removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / preclustercommand.h

diff --git a/preclustercommand.h b/preclustercommand.h
index de6a5727575a7f35d2605239968a37435faa388f..d8ee57de9424e623d0455e0327e6f636ce569135 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -31,9 +31,16 @@ class PreClusterCommand : public Command {
        
 public:
        PreClusterCommand(string);
-       ~PreClusterCommand();
-       int execute();  
-       void help();
+       PreClusterCommand();
+       ~PreClusterCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "pre.cluster";                         }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        int diffs, length;
@@ -44,6 +51,8 @@ private:
        map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
        map<string, int>::iterator itSize; 
 //     map<string, bool> active; //maps sequence name to whether it has already been merged or not.
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        int readFASTA();
        void readNameFile();