X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=81267d1604ca2ba2a4551b2520cc6eeee7182a0f;hb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102;hp=64eac8d57affc1090bbc324bb76ccb6f7fa5648d;hpb=a98eb683e17d8e49583bf2d215ab7562a4cdca75;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 64eac8d..81267d1 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -21,27 +21,38 @@ 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;
 	SequenceDB alignDB;
 
-	string countends, output, fastafile, calc, outputDir, oldfastafile, column;
+	string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
+
 	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);