X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.h;h=38bcd37cf1ffc33a8ee3572c6f24053e1372c1fc;hb=ae57e166b2ed7b475ec3f466106bd76fabadd063;hp=8302fedc78717b73a642d28f08d8a173ad2fc77b;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/preclustercommand.h b/preclustercommand.h
index 8302fed..38bcd37 100644
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -39,14 +39,16 @@ public:
 	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
@@ -60,6 +62,8 @@ private:
 	//int readNamesFASTA();
 	int calcMisMatches(string, string);
 	void printData(string, string); //fasta filename, names file name
+	int process();
+	int loadSeqs(map<string, string>&, vector<Sequence>&);
 };
 
 /************************************************************/