X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=3e3dc7098a768461c67dc1d45751e50891ccc9c2;hb=cdf9083dc32543cc640e72e9ca3aee0323cbad45;hp=bf463a00d238cd6da3b21213f0d393ee6ff895c9;hpb=7bf581f8c46b08eb3bb40715dac94695edee4a67;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index bf463a0..3e3dc70 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -21,7 +21,12 @@ class DistanceCommand : public Command {
 
 public:
 	DistanceCommand(string);
+	DistanceCommand();
 	~DistanceCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();	
 	void help();
 	
@@ -38,11 +43,12 @@ private:
 
 	int processors, numNewFasta;
 	float cutoff;
-	map<int, int> processIDS;   //end line, processid
+	vector<int> processIDS;   //end line, processid
 	vector<linePair*> lines;
 	
 	bool abort;
-	vector<string>  Estimators; //holds estimators to be used
+	vector<string>  Estimators, outputNames; //holds estimators to be used
+	map<string, vector<string> > outputTypes;
 	
 	//void m->appendFiles(string, string);
 	void createProcesses(string);