1.19.0

[mothur.git] / preclustercommand.h

diff --git a/preclustercommand.h b/preclustercommand.h
index 643a36783594cf6d0716e2e4b79fedf3413a6861..d8ee57de9424e623d0455e0327e6f636ce569135 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -30,10 +30,17 @@ struct seqPNode {
 class PreClusterCommand : public Command {
        
 public:
-       PreClusterCommand(string);      
-       ~PreClusterCommand();
-       int execute();  
-       void help();
+       PreClusterCommand(string);
+       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();