X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=81267d1604ca2ba2a4551b2520cc6eeee7182a0f;hb=fd98ee6efb944d38bbd61fc36ea9fea2557e3830;hp=bf463a00d238cd6da3b21213f0d393ee6ff895c9;hpb=7bf581f8c46b08eb3bb40715dac94695edee4a67;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index bf463a0..81267d1 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -21,14 +21,24 @@ class DistanceCommand : public Command {
 
 public:
 	DistanceCommand(string);
-	~DistanceCommand();
-	int execute();	
-	void help();
+	DistanceCommand();
+	~DistanceCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "dist.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";	}
+	string getHelpString();	
+	string getCitation() { return "Schloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844. \nhttp://www.mothur.org/wiki/Dist.seqs"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	struct linePair {
+	struct distlinePair {
 		int start;
 		int end;
+		
 	};
 	
 	Dist* distCalculator;
@@ -38,11 +48,11 @@ private:
 
 	int processors, numNewFasta;
 	float cutoff;
-	map<int, int> processIDS;   //end line, processid
-	vector<linePair*> lines;
+	vector<int> processIDS;   //end line, processid
+	vector<distlinePair> lines;
 	
 	bool abort;
-	vector<string>  Estimators; //holds estimators to be used
+	vector<string>  Estimators, outputNames; //holds estimators to be used
 	
 	//void m->appendFiles(string, string);
 	void createProcesses(string);