X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.h;h=38bcd37cf1ffc33a8ee3572c6f24053e1372c1fc;hb=8c8acb6218f58f662466e4111ab8aa4da0caf93c;hp=de6a5727575a7f35d2605239968a37435faa388f;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/preclustercommand.h b/preclustercommand.h
index de6a572..38bcd37 100644
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -31,25 +31,39 @@ 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();	
+	string getCitation() { return "http://www.mothur.org/wiki/Pre.cluster"; }
+	string getDescription()		{ return "implements a pseudo-single linkage algorithm with the goal of removing sequences that are likely due to pyrosequencing errors"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	int diffs, length;
-	bool abort;
-	string fastafile, namefile, outputDir;
+	bool abort, bygroup;
+	string fastafile, namefile, outputDir, groupfile;
 	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, 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();
 	//int readNamesFASTA();
 	int calcMisMatches(string, string);
 	void printData(string, string); //fasta filename, names file name
+	int process();
+	int loadSeqs(map<string, string>&, vector<Sequence>&);
 };
 
 /************************************************************/