added summary, collect, and scale parameters to phylo.diversity command.

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index 37b9edb80224de6d7b7be0f722152e0bdd782b11..c8e01749de20baac9fe523e9cbf0b5f158b35941 100644 (file)
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -26,12 +26,10 @@
        The cluster() command outputs three files *.list, *.rabund, and *.sabund.   */
 
 
-class GlobalData;
-
 class ClusterCommand : public Command {
        
 public:
-       ClusterCommand(string); 
+       ClusterCommand(string);
        ~ClusterCommand();
        int execute();  
        void help();
@@ -44,17 +42,21 @@ private:
        RAbundVector* rabund;
        RAbundVector oldRAbund;
        ListVector oldList;
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
-       bool abort;
 
-       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