X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.h;h=d8ee57de9424e623d0455e0327e6f636ce569135;hb=65f2be9d8f9b4cf72b4aafd800fdd11ad26435fd;hp=de6a5727575a7f35d2605239968a37435faa388f;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/preclustercommand.h b/preclustercommand.h
index de6a572..d8ee57d 100644
--- 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();