worked on trim.seqs

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index 1487b3e8985420b096959fdb2737b8ce9f86e7c5..c8e01749de20baac9fe523e9cbf0b5f158b35941 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"
@@ -29,14 +26,13 @@
        The cluster() command outputs three files *.list, *.rabund, and *.sabund.   */
 
 
-class GlobalData;
-
 class ClusterCommand : public Command {
        
 public:
-       ClusterCommand();       
+       ClusterCommand(string);
        ~ClusterCommand();
        int execute();  
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -46,13 +42,21 @@ private:
        RAbundVector* rabund;
        RAbundVector oldRAbund;
        ListVector oldList;
-       
-       string method, fileroot, tag;
+
+       bool abort, hard;
+
+       string method, fileroot, tag, outputDir;
        double cutoff;
+       string showabund, timing;
        int precision, length;
        ofstream sabundFile, rabundFile, listFile;
+
+       bool print_start;
+       time_t start;
+       unsigned long loops;
        
        void printData(string label);
+       vector<string> outputNames;
 };
 
-#endif
\ No newline at end of file
+#endif