X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapsimcommand.h;h=a26018062f28c4406dd83a518f67ee78b388d227;hb=6e81846c8e5b2614f6b06643a9f558fb0e6669fa;hp=33696a33ac87b34bedea636810b32e4daa09be8c;hpb=f15f7092c97277337d4fdd9ef674015c15a13220;p=mothur.git

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index 33696a3..a260180 100644
--- a/heatmapsimcommand.h
+++ b/heatmapsimcommand.h
@@ -21,9 +21,10 @@ class GlobalData;
 class HeatMapSimCommand : public Command {
 
 public:
-	HeatMapSimCommand();
+	HeatMapSimCommand(string);
 	~HeatMapSimCommand();
 	int execute();
+	void help();
 	
 private:
 	GlobalData* globaldata;
@@ -33,6 +34,17 @@ private:
 	vector<Calculator*> heatCalculators;
 	ValidCalculators* validCalculator;
 	HeatMapSim* heatmap;
+	OptionParser* parser;
+	map<string, string> parameters;
+	map<string, string>::iterator it;
+	bool abort, allLines;
+	set<string> labels; //holds labels to be used
+	string format, groups, label, calc, phylipfile, columnfile, namefile, outputDir;
+	vector<string> Estimators, Groups, outputNames;
+	
+	int runCommandShared();
+	int runCommandDist();
+
 
 };