X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.h;h=d8ee57de9424e623d0455e0327e6f636ce569135;hb=0d4b21e5ccc56276b0c18d17d8e75d94ce1df4e7;hp=3a1157d1979935e990f45e1f3202d4fe74525574;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/preclustercommand.h b/preclustercommand.h
index 3a1157d..d8ee57d 100644
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -30,22 +30,33 @@ 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;
 	bool abort;
 	string fastafile, namefile, outputDir;
 	vector<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
-//	map<string, string> names; //represents the names file first column maps to second column
-//	map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
+	map<string, string> names; //represents the names file first column maps to second column
+	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();
-	int readNamesFASTA();
+	void readNameFile();
+	//int readNamesFASTA();
 	int calcMisMatches(string, string);
 	void printData(string, string); //fasta filename, names file name
 };