added shhh.seqs command

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index 5dbeb73e2a5e133669f1d5ffd0d61a85731ed9a5..787f835a0f33d1d157aeab41568286c28a752520 100644 (file)
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -9,10 +9,8 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include "globaldata.hpp"
 #include "command.hpp"
+#include "globaldata.hpp"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
@@ -28,14 +26,18 @@
        The cluster() command outputs three files *.list, *.rabund, and *.sabund.   */
 
 
-class GlobalData;
-
 class ClusterCommand : public Command {
        
 public:
-       ClusterCommand();       
+       ClusterCommand(string);
+       ClusterCommand();
        ~ClusterCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -45,13 +47,22 @@ 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;
+       map<string, vector<string> > outputTypes;
 };
 
 #endif