X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.h;h=d8ee57de9424e623d0455e0327e6f636ce569135;hb=fee6c80b2ca01d5efd0da8a70bdf07475b23e9da;hp=a26fda41cba8e316fd8649604e6934a5960f22f4;hpb=51d85e945d26324e50d6406829ce006ccc9eb1c0;p=mothur.git

diff --git a/preclustercommand.h b/preclustercommand.h
index a26fda4..d8ee57d 100644
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -20,8 +20,9 @@ struct seqPNode {
 	int numIdentical;
 	Sequence seq;
 	string names;
+	bool active;
 	seqPNode() {}
-	seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm) {}
+	seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm), active(1) {}
 	~seqPNode() {}
 };
 /************************************************************/
@@ -30,25 +31,34 @@ 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;
 	bool abort;
 	string fastafile, namefile, outputDir;
-	list<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
+	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(ofstream&, ofstream&, seqPNode); //fasta filename, names file name
+	void printData(string, string); //fasta filename, names file name
 };
 
 /************************************************************/