added an alignreport option to screen seqs

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index 1487b3e8985420b096959fdb2737b8ce9f86e7c5..44ce6f9f6833a8fd5181bcff64880bfe8f4d4f88 100644 (file)
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -9,11 +9,8 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
-#include "globaldata.hpp"
 #include "command.hpp"
+#include "globaldata.hpp"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
@@ -34,9 +31,10 @@ class GlobalData;
 class ClusterCommand : public Command {
        
 public:
-       ClusterCommand();       
+       ClusterCommand(string); 
        ~ClusterCommand();
        int execute();  
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -46,7 +44,9 @@ private:
        RAbundVector* rabund;
        RAbundVector oldRAbund;
        ListVector oldList;
-       
+
+       bool abort;
+
        string method, fileroot, tag;
        double cutoff;
        int precision, length;
@@ -55,4 +55,4 @@ private:
        void printData(string label);
 };
 
-#endif
\ No newline at end of file
+#endif