*);
+       int convertPhylip2Column(NameAssignment*&);
+    int convertPhylip2Column(CountTable*&);
 };
 
 /******************************************************/